From fb6003f5b06739509bac67b0fcde93ec0bbddddd Mon Sep 17 00:00:00 2001
From: Andrey Solovyev <a.solovyev39@gmail.com>
Date: Thu, 18 Jun 2020 15:16:12 +0100
Subject: [PATCH 01/11] initial work on data import wrappers

---
 .../atlas_import_classifiers.xml              |  0
 .../atlas_import_experiment_data.xml          | 60 +++++++++++++++++++
 .../atlas-data-import/atlas_import_macros.xml | 35 +++++++++++
 .../atlas_import_sdrf_files.xml               |  0
 4 files changed, 95 insertions(+)
 create mode 100644 tools/tertiary-analysis/atlas-data-import/atlas_import_classifiers.xml
 create mode 100644 tools/tertiary-analysis/atlas-data-import/atlas_import_experiment_data.xml
 create mode 100644 tools/tertiary-analysis/atlas-data-import/atlas_import_macros.xml
 create mode 100644 tools/tertiary-analysis/atlas-data-import/atlas_import_sdrf_files.xml

diff --git a/tools/tertiary-analysis/atlas-data-import/atlas_import_classifiers.xml b/tools/tertiary-analysis/atlas-data-import/atlas_import_classifiers.xml
new file mode 100644
index 00000000..e69de29b
diff --git a/tools/tertiary-analysis/atlas-data-import/atlas_import_experiment_data.xml b/tools/tertiary-analysis/atlas-data-import/atlas_import_experiment_data.xml
new file mode 100644
index 00000000..e82a1c7f
--- /dev/null
+++ b/tools/tertiary-analysis/atlas-data-import/atlas_import_experiment_data.xml
@@ -0,0 +1,60 @@
+<tool id="atlas_import_experiment_data" name="Atlas import: get experiment data" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
+    <description>Obtain study data from Single Cell Expression Atlas</description>
+    <macros>
+         <import>atlas_import_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        get_experiment_data.R --accession-code "${accession_code}" --matrix-type "${matrix_type}" --get-sdrf "${get_sdrf}" --get-condensed-sdrf "${get_condensed_sdrf}" --get-marker-genes "${get_marker_genes}" 
+
+        #if $config_file 
+        --config-file "${config_file}" 
+        #end if
+        #if $decorated_rows 
+        --decorated-rows "${decorated_rows}" 
+        #end if
+        #if $use_default_expr_names 
+        --use-default-expr-names "${use_default_expr_names}" 
+        #end if
+        #if $exp_data_dir 
+        --exp-data-dir "${exp_data_dir}" 
+        #end if
+        #if $get_idf 
+        --get-idf "${get_idf}" 
+        #end if
+        #if $number_of_clusters 
+        --number-of-clusters  "${number_of_clusters}" 
+        #end if
+        #if $use_full_names
+        --use-full-names  "${use_full_names}" 
+        #end if
+    ]]></command>
+    <inputs>
+        <param type="text" name="accession_code" label="Accession code" help="Accession code of dataset to be downloaded" />
+        <param type="select" name="matrix_type" label="Matrix type"  help="Type of matrix to be imported">
+            <option value="raw">Raw</option>
+            <option value="filtered">Filtered</option>
+            <option value="tpm">TPM-normalised</option>
+            <option value="cpm">CPM-normalised</option>
+        </param>
+        <param type="boolean" name="get_sdrf" checked="false"  label="Import SDRF file" help="Boolean indicating whether SDRF file needs to be imported" />
+        <param type="boolean" name="get_idf" checked="false"  label="Import IDF file" help="Boolean indicating whether IDF file needs to be imported" />
+        <param type="boolean" name="get_condensed_sdrf" checked="false"  label="Get condensed SDRF file" help="Boolean indicating whether condensed SDRF file needs to be imported" />
+        <param type="boolean" name="get_marker_genes" checked="false"  label="Import marker genes" help="Boolean indicating whether marker genes should be imported" />
+        <param type="data" name="config_file" label="Config file" format="yml" help="Config file with user-provided parameters" />
+        <param type="boolean" name="decorated_rows" checked="false"  label="Decorated rows" help="Boolean indicating whether a decorated version of the rows should be imported" />
+        <param type="boolean" name="use_default_expr_names" checked="false"  label="Use default expr names" help="Should default (non 10x-type) file names be used for expression data? Default: FALSE" />
+        <param type="text" name="exp_data_dir" label="Expression data dir" help="Name of the directory with expression data" />
+        <param type="integer" name="number_of_clusters" label="Number of clusters" help="Number of clusters in marker genes file" />
+        <param type="boolean" name="use_full_names" checked="false"  label="Use full names" help="Should non-expression data files be named with full file names? Default: FALSE" />
+    </inputs>
+    <outputs>
+        
+    </outputs>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tools/tertiary-analysis/atlas-data-import/atlas_import_macros.xml b/tools/tertiary-analysis/atlas-data-import/atlas_import_macros.xml
new file mode 100644
index 00000000..876c5709
--- /dev/null
+++ b/tools/tertiary-analysis/atlas-data-import/atlas_import_macros.xml
@@ -0,0 +1,35 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.0</token>
+    <token name="@HELP@">More information can be found at https://github.com/ebi-gene-expression-group/atlas-data-import</token>
+    <token name="@PROFILE@">18.01</token>
+    <xml name="requirements">
+      <requirements>
+        <requirement type="package" version="0.0.6">atlas-data-import</requirement>
+            <yield/>
+      </requirements>
+    </xml>
+    <xml name="version">
+      <version_command><![CDATA[
+        conda list | grep atlas-data-import | egrep -o [0-9]\.[0-9]\.[0-9]
+    ]]></version_command>
+    </xml>
+    <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+0.0.6+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
+    ]]></token>
+    <xml name="citations">
+      <citations>
+        <citation type="bibtex">
+          @misc{github-atlas-data-import.git,
+            author = {Andrey Solovyev, EBI Gene Expression Team},
+            year = {2020},
+            title = {Scripts for extracting expression- and metadata from SCXA in a programmatic way},
+            publisher = {GitHub},
+            journal = {GitHub repository},
+            url = {https://github.com/ebi-gene-expression-group/atlas-data-import.git},
+          }
+        </citation>
+        <yield />
+      </citations>
+    </xml>
+</macros>
diff --git a/tools/tertiary-analysis/atlas-data-import/atlas_import_sdrf_files.xml b/tools/tertiary-analysis/atlas-data-import/atlas_import_sdrf_files.xml
new file mode 100644
index 00000000..e69de29b

From 891e9e54c97b21efc9c359e4972f6034116e0b2c Mon Sep 17 00:00:00 2001
From: Andrey Solovyev <a.solovyev39@gmail.com>
Date: Mon, 22 Jun 2020 16:13:35 +0100
Subject: [PATCH 02/11] add new wrappers and merge the old atlas import wrapper

---
 .../atlas_import_classifiers.xml              |  29 ++++
 .../atlas_import_experiment_data.xml          |  25 ++--
 .../atlas_import_sdrf_files.xml               |  33 ++++
 .../data-scxa/atlas-retrieve-macros.xml       |  35 +++++
 .../atlas_import_experiment_data.xml          | 141 ++++++++++++++++++
 .../data-scxa/retrieve-classifiers.xml        |  29 ++++
 .../data-scxa/retrieve-scxa.xml               | 119 ---------------
 .../data-scxa/retrieve-sdrf-files.xml         |  33 ++++
 8 files changed, 314 insertions(+), 130 deletions(-)
 create mode 100644 tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml
 create mode 100644 tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml
 create mode 100644 tools/tertiary-analysis/data-scxa/retrieve-classifiers.xml
 delete mode 100644 tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
 create mode 100644 tools/tertiary-analysis/data-scxa/retrieve-sdrf-files.xml

diff --git a/tools/tertiary-analysis/atlas-data-import/atlas_import_classifiers.xml b/tools/tertiary-analysis/atlas-data-import/atlas_import_classifiers.xml
index e69de29b..ff547252 100644
--- a/tools/tertiary-analysis/atlas-data-import/atlas_import_classifiers.xml
+++ b/tools/tertiary-analysis/atlas-data-import/atlas_import_classifiers.xml
@@ -0,0 +1,29 @@
+<tool id="atlas_import_classifiers" name="Atlas import: get classifiers" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
+    <description>Import pre-trained classifiers from Single Cell Expression Atlas</description>
+    <macros>
+         <import>atlas_import_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        import_classifiers.R  --tool "${tool}" --classifiers-output-dir "${classifier_output_dir}"
+
+        #if $config_file 
+        --config-file "${config_file}" 
+        #end if
+    ]]></command>
+    <inputs>
+        <param type="data" name="config_file" label="Config file" format="yml" help="Config file with user-provided parameters" />
+        <param type="text" name="tool" label="Tool" help="For which tool should the classifiers be imported?" />
+    </inputs>
+    <outputs>
+        <collection name="imported_classifiers" type="list" label="Collection of imported classifiers">
+            <discover_datasets pattern="__name_and_ext__" directory="${classifier_output_dir}" />
+        </collection>
+    </outputs>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file
diff --git a/tools/tertiary-analysis/atlas-data-import/atlas_import_experiment_data.xml b/tools/tertiary-analysis/atlas-data-import/atlas_import_experiment_data.xml
index e82a1c7f..8d41d06e 100644
--- a/tools/tertiary-analysis/atlas-data-import/atlas_import_experiment_data.xml
+++ b/tools/tertiary-analysis/atlas-data-import/atlas_import_experiment_data.xml
@@ -16,18 +16,12 @@
         #if $use_default_expr_names 
         --use-default-expr-names "${use_default_expr_names}" 
         #end if
-        #if $exp_data_dir 
-        --exp-data-dir "${exp_data_dir}" 
-        #end if
         #if $get_idf 
         --get-idf "${get_idf}" 
         #end if
         #if $number_of_clusters 
         --number-of-clusters  "${number_of_clusters}" 
         #end if
-        #if $use_full_names
-        --use-full-names  "${use_full_names}" 
-        #end if
     ]]></command>
     <inputs>
         <param type="text" name="accession_code" label="Accession code" help="Accession code of dataset to be downloaded" />
@@ -37,19 +31,28 @@
             <option value="tpm">TPM-normalised</option>
             <option value="cpm">CPM-normalised</option>
         </param>
-        <param type="boolean" name="get_sdrf" checked="false"  label="Import SDRF file" help="Boolean indicating whether SDRF file needs to be imported" />
-        <param type="boolean" name="get_idf" checked="false"  label="Import IDF file" help="Boolean indicating whether IDF file needs to be imported" />
+        <param type="boolean" name="get_sdrf" checked="false" label="Import SDRF file" help="Boolean indicating whether SDRF file needs to be imported" />
+        <param type="boolean" name="get_idf" checked="false" label="Import IDF file" help="Boolean indicating whether IDF file needs to be imported" />
         <param type="boolean" name="get_condensed_sdrf" checked="false"  label="Get condensed SDRF file" help="Boolean indicating whether condensed SDRF file needs to be imported" />
         <param type="boolean" name="get_marker_genes" checked="false"  label="Import marker genes" help="Boolean indicating whether marker genes should be imported" />
         <param type="data" name="config_file" label="Config file" format="yml" help="Config file with user-provided parameters" />
         <param type="boolean" name="decorated_rows" checked="false"  label="Decorated rows" help="Boolean indicating whether a decorated version of the rows should be imported" />
         <param type="boolean" name="use_default_expr_names" checked="false"  label="Use default expr names" help="Should default (non 10x-type) file names be used for expression data? Default: FALSE" />
-        <param type="text" name="exp_data_dir" label="Expression data dir" help="Name of the directory with expression data" />
         <param type="integer" name="number_of_clusters" label="Number of clusters" help="Number of clusters in marker genes file" />
-        <param type="boolean" name="use_full_names" checked="false"  label="Use full names" help="Should non-expression data files be named with full file names? Default: FALSE" />
     </inputs>
     <outputs>
-        
+        <data name="expr_mtx" format="txt" from_work_dir="${accession_code}/10x_data/matrix.mtx" />
+        <data name="barcodes" format="txt" from_work_dir="${accession_code}/10x_data/barcodes.tsv" />
+        <data name="genes" format="txt" from_work_dir="${accession_code}/10x_data/genes.tsv" />
+        <data name="sdrf" format="txt" from_work_dir="${accession_code}/sdrf.txt">
+            <filter>get_sdrf==True</filter>
+        </data>
+        <data name="idf" format="txt" from_work_dir="${accession_code}/idf.txt">
+            <filter>get_idf==True</filter>
+        </data>
+        <data name="marker_genes" format="txt" from_work_dir="${accession_code}/marker_genes_${number_of_clusters}.tsv">
+            <filter>get_marker_genes==True</filter>
+        </data>
     </outputs>
     <help><![CDATA[
     @HELP@
diff --git a/tools/tertiary-analysis/atlas-data-import/atlas_import_sdrf_files.xml b/tools/tertiary-analysis/atlas-data-import/atlas_import_sdrf_files.xml
index e69de29b..eb7299b1 100644
--- a/tools/tertiary-analysis/atlas-data-import/atlas_import_sdrf_files.xml
+++ b/tools/tertiary-analysis/atlas-data-import/atlas_import_sdrf_files.xml
@@ -0,0 +1,33 @@
+<tool id="atlas_import_sdrf_files" name="Atlas import: get sdrf files" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
+    <description>Import sdrf files from Single Cell Expression Atlas</description>
+    <macros>
+         <import>atlas_import_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        import_sdrf_files.R --sdrf-output-dir "${sdrf_output_dir}"
+
+        #if $config_file 
+        --config-file "${config_file}" 
+        #end if
+        #if $get_condensed_sdrf 
+        --get-condensed-sdrf "${get_condensed_sdrf}" 
+        #end if
+
+    ]]></command>
+    <inputs>
+        <param type="data" name="config_file" label="Config file" format="yml" help="Config file with user-provided parameters" />
+        <param type="boolean" name="get_condensed_sdrf" checked="false"  label="Get condensed sdrf files" help="Boolean indicating whether condensed SDRF files should be imported" />
+    </inputs>
+    <outputs>
+        <collection name="imported_sdrf_files" type="list" label="Collection of imported classifiers">
+            <discover_datasets pattern="__name_and_ext__" directory="${sdrf_output_dir}" />
+        </collection>
+    </outputs>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file
diff --git a/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml b/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml
new file mode 100644
index 00000000..876c5709
--- /dev/null
+++ b/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml
@@ -0,0 +1,35 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.0</token>
+    <token name="@HELP@">More information can be found at https://github.com/ebi-gene-expression-group/atlas-data-import</token>
+    <token name="@PROFILE@">18.01</token>
+    <xml name="requirements">
+      <requirements>
+        <requirement type="package" version="0.0.6">atlas-data-import</requirement>
+            <yield/>
+      </requirements>
+    </xml>
+    <xml name="version">
+      <version_command><![CDATA[
+        conda list | grep atlas-data-import | egrep -o [0-9]\.[0-9]\.[0-9]
+    ]]></version_command>
+    </xml>
+    <token name="@VERSION_HISTORY@"><![CDATA[
+**Version history**
+0.0.6+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
+    ]]></token>
+    <xml name="citations">
+      <citations>
+        <citation type="bibtex">
+          @misc{github-atlas-data-import.git,
+            author = {Andrey Solovyev, EBI Gene Expression Team},
+            year = {2020},
+            title = {Scripts for extracting expression- and metadata from SCXA in a programmatic way},
+            publisher = {GitHub},
+            journal = {GitHub repository},
+            url = {https://github.com/ebi-gene-expression-group/atlas-data-import.git},
+          }
+        </citation>
+        <yield />
+      </citations>
+    </xml>
+</macros>
diff --git a/tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml b/tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml
new file mode 100644
index 00000000..0ed5a865
--- /dev/null
+++ b/tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml
@@ -0,0 +1,141 @@
+<tool id="atlas_import_experiment_data" name="Atlas import: get experiment data" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
+    <description>Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA)</description>
+    <macros>
+         <import>atlas-retrieve-macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        get_experiment_data.R --accession-code "${accession_code}" --matrix-type "${matrix_type}" --get-sdrf "${get_sdrf}" --get-condensed-sdrf "${get_condensed_sdrf}" --get-marker-genes "${get_marker_genes}" 
+
+        #if $config_file 
+        --config-file "${config_file}" 
+        #end if
+        #if $get_exp_design
+        --get-exp-design "${get_exp_design}"
+        #end if 
+        #if $decorated_rows 
+        --decorated-rows "${decorated_rows}" 
+        #end if
+        #if $use_default_expr_names 
+        --use-default-expr-names "${use_default_expr_names}" 
+        #end if
+        #if $get_idf 
+        --get-idf "${get_idf}" 
+        #end if
+        #if $number_of_clusters 
+        --number-of-clusters  "${number_of_clusters}" 
+        #end if
+    ]]></command>
+    <inputs>
+        <param type="text" name="accession_code" label="SC-Atlas experiment accession" value="E-GEOD-100058" help="EBI Single Cell Atlas accession for the experiment that you want to retrieve." />
+        <param type="select" name="matrix_type" label="Choose the type of matrix to download"  help="Type of matrix to be imported">
+            <option value="raw">Raw</option>
+            <option value="filtered">Filtered Counts</option>
+            <option value="tpm">TPM-normalised</option>
+            <option value="cpm">CPM-normalised</option>
+        </param>
+        <param type="boolean" name="get_sdrf" checked="false" label="Import SDRF file" help="Boolean indicating whether SDRF file needs to be imported" />
+        <param type="boolean" name="get_exp_design" checked="false" label="Import experiment design file" help="Boolean indicating whether experiment design file needs to be imported" />
+        <param type="boolean" name="get_idf" checked="false" label="Import IDF file" help="Boolean indicating whether IDF file needs to be imported" />
+        <param type="boolean" name="get_condensed_sdrf" checked="false"  label="Get condensed SDRF file" help="Boolean indicating whether condensed SDRF file needs to be imported" />
+        <param type="boolean" name="get_marker_genes" checked="false"  label="Import marker genes" help="Boolean indicating whether marker genes should be imported" />
+        <param type="data" name="config_file" label="Config file" format="yml" help="Config file with user-provided parameters" />
+        <param type="boolean" name="decorated_rows" checked="false"  label="Decorated rows" help="Boolean indicating whether a decorated version of the rows should be imported" />
+        <param type="boolean" name="use_default_expr_names" checked="false"  label="Use default expr names" help="Should default (non 10x-type) file names be used for expression data? Default: FALSE" />
+        <param type="integer" name="number_of_clusters" label="Number of clusters" help="Number of clusters in marker genes file" />
+    </inputs>
+    <outputs>
+        <data name="expr_mtx" format="txt" from_work_dir="${accession_code}/10x_data/matrix.mtx" label="${tool.name} on ${on_string} ${accession} matrix.mtx (${matrix_type.value_label})" />
+        <data name="barcodes" format="txt" from_work_dir="${accession_code}/10x_data/barcodes.tsv" label="${tool.name} on ${on_string} ${accession} barcodes.tsv (${matrix_type.value_label})" />
+        <data name="genes" format="txt" from_work_dir="${accession_code}/10x_data/genes.tsv" label="${tool.name} on ${on_string} ${accession} genes.tsv (${matrix_type.value_label})" />
+        <data name="sdrf" format="txt" from_work_dir="${accession_code}/sdrf.txt" label="${tool.name} on ${on_string} ${accession} sdrf.txt (${matrix_type.value_label})" >
+            <filter>get_sdrf</filter>
+        </data>
+        <data name="idf" format="txt" from_work_dir="${accession_code}/idf.txt" label="${tool.name} on ${on_string} ${accession} idf.txt (${matrix_type.value_label})">
+            <filter>get_idf</filter>
+        </data>
+        <data name="marker_genes" format="txt" from_work_dir="${accession_code}/marker_genes_${number_of_clusters}.tsv" >
+            <filter>get_marker_genes</filter>
+        </data>
+        <data name="exp_design" format="txt" from_work_dir="${accession_code}/exp_design.tsv" >
+            <filter>get_exp_design</filter>
+        </data>
+    </outputs>
+    <help><![CDATA[
+=================================================================================
+Gene expression analysis in single cells across species and biological conditions
+=================================================================================
+
+Single Cell Expression Atlas supports research in single cell transcriptomics.
+The Atlas annotates publicly available single cell RNA-Seq experiments with
+ontology identifiers and re-analyses them using standardised pipelines available
+through iRAP, our RNA-Seq analysis toolkit. The browser enables visualisation of
+clusters of cells, their annotations and supports searches for gene expression
+within and across studies.
+
+For more information check https://www.ebi.ac.uk/gxa/sc/home
+
+EBI SCXA Data Retrieval
+-----------------------
+
+The data retrieval tool presented here allows the user to retrieve expression matrices
+and metadata for any public experiment available at EBI Single Cell Expression Atlas.
+
+To use it, simply set the accession for the desired experiment and choose the type of
+matrix that you want to download:
+
+:Raw counts:
+  Un-normalised, unfiltered version of the expression data. 
+
+:Filtered counts:
+  This should be the default choice for running clustering and another analysis
+  methods where you will introduce scaling and normalization of the data. The filtering
+  is based on the quality control applied by iRAP prior to pseudo-alignment and quantification.
+
+:TPMs:
+  TPM stands for Transcripts Per Kilobase Million, and as the name implies, this has been
+  already normalized/scaled. You should keep this in mind when using this data
+  on methods that will try to normalise data as part of their procedure. Due to technical
+  particularities in the current Atlas SC pipeline, TPMs available here are not filtered.
+  **Note: droplet databases won't have TPM data**
+
+:CPMS:
+  CPM normalisation stands for Counts Per Kilobase Million. As TPMs, these matrices are already normalised/scaled. You should keep this in mind when using this data on methods that will try to normalise data as part of their procedure.   
+
+Outputs will be:
+
+:Matrix (txt):
+  Contains the expression values for genes (rows) and samples/runs/cells (columns),
+  in either raw filtered counts or filtered tpms depending on the choice made. This
+  text file is formatted as a Matrix Market file, and as such it is accompanied by
+  separate files for the gene identifiers and the samples/runs/cells identifiers.
+
+:Genes (tsv):
+  Identifiers (column repeated) for the genes present in the matrix of expression,
+  in the same order as the matrix rows.
+
+:Barcodes (tsv):
+  Identifiers for the cells, samples or runs of the data matrix. The file is ordered
+  to match the columns of the matrix.
+
+Optional outputs: 
+
+:Experiment Design file (tsv):
+  Contains metadata for the different cells/samples/runs of the experiment.
+  Please note that this file is generated before the filtering step, and while not
+  often, it might be the case that it contains more cells/samples/runs than the matrix.
+
+:SDRF file (txt):
+  Similar to Experiment Design file, contains information on individual cells/sequencing runs. Might contain information on technical duplicates. 
+
+:IDF file (txt): 
+  IDF file holds general information about the sequencing experiment and interpretation of the fields in SDRF/metadata files. 
+  
+:Marker gene file (txt):
+  File containing information on marker genes that differentiate cell types present in the sequencing experiment. 
+
+@HELP@
+@VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff --git a/tools/tertiary-analysis/data-scxa/retrieve-classifiers.xml b/tools/tertiary-analysis/data-scxa/retrieve-classifiers.xml
new file mode 100644
index 00000000..a14561aa
--- /dev/null
+++ b/tools/tertiary-analysis/data-scxa/retrieve-classifiers.xml
@@ -0,0 +1,29 @@
+<tool id="atlas_import_classifiers" name="Atlas import: get classifiers" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
+    <description>Import pre-trained classifiers from Single Cell Expression Atlas</description>
+    <macros>
+         <import>atlas-retrieve-macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        import_classifiers.R  --tool "${tool}" --classifiers-output-dir "${classifier_output_dir}"
+
+        #if $config_file 
+        --config-file "${config_file}" 
+        #end if
+    ]]></command>
+    <inputs>
+        <param type="data" name="config_file" label="Config file" format="yml" help="Config file with user-provided parameters" />
+        <param type="text" name="tool" label="Tool" help="For which tool should the classifiers be imported?" />
+    </inputs>
+    <outputs>
+        <collection name="imported_classifiers" type="list" label="Collection of imported classifiers">
+            <discover_datasets pattern="__name_and_ext__" directory="${classifier_output_dir}" />
+        </collection>
+    </outputs>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file
diff --git a/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml b/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
deleted file mode 100644
index 595337d1..00000000
--- a/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
+++ /dev/null
@@ -1,119 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<tool id="retrieve_scxa" name="EBI SCXA Data Retrieval" version="v0.0.2+galaxy2">
-  <description>Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA)</description>
-  <requirements>
-    <requirement type="package" version="1.20.1">wget</requirement>
-  </requirements>
-  <command detect_errors="exit_code"><![CDATA[
-
-#if str($matrix_type) == "tpm":
-
-wget -O exp_quant.zip
-    'https://www.ebi.ac.uk/gxa/sc/experiment/${accession}/download/zip?fileType=quantification-filtered&accessKey=' &&
-unzip exp_quant.zip;
-mv '${accession}'.expression_tpm.mtx ${matrix_mtx} &&
-awk '{OFS="\t"; print \$2,\$2}' '${accession}'.expression_tpm.mtx_rows > ${genes_tsv} &&
-cut -f2 '${accession}'.expression_tpm.mtx_cols > ${barcode_tsv};
-
-#else if str($matrix_type) == "raw":
-
-wget -O ${matrix_mtx} 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.mtx';
-wget -qO - 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.mtx_cols' | cut -f2 > ${barcode_tsv};
-wget -qO - 'ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/sc_experiments/${accession}/${accession}.aggregated_filtered_counts.decorated.mtx_rows' |
-  awk -F'\t' '{ if (length($2) == 0) { print $1"\t"$1 } else { print $0 } }' > ${genes_tsv};
-
-#end if
-
-wget -O exp_design.tsv
-    'https://www.ebi.ac.uk/gxa/sc/experiment/${accession}/download?fileType=experiment-design&accessKey=';
-
-]]></command>
-
-  <inputs>
-    <param name="accession" type="text" value="E-GEOD-100058" label="SC-Atlas experiment accession" help="EBI Single Cell Atlas accession for the experiment that you want to retrieve."/>
-    <param name="matrix_type" type="select" label="Choose the type of matrix to download" help="Raw filtered counts or (non-filtered) TPMs">
-      <option value="raw" selected="true">Raw filtered counts</option>
-      <option value="tpm">TPMs</option>
-    </param>
-  </inputs>
-
-  <outputs>
-    <data name="matrix_mtx" format="txt" label="${tool.name} on ${on_string} ${accession} matrix.mtx (${matrix_type.value_label})"/>
-    <data name="genes_tsv" format="tsv" label="${tool.name} on ${on_string} ${accession} genes.tsv (${matrix_type.value_label})"/>
-    <data name="barcode_tsv" format="tsv" label="${tool.name} on ${on_string} ${accession} barcodes.tsv (${matrix_type.value_label})"/>
-    <data name="design_tsv" format="tsv" from_work_dir="exp_design.tsv" label="${tool.name} on ${on_string} ${accession} exp_design.tsv"/>
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="accession" value="E-GEOD-100058"/>
-      <param name="matrix_type" value="tpm"/>
-      <output name="matrix_mtx" file="E-GEOD-100058.expression_tpm.mtx" ftype="txt"/>
-      <output name="genes_tsv" file="E-GEOD-100058.genes.tsv" ftype="tsv"/>
-      <output name="barcode_tsv" file="E-GEOD-100058.barcodes.tsv" ftype="tsv"/>
-      <output name="design_tsv" file="E-GEOD-100058.exp_design.tsv" ftype="tsv"/>
-    </test>
-  </tests>
-
-  <help><![CDATA[
-=================================================================================
-Gene expression analysis in single cells across species and biological conditions
-=================================================================================
-
-Single Cell Expression Atlas supports research in single cell transcriptomics.
-The Atlas annotates publicly available single cell RNA-Seq experiments with
-ontology identifiers and re-analyses them using standardised pipelines available
-through iRAP, our RNA-Seq analysis toolkit. The browser enables visualisation of
-clusters of cells, their annotations and supports searches for gene expression
-within and across studies.
-
-For more information check https://www.ebi.ac.uk/gxa/sc/home
-
-EBI SCXA Data Retrieval
------------------------
-
-The data retrieval tool presented here allows the user to retrieve expression matrices
-and metadata for any public experiment available at EBI Single Cell Expression Atlas.
-
-To use it, simply set the accession for the desired experiment and choose the type of
-matrix that you want to download:
-
-:Raw filtered counts:
-  This should be the default choice for running clustering and another analysis
-  methods where you will introduce scaling and normalization of the data. The filtering
-  is based on the quality control applied by iRAP prior to pseudo-alignment and quantification.
-
-:TPMs:
-  TPM stands for Transcripts Per Kilobase Million, and as the name implies, this has been
-  already normalized/scaled. You should keep this in mind when using this data
-  on methods that will try to normalise data as part of their procedure. Due to technical
-  particularities in the current Atlas SC pipeline, TPMs available here are not filtered.
-  **Note: droplet databases won't have TPM data**
-
-Outputs will be:
-
-:Matrix (txt):
-  Contains the expression values for genes (rows) and samples/runs/cells (columns),
-  in either raw filtered counts or filtered tpms depending on the choice made. This
-  text file is formatted as a Matrix Market file, and as such it is accompanied by
-  separate files for the gene identifiers and the samples/runs/cells identifiers.
-
-:Genes (tsv):
-  Identifiers (column repeated) for the genes present in the matrix of expression,
-  in the same order as the matrix rows.
-
-:Barcodes (tsv):
-  Identifiers for the cells, samples or runs of the data matrix. The file is ordered
-  to match the columns of the matrix.
-
-:Experiment Design file (tsv):
-  Contains metadata for the different cells/samples/runs of the experiment.
-  Please note that this file is generated before the filtering step, and while not
-  often, it might be the case that it contains more cells/samples/runs than the matrix.
-
-]]></help>
-  <citations>
-    <citation type="doi">10.1093/nar/gkv1045</citation>
-    <citation type="doi">10.1101/2020.04.08.032698</citation>
-  </citations>
-</tool>
diff --git a/tools/tertiary-analysis/data-scxa/retrieve-sdrf-files.xml b/tools/tertiary-analysis/data-scxa/retrieve-sdrf-files.xml
new file mode 100644
index 00000000..eb94e2ec
--- /dev/null
+++ b/tools/tertiary-analysis/data-scxa/retrieve-sdrf-files.xml
@@ -0,0 +1,33 @@
+<tool id="atlas_import_sdrf_files" name="Atlas import: get sdrf files" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
+    <description>Import sdrf files from Single Cell Expression Atlas</description>
+    <macros>
+         <import>atlas-retrieve-macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        import_sdrf_files.R --sdrf-output-dir "${sdrf_output_dir}"
+
+        #if $config_file 
+        --config-file "${config_file}" 
+        #end if
+        #if $get_condensed_sdrf 
+        --get-condensed-sdrf "${get_condensed_sdrf}" 
+        #end if
+
+    ]]></command>
+    <inputs>
+        <param type="data" name="config_file" label="Config file" format="yml" help="Config file with user-provided parameters" />
+        <param type="boolean" name="get_condensed_sdrf" checked="false"  label="Get condensed sdrf files" help="Boolean indicating whether condensed SDRF files should be imported" />
+    </inputs>
+    <outputs>
+        <collection name="imported_sdrf_files" type="list" label="Collection of imported classifiers">
+            <discover_datasets pattern="__name_and_ext__" directory="${sdrf_output_dir}" />
+        </collection>
+    </outputs>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file

From cc22b6e3c29ab2d6c9a27ce5eb02d4b4f1b4ff5f Mon Sep 17 00:00:00 2001
From: Andrey Solovyev <a.solovyev39@gmail.com>
Date: Thu, 25 Jun 2020 15:44:42 +0100
Subject: [PATCH 03/11] rename file

---
 .../retrieve-classification-data.xml          | 59 +++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 tools/tertiary-analysis/data-scxa/retrieve-classification-data.xml

diff --git a/tools/tertiary-analysis/data-scxa/retrieve-classification-data.xml b/tools/tertiary-analysis/data-scxa/retrieve-classification-data.xml
new file mode 100644
index 00000000..2ffffd7e
--- /dev/null
+++ b/tools/tertiary-analysis/data-scxa/retrieve-classification-data.xml
@@ -0,0 +1,59 @@
+<tool id="atlas_import_classifiers" name="Atlas import: get classifiers" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
+    <description>Import pre-trained classifiers and SDRF files for a range of studies from Single Cell Expression Atlas</description>
+    <macros>
+         <import>atlas-retrieve-macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        import_classification_data.R  --tool "${tool}" --classifiers-output-dir "${classifier_output_dir}"
+
+        #if $config_file 
+        --config-file "${config_file}" 
+        #end if
+        #if $get_sdrf 
+        --get-sdrf "${get_sdrf}" 
+        #end if
+        #if $condensed_sdrf 
+        --condensed-sdrf "${condensed_sdrf}" 
+        #end if
+        #if $sdrf_output_dir 
+        --sdrf-output-dir "${sdrf_output_dir}" 
+        #end if
+        #if $get_tool_perf_table 
+        --get-tool-perf-table "${get_tool_perf_table}" 
+        #end if
+        #if $tool_perf_table_output_path 
+        --tool-perf-table-output-path "${tool_perf_table_output_path}" 
+        #end if
+
+    ]]></command>
+    <inputs>
+        <param type="data" name="config_file" label="Config file" format="yml" help="Config file with user-provided parameters" />
+        <param type="text" name="tool" label="Tool" help="For which tool should the classifiers be imported?" />
+        <conditional name="get_sdrf">
+        <param name="import_sdrf_files" type="boolean" checked="false" label="Import SDRF files for the given experiments?" help="If specified, SDRF files will also be imported"/>
+        <when value="true" >
+          <param name="condensed_sdrf" type="boolean" label="Import condensed version of SDRF files?" checked="false" help="Should condensed SDRF files be imported? By default, normal version is imported." />
+        </when>
+        <when value="false">
+          <param name="condensed_sdrf" type="hidden" value="NULL" />
+        </when>
+      </conditional>
+    </inputs>
+    <outputs>
+        <collection name="imported_classifiers" type="list" label="Collection of imported classifiers">
+            <discover_datasets pattern="__name_and_ext__" directory="${classifier_output_dir}" />
+        </collection>
+        <collection name="imported_sdrfs" type="list" label="Collection of imported SDRF files">
+            <discover_datasets pattern="__name_and_ext__" directory="${sdrf_output_dir}" />
+            <filter>get_sdrf['import_sdrf_files']</filter>
+        </collection>
+        <data name="tool_perf_table_output_path" format="tsv" />
+    </outputs>
+    <help><![CDATA[
+    @HELP@
+    
+    @VERSION_HISTORY@
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file

From e4756b05beb40b58d467da010c0d060488b09488 Mon Sep 17 00:00:00 2001
From: Andrey Solovyev <a.solovyev39@gmail.com>
Date: Fri, 3 Jul 2020 14:40:52 +0100
Subject: [PATCH 04/11] update wrappers

---
 .../data-scxa/atlas-retrieve-macros.xml       |  2 +-
 .../atlas_import_experiment_data.xml          |  7 ++--
 .../retrieve-classification-data.xml          | 32 +++++++++---------
 .../data-scxa/retrieve-classifiers.xml        | 29 ----------------
 .../data-scxa/retrieve-sdrf-files.xml         | 33 -------------------
 5 files changed, 21 insertions(+), 82 deletions(-)
 delete mode 100644 tools/tertiary-analysis/data-scxa/retrieve-classifiers.xml
 delete mode 100644 tools/tertiary-analysis/data-scxa/retrieve-sdrf-files.xml

diff --git a/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml b/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml
index 876c5709..36d480c9 100644
--- a/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml
+++ b/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml
@@ -4,7 +4,7 @@
     <token name="@PROFILE@">18.01</token>
     <xml name="requirements">
       <requirements>
-        <requirement type="package" version="0.0.6">atlas-data-import</requirement>
+        <requirement type="package" version="0.0.9">atlas-data-import</requirement>
             <yield/>
       </requirements>
     </xml>
diff --git a/tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml b/tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml
index 0ed5a865..1605ccbd 100644
--- a/tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml
+++ b/tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml
@@ -1,5 +1,5 @@
 <tool id="atlas_import_experiment_data" name="Atlas import: get experiment data" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
-    <description>Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA)</description>
+    <description>Retrieve expression matrices and metadata from EBI Single Cell Expression Atlas (SCXA)</description>
     <macros>
          <import>atlas-retrieve-macros.xml</import>
     </macros>
@@ -39,7 +39,7 @@
         <param type="boolean" name="get_idf" checked="false" label="Import IDF file" help="Boolean indicating whether IDF file needs to be imported" />
         <param type="boolean" name="get_condensed_sdrf" checked="false"  label="Get condensed SDRF file" help="Boolean indicating whether condensed SDRF file needs to be imported" />
         <param type="boolean" name="get_marker_genes" checked="false"  label="Import marker genes" help="Boolean indicating whether marker genes should be imported" />
-        <param type="data" name="config_file" label="Config file" format="yml" help="Config file with user-provided parameters" />
+        <param type="data" name="config_file" label="Config file" optional="true" format="yml" help="Config file with user-provided parameters" />
         <param type="boolean" name="decorated_rows" checked="false"  label="Decorated rows" help="Boolean indicating whether a decorated version of the rows should be imported" />
         <param type="boolean" name="use_default_expr_names" checked="false"  label="Use default expr names" help="Should default (non 10x-type) file names be used for expression data? Default: FALSE" />
         <param type="integer" name="number_of_clusters" label="Number of clusters" help="Number of clusters in marker genes file" />
@@ -51,6 +51,9 @@
         <data name="sdrf" format="txt" from_work_dir="${accession_code}/sdrf.txt" label="${tool.name} on ${on_string} ${accession} sdrf.txt (${matrix_type.value_label})" >
             <filter>get_sdrf</filter>
         </data>
+        <data name="condensed_sdrf" format="txt" from_work_dir="${accession_code}/condensed-sdrf.tsv" label="${tool.name} on ${on_string} ${accession} condensed-sdrf.tsv (${matrix_type.value_label})" >
+            <filter>get_condensed_sdrf</filter>
+        </data>
         <data name="idf" format="txt" from_work_dir="${accession_code}/idf.txt" label="${tool.name} on ${on_string} ${accession} idf.txt (${matrix_type.value_label})">
             <filter>get_idf</filter>
         </data>
diff --git a/tools/tertiary-analysis/data-scxa/retrieve-classification-data.xml b/tools/tertiary-analysis/data-scxa/retrieve-classification-data.xml
index 2ffffd7e..ebd69904 100644
--- a/tools/tertiary-analysis/data-scxa/retrieve-classification-data.xml
+++ b/tools/tertiary-analysis/data-scxa/retrieve-classification-data.xml
@@ -5,21 +5,16 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        import_classification_data.R  --tool "${tool}" --classifiers-output-dir "${classifier_output_dir}"
+        import_classification_data.R  --tool "${tool}" 
 
         #if $config_file 
         --config-file "${config_file}" 
         #end if
-        #if $get_sdrf 
-        --get-sdrf "${get_sdrf}" 
+        #if $import_sdrf_files.get_sdrf 
+        --get-sdrf "${import_sdrf_files.get_sdrf}" 
+        --condensed-sdrf "${import_sdrf_files.condensed_sdrf}" 
         #end if
-        #if $condensed_sdrf 
-        --condensed-sdrf "${condensed_sdrf}" 
-        #end if
-        #if $sdrf_output_dir 
-        --sdrf-output-dir "${sdrf_output_dir}" 
-        #end if
-        #if $get_tool_perf_table 
+        #if $get_tool_perf_table
         --get-tool-perf-table "${get_tool_perf_table}" 
         #end if
         #if $tool_perf_table_output_path 
@@ -28,10 +23,10 @@
 
     ]]></command>
     <inputs>
-        <param type="data" name="config_file" label="Config file" format="yml" help="Config file with user-provided parameters" />
+        <param type="data" name="config_file" label="Config file" format="yml" optional="true" help="Config file with user-provided parameters" />
         <param type="text" name="tool" label="Tool" help="For which tool should the classifiers be imported?" />
-        <conditional name="get_sdrf">
-        <param name="import_sdrf_files" type="boolean" checked="false" label="Import SDRF files for the given experiments?" help="If specified, SDRF files will also be imported"/>
+        <conditional name="import_sdrf_files">
+        <param name="get_sdrf" type="boolean" checked="false" label="Import SDRF files for the given experiments?" help="If specified, SDRF files will be imported"/>
         <when value="true" >
           <param name="condensed_sdrf" type="boolean" label="Import condensed version of SDRF files?" checked="false" help="Should condensed SDRF files be imported? By default, normal version is imported." />
         </when>
@@ -39,16 +34,19 @@
           <param name="condensed_sdrf" type="hidden" value="NULL" />
         </when>
       </conditional>
+      <param name="get_tool_perf_table" type="boolean" checked="false" label="Import tool performance table" help="If specified, tool performance table will be imported"/>
     </inputs>
     <outputs>
         <collection name="imported_classifiers" type="list" label="Collection of imported classifiers">
-            <discover_datasets pattern="__name_and_ext__" directory="${classifier_output_dir}" />
+            <discover_datasets pattern="__name_and_ext__" directory="imported_classifiers" />
         </collection>
         <collection name="imported_sdrfs" type="list" label="Collection of imported SDRF files">
-            <discover_datasets pattern="__name_and_ext__" directory="${sdrf_output_dir}" />
-            <filter>get_sdrf['import_sdrf_files']</filter>
+            <discover_datasets pattern="__name_and_ext__" directory="imported_SDRFs" />
+            <filter>import_sdrf_files['get_sdrf']</filter>
         </collection>
-        <data name="tool_perf_table_output_path" format="tsv" />
+        <data name="tool_perf_table_output_path" format="tsv">
+            <filter>get_tool_perf_table</filter>
+        </data>
     </outputs>
     <help><![CDATA[
     @HELP@
diff --git a/tools/tertiary-analysis/data-scxa/retrieve-classifiers.xml b/tools/tertiary-analysis/data-scxa/retrieve-classifiers.xml
deleted file mode 100644
index a14561aa..00000000
--- a/tools/tertiary-analysis/data-scxa/retrieve-classifiers.xml
+++ /dev/null
@@ -1,29 +0,0 @@
-<tool id="atlas_import_classifiers" name="Atlas import: get classifiers" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
-    <description>Import pre-trained classifiers from Single Cell Expression Atlas</description>
-    <macros>
-         <import>atlas-retrieve-macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <command detect_errors="exit_code"><![CDATA[
-        import_classifiers.R  --tool "${tool}" --classifiers-output-dir "${classifier_output_dir}"
-
-        #if $config_file 
-        --config-file "${config_file}" 
-        #end if
-    ]]></command>
-    <inputs>
-        <param type="data" name="config_file" label="Config file" format="yml" help="Config file with user-provided parameters" />
-        <param type="text" name="tool" label="Tool" help="For which tool should the classifiers be imported?" />
-    </inputs>
-    <outputs>
-        <collection name="imported_classifiers" type="list" label="Collection of imported classifiers">
-            <discover_datasets pattern="__name_and_ext__" directory="${classifier_output_dir}" />
-        </collection>
-    </outputs>
-    <help><![CDATA[
-    @HELP@
-    
-    @VERSION_HISTORY@
-    ]]></help>
-    <expand macro="citations" />
-</tool>
\ No newline at end of file
diff --git a/tools/tertiary-analysis/data-scxa/retrieve-sdrf-files.xml b/tools/tertiary-analysis/data-scxa/retrieve-sdrf-files.xml
deleted file mode 100644
index eb94e2ec..00000000
--- a/tools/tertiary-analysis/data-scxa/retrieve-sdrf-files.xml
+++ /dev/null
@@ -1,33 +0,0 @@
-<tool id="atlas_import_sdrf_files" name="Atlas import: get sdrf files" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
-    <description>Import sdrf files from Single Cell Expression Atlas</description>
-    <macros>
-         <import>atlas-retrieve-macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <command detect_errors="exit_code"><![CDATA[
-        import_sdrf_files.R --sdrf-output-dir "${sdrf_output_dir}"
-
-        #if $config_file 
-        --config-file "${config_file}" 
-        #end if
-        #if $get_condensed_sdrf 
-        --get-condensed-sdrf "${get_condensed_sdrf}" 
-        #end if
-
-    ]]></command>
-    <inputs>
-        <param type="data" name="config_file" label="Config file" format="yml" help="Config file with user-provided parameters" />
-        <param type="boolean" name="get_condensed_sdrf" checked="false"  label="Get condensed sdrf files" help="Boolean indicating whether condensed SDRF files should be imported" />
-    </inputs>
-    <outputs>
-        <collection name="imported_sdrf_files" type="list" label="Collection of imported classifiers">
-            <discover_datasets pattern="__name_and_ext__" directory="${sdrf_output_dir}" />
-        </collection>
-    </outputs>
-    <help><![CDATA[
-    @HELP@
-    
-    @VERSION_HISTORY@
-    ]]></help>
-    <expand macro="citations" />
-</tool>
\ No newline at end of file

From 04a9cf52b275fdde8ffa38caac947aa2cdf543b2 Mon Sep 17 00:00:00 2001
From: Andrey Solovyev <a.solovyev39@gmail.com>
Date: Mon, 6 Jul 2020 16:42:00 +0100
Subject: [PATCH 05/11] rename wrapper

---
 ..._experiment_data.xml => retrieve-scxa.xml} | 30 +++++++++----------
 1 file changed, 15 insertions(+), 15 deletions(-)
 rename tools/tertiary-analysis/data-scxa/{atlas_import_experiment_data.xml => retrieve-scxa.xml} (82%)

diff --git a/tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml b/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
similarity index 82%
rename from tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml
rename to tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
index 1605ccbd..4473966f 100644
--- a/tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml
+++ b/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
@@ -1,11 +1,11 @@
-<tool id="atlas_import_experiment_data" name="Atlas import: get experiment data" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
+<tool id="retrieve_scxa" name="Atlas import: get experiment data" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
     <description>Retrieve expression matrices and metadata from EBI Single Cell Expression Atlas (SCXA)</description>
     <macros>
          <import>atlas-retrieve-macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        get_experiment_data.R --accession-code "${accession_code}" --matrix-type "${matrix_type}" --get-sdrf "${get_sdrf}" --get-condensed-sdrf "${get_condensed_sdrf}" --get-marker-genes "${get_marker_genes}" 
+        get_experiment_data.R --accesssion-code "${accession_code}" --matrix-type "${matrix_type}" --get-sdrf "${get_sdrf}" --get-condensed-sdrf "${get_condensed_sdrf}" --get-marker-genes "${get_marker_genes}" 
 
         #if $config_file 
         --config-file "${config_file}" 
@@ -28,7 +28,7 @@
     ]]></command>
     <inputs>
         <param type="text" name="accession_code" label="SC-Atlas experiment accession" value="E-GEOD-100058" help="EBI Single Cell Atlas accession for the experiment that you want to retrieve." />
-        <param type="select" name="matrix_type" label="Choose the type of matrix to download"  help="Type of matrix to be imported">
+        <param type="select" name="matrix_type" label="Choose the type of matrix to download" help="Type of matrix to be imported">
             <option value="raw">Raw</option>
             <option value="filtered">Filtered Counts</option>
             <option value="tpm">TPM-normalised</option>
@@ -37,30 +37,30 @@
         <param type="boolean" name="get_sdrf" checked="false" label="Import SDRF file" help="Boolean indicating whether SDRF file needs to be imported" />
         <param type="boolean" name="get_exp_design" checked="false" label="Import experiment design file" help="Boolean indicating whether experiment design file needs to be imported" />
         <param type="boolean" name="get_idf" checked="false" label="Import IDF file" help="Boolean indicating whether IDF file needs to be imported" />
-        <param type="boolean" name="get_condensed_sdrf" checked="false"  label="Get condensed SDRF file" help="Boolean indicating whether condensed SDRF file needs to be imported" />
-        <param type="boolean" name="get_marker_genes" checked="false"  label="Import marker genes" help="Boolean indicating whether marker genes should be imported" />
+        <param type="boolean" name="get_condensed_sdrf" checked="false" label="Get condensed SDRF file" help="Boolean indicating whether condensed SDRF file needs to be imported" />
+        <param type="boolean" name="get_marker_genes" checked="false" label="Import marker genes" help="Boolean indicating whether marker genes should be imported" />
         <param type="data" name="config_file" label="Config file" optional="true" format="yml" help="Config file with user-provided parameters" />
-        <param type="boolean" name="decorated_rows" checked="false"  label="Decorated rows" help="Boolean indicating whether a decorated version of the rows should be imported" />
+        <param type="boolean" name="decorated_rows" checked="false" label="Decorated rows" help="Boolean indicating whether a decorated version of the rows should be imported" />
         <param type="boolean" name="use_default_expr_names" checked="false"  label="Use default expr names" help="Should default (non 10x-type) file names be used for expression data? Default: FALSE" />
-        <param type="integer" name="number_of_clusters" label="Number of clusters" help="Number of clusters in marker genes file" />
+        <param type="integer" name="number_of_clusters" value="0" label="Number of clusters" help="Number of clusters in marker genes file" />
     </inputs>
     <outputs>
-        <data name="expr_mtx" format="txt" from_work_dir="${accession_code}/10x_data/matrix.mtx" label="${tool.name} on ${on_string} ${accession} matrix.mtx (${matrix_type.value_label})" />
-        <data name="barcodes" format="txt" from_work_dir="${accession_code}/10x_data/barcodes.tsv" label="${tool.name} on ${on_string} ${accession} barcodes.tsv (${matrix_type.value_label})" />
-        <data name="genes" format="txt" from_work_dir="${accession_code}/10x_data/genes.tsv" label="${tool.name} on ${on_string} ${accession} genes.tsv (${matrix_type.value_label})" />
-        <data name="sdrf" format="txt" from_work_dir="${accession_code}/sdrf.txt" label="${tool.name} on ${on_string} ${accession} sdrf.txt (${matrix_type.value_label})" >
+        <data name="expr_mtx" format="txt" from_work_dir="${accession_code}/10x_data/matrix.mtx" label="${tool.name} on ${on_string} ${accession_code} matrix.mtx (${matrix_type.value_label})" />
+        <data name="barcodes" format="txt" from_work_dir="${accession_code}/10x_data/barcodes.tsv" label="${tool.name} on ${on_string} ${accession_code} barcodes.tsv (${matrix_type.value_label})" />
+        <data name="genes" format="txt" from_work_dir="${accession_code}/10x_data/genes.tsv" label="${tool.name} on ${on_string} ${accession_code} genes.tsv (${matrix_type.value_label})" />
+        <data name="sdrf" format="txt" from_work_dir="${accession_code}/sdrf.txt" label="${tool.name} on ${on_string} ${accession_code} sdrf.txt (${matrix_type.value_label})" >
             <filter>get_sdrf</filter>
         </data>
-        <data name="condensed_sdrf" format="txt" from_work_dir="${accession_code}/condensed-sdrf.tsv" label="${tool.name} on ${on_string} ${accession} condensed-sdrf.tsv (${matrix_type.value_label})" >
+        <data name="condensed_sdrf" format="txt" from_work_dir="${accession_code}/condensed-sdrf.tsv" label="${tool.name} on ${on_string} ${accession_code} condensed-sdrf.tsv (${matrix_type.value_label})" >
             <filter>get_condensed_sdrf</filter>
         </data>
-        <data name="idf" format="txt" from_work_dir="${accession_code}/idf.txt" label="${tool.name} on ${on_string} ${accession} idf.txt (${matrix_type.value_label})">
+        <data name="idf" format="txt" from_work_dir="${accession_code}/idf.txt" label="${tool.name} on ${on_string} ${accession_code} idf.txt (${matrix_type.value_label})">
             <filter>get_idf</filter>
         </data>
-        <data name="marker_genes" format="txt" from_work_dir="${accession_code}/marker_genes_${number_of_clusters}.tsv" >
+        <data name="marker_genes" from_work_dir="${accession_code}/marker_genes_${number_of_clusters}.tsv" format="txt"  >
             <filter>get_marker_genes</filter>
         </data>
-        <data name="exp_design" format="txt" from_work_dir="${accession_code}/exp_design.tsv" >
+        <data name="exp_design" from_work_dir="${accession_code}/exp_design.tsv" format="txt"  >
             <filter>get_exp_design</filter>
         </data>
     </outputs>

From 14a4e30e241a6def36eeb958e2e00f7e335f2ef5 Mon Sep 17 00:00:00 2001
From: Andrey Solovyev <a.solovyev39@gmail.com>
Date: Tue, 7 Jul 2020 11:44:57 +0100
Subject: [PATCH 06/11] bump wrapper version

---
 .../dropletutils/dropletutils-read-10x.xml    | 25 +++++++++----------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/tools/tertiary-analysis/dropletutils/dropletutils-read-10x.xml b/tools/tertiary-analysis/dropletutils/dropletutils-read-10x.xml
index 8cdc2ab4..c8691bec 100644
--- a/tools/tertiary-analysis/dropletutils/dropletutils-read-10x.xml
+++ b/tools/tertiary-analysis/dropletutils/dropletutils-read-10x.xml
@@ -1,24 +1,23 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="dropletutils_read_10x" name="DropletUtils Read10x" version="@TOOL_VERSION@+galaxy1">
+<tool id="dropletutils_read_10x" name="DropletUtils Read10x" version="@TOOL_VERSION@+galaxy2">
   <description>into SingleCellExperiment object</description>
   <macros>
     <import>dropletutils_macros.xml</import>
   </macros>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
-ln -s '${matrix}' matrix.mtx &&
-ln -s '${genes}' genes.tsv &&
-ln -s '${barcodes}' barcodes.tsv &&
-dropletutils-read-10x-counts.R
-    -s .
-    -c TRUE
-    -o '${output_rds}'
-
-#if $add_metadata.add_metadata_file 
---metadata-files "${add_metadata.metadata_files}"
---cell-id-column "${add_metadata.cell_id_column}" 
-#end if
+      ln -s '${matrix}' matrix.mtx &&
+      ln -s '${genes}' genes.tsv &&
+      ln -s '${barcodes}' barcodes.tsv &&
+      dropletutils-read-10x-counts.R
+          -s .
+          -c TRUE
+          -o '${output_rds}'
 
+      #if $add_metadata.add_metadata_file 
+      --metadata-files "${add_metadata.metadata_files}"
+      --cell-id-column "${add_metadata.cell_id_column}" 
+      #end if
 ]]></command>
 
   <inputs>

From 9db4b8b7eacb77f314aba99169c5623eff6d868e Mon Sep 17 00:00:00 2001
From: Andrey Solovyev <a.solovyev39@gmail.com>
Date: Tue, 7 Jul 2020 11:53:08 +0100
Subject: [PATCH 07/11] Revert "rename wrapper"

This reverts commit 04a9cf52b275fdde8ffa38caac947aa2cdf543b2.
---
 ...a.xml => atlas_import_experiment_data.xml} | 30 +++++++++----------
 1 file changed, 15 insertions(+), 15 deletions(-)
 rename tools/tertiary-analysis/data-scxa/{retrieve-scxa.xml => atlas_import_experiment_data.xml} (82%)

diff --git a/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml b/tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml
similarity index 82%
rename from tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
rename to tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml
index 4473966f..1605ccbd 100644
--- a/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
+++ b/tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml
@@ -1,11 +1,11 @@
-<tool id="retrieve_scxa" name="Atlas import: get experiment data" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
+<tool id="atlas_import_experiment_data" name="Atlas import: get experiment data" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
     <description>Retrieve expression matrices and metadata from EBI Single Cell Expression Atlas (SCXA)</description>
     <macros>
          <import>atlas-retrieve-macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        get_experiment_data.R --accesssion-code "${accession_code}" --matrix-type "${matrix_type}" --get-sdrf "${get_sdrf}" --get-condensed-sdrf "${get_condensed_sdrf}" --get-marker-genes "${get_marker_genes}" 
+        get_experiment_data.R --accession-code "${accession_code}" --matrix-type "${matrix_type}" --get-sdrf "${get_sdrf}" --get-condensed-sdrf "${get_condensed_sdrf}" --get-marker-genes "${get_marker_genes}" 
 
         #if $config_file 
         --config-file "${config_file}" 
@@ -28,7 +28,7 @@
     ]]></command>
     <inputs>
         <param type="text" name="accession_code" label="SC-Atlas experiment accession" value="E-GEOD-100058" help="EBI Single Cell Atlas accession for the experiment that you want to retrieve." />
-        <param type="select" name="matrix_type" label="Choose the type of matrix to download" help="Type of matrix to be imported">
+        <param type="select" name="matrix_type" label="Choose the type of matrix to download"  help="Type of matrix to be imported">
             <option value="raw">Raw</option>
             <option value="filtered">Filtered Counts</option>
             <option value="tpm">TPM-normalised</option>
@@ -37,30 +37,30 @@
         <param type="boolean" name="get_sdrf" checked="false" label="Import SDRF file" help="Boolean indicating whether SDRF file needs to be imported" />
         <param type="boolean" name="get_exp_design" checked="false" label="Import experiment design file" help="Boolean indicating whether experiment design file needs to be imported" />
         <param type="boolean" name="get_idf" checked="false" label="Import IDF file" help="Boolean indicating whether IDF file needs to be imported" />
-        <param type="boolean" name="get_condensed_sdrf" checked="false" label="Get condensed SDRF file" help="Boolean indicating whether condensed SDRF file needs to be imported" />
-        <param type="boolean" name="get_marker_genes" checked="false" label="Import marker genes" help="Boolean indicating whether marker genes should be imported" />
+        <param type="boolean" name="get_condensed_sdrf" checked="false"  label="Get condensed SDRF file" help="Boolean indicating whether condensed SDRF file needs to be imported" />
+        <param type="boolean" name="get_marker_genes" checked="false"  label="Import marker genes" help="Boolean indicating whether marker genes should be imported" />
         <param type="data" name="config_file" label="Config file" optional="true" format="yml" help="Config file with user-provided parameters" />
-        <param type="boolean" name="decorated_rows" checked="false" label="Decorated rows" help="Boolean indicating whether a decorated version of the rows should be imported" />
+        <param type="boolean" name="decorated_rows" checked="false"  label="Decorated rows" help="Boolean indicating whether a decorated version of the rows should be imported" />
         <param type="boolean" name="use_default_expr_names" checked="false"  label="Use default expr names" help="Should default (non 10x-type) file names be used for expression data? Default: FALSE" />
-        <param type="integer" name="number_of_clusters" value="0" label="Number of clusters" help="Number of clusters in marker genes file" />
+        <param type="integer" name="number_of_clusters" label="Number of clusters" help="Number of clusters in marker genes file" />
     </inputs>
     <outputs>
-        <data name="expr_mtx" format="txt" from_work_dir="${accession_code}/10x_data/matrix.mtx" label="${tool.name} on ${on_string} ${accession_code} matrix.mtx (${matrix_type.value_label})" />
-        <data name="barcodes" format="txt" from_work_dir="${accession_code}/10x_data/barcodes.tsv" label="${tool.name} on ${on_string} ${accession_code} barcodes.tsv (${matrix_type.value_label})" />
-        <data name="genes" format="txt" from_work_dir="${accession_code}/10x_data/genes.tsv" label="${tool.name} on ${on_string} ${accession_code} genes.tsv (${matrix_type.value_label})" />
-        <data name="sdrf" format="txt" from_work_dir="${accession_code}/sdrf.txt" label="${tool.name} on ${on_string} ${accession_code} sdrf.txt (${matrix_type.value_label})" >
+        <data name="expr_mtx" format="txt" from_work_dir="${accession_code}/10x_data/matrix.mtx" label="${tool.name} on ${on_string} ${accession} matrix.mtx (${matrix_type.value_label})" />
+        <data name="barcodes" format="txt" from_work_dir="${accession_code}/10x_data/barcodes.tsv" label="${tool.name} on ${on_string} ${accession} barcodes.tsv (${matrix_type.value_label})" />
+        <data name="genes" format="txt" from_work_dir="${accession_code}/10x_data/genes.tsv" label="${tool.name} on ${on_string} ${accession} genes.tsv (${matrix_type.value_label})" />
+        <data name="sdrf" format="txt" from_work_dir="${accession_code}/sdrf.txt" label="${tool.name} on ${on_string} ${accession} sdrf.txt (${matrix_type.value_label})" >
             <filter>get_sdrf</filter>
         </data>
-        <data name="condensed_sdrf" format="txt" from_work_dir="${accession_code}/condensed-sdrf.tsv" label="${tool.name} on ${on_string} ${accession_code} condensed-sdrf.tsv (${matrix_type.value_label})" >
+        <data name="condensed_sdrf" format="txt" from_work_dir="${accession_code}/condensed-sdrf.tsv" label="${tool.name} on ${on_string} ${accession} condensed-sdrf.tsv (${matrix_type.value_label})" >
             <filter>get_condensed_sdrf</filter>
         </data>
-        <data name="idf" format="txt" from_work_dir="${accession_code}/idf.txt" label="${tool.name} on ${on_string} ${accession_code} idf.txt (${matrix_type.value_label})">
+        <data name="idf" format="txt" from_work_dir="${accession_code}/idf.txt" label="${tool.name} on ${on_string} ${accession} idf.txt (${matrix_type.value_label})">
             <filter>get_idf</filter>
         </data>
-        <data name="marker_genes" from_work_dir="${accession_code}/marker_genes_${number_of_clusters}.tsv" format="txt"  >
+        <data name="marker_genes" format="txt" from_work_dir="${accession_code}/marker_genes_${number_of_clusters}.tsv" >
             <filter>get_marker_genes</filter>
         </data>
-        <data name="exp_design" from_work_dir="${accession_code}/exp_design.tsv" format="txt"  >
+        <data name="exp_design" format="txt" from_work_dir="${accession_code}/exp_design.tsv" >
             <filter>get_exp_design</filter>
         </data>
     </outputs>

From eac6424d788181325d92f232ac62526d363201c7 Mon Sep 17 00:00:00 2001
From: Andrey Solovyev <a.solovyev39@gmail.com>
Date: Tue, 7 Jul 2020 12:15:53 +0100
Subject: [PATCH 08/11] fix erroneous commits

---
 ..._experiment_data.xml => retrieve-scxa.xml} | 30 +++++++++----------
 1 file changed, 15 insertions(+), 15 deletions(-)
 rename tools/tertiary-analysis/data-scxa/{atlas_import_experiment_data.xml => retrieve-scxa.xml} (82%)

diff --git a/tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml b/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
similarity index 82%
rename from tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml
rename to tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
index 1605ccbd..4473966f 100644
--- a/tools/tertiary-analysis/data-scxa/atlas_import_experiment_data.xml
+++ b/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
@@ -1,11 +1,11 @@
-<tool id="atlas_import_experiment_data" name="Atlas import: get experiment data" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
+<tool id="retrieve_scxa" name="Atlas import: get experiment data" version="@TOOL_VERSION@+galaxy0"  profile="@PROFILE@">
     <description>Retrieve expression matrices and metadata from EBI Single Cell Expression Atlas (SCXA)</description>
     <macros>
          <import>atlas-retrieve-macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        get_experiment_data.R --accession-code "${accession_code}" --matrix-type "${matrix_type}" --get-sdrf "${get_sdrf}" --get-condensed-sdrf "${get_condensed_sdrf}" --get-marker-genes "${get_marker_genes}" 
+        get_experiment_data.R --accesssion-code "${accession_code}" --matrix-type "${matrix_type}" --get-sdrf "${get_sdrf}" --get-condensed-sdrf "${get_condensed_sdrf}" --get-marker-genes "${get_marker_genes}" 
 
         #if $config_file 
         --config-file "${config_file}" 
@@ -28,7 +28,7 @@
     ]]></command>
     <inputs>
         <param type="text" name="accession_code" label="SC-Atlas experiment accession" value="E-GEOD-100058" help="EBI Single Cell Atlas accession for the experiment that you want to retrieve." />
-        <param type="select" name="matrix_type" label="Choose the type of matrix to download"  help="Type of matrix to be imported">
+        <param type="select" name="matrix_type" label="Choose the type of matrix to download" help="Type of matrix to be imported">
             <option value="raw">Raw</option>
             <option value="filtered">Filtered Counts</option>
             <option value="tpm">TPM-normalised</option>
@@ -37,30 +37,30 @@
         <param type="boolean" name="get_sdrf" checked="false" label="Import SDRF file" help="Boolean indicating whether SDRF file needs to be imported" />
         <param type="boolean" name="get_exp_design" checked="false" label="Import experiment design file" help="Boolean indicating whether experiment design file needs to be imported" />
         <param type="boolean" name="get_idf" checked="false" label="Import IDF file" help="Boolean indicating whether IDF file needs to be imported" />
-        <param type="boolean" name="get_condensed_sdrf" checked="false"  label="Get condensed SDRF file" help="Boolean indicating whether condensed SDRF file needs to be imported" />
-        <param type="boolean" name="get_marker_genes" checked="false"  label="Import marker genes" help="Boolean indicating whether marker genes should be imported" />
+        <param type="boolean" name="get_condensed_sdrf" checked="false" label="Get condensed SDRF file" help="Boolean indicating whether condensed SDRF file needs to be imported" />
+        <param type="boolean" name="get_marker_genes" checked="false" label="Import marker genes" help="Boolean indicating whether marker genes should be imported" />
         <param type="data" name="config_file" label="Config file" optional="true" format="yml" help="Config file with user-provided parameters" />
-        <param type="boolean" name="decorated_rows" checked="false"  label="Decorated rows" help="Boolean indicating whether a decorated version of the rows should be imported" />
+        <param type="boolean" name="decorated_rows" checked="false" label="Decorated rows" help="Boolean indicating whether a decorated version of the rows should be imported" />
         <param type="boolean" name="use_default_expr_names" checked="false"  label="Use default expr names" help="Should default (non 10x-type) file names be used for expression data? Default: FALSE" />
-        <param type="integer" name="number_of_clusters" label="Number of clusters" help="Number of clusters in marker genes file" />
+        <param type="integer" name="number_of_clusters" value="0" label="Number of clusters" help="Number of clusters in marker genes file" />
     </inputs>
     <outputs>
-        <data name="expr_mtx" format="txt" from_work_dir="${accession_code}/10x_data/matrix.mtx" label="${tool.name} on ${on_string} ${accession} matrix.mtx (${matrix_type.value_label})" />
-        <data name="barcodes" format="txt" from_work_dir="${accession_code}/10x_data/barcodes.tsv" label="${tool.name} on ${on_string} ${accession} barcodes.tsv (${matrix_type.value_label})" />
-        <data name="genes" format="txt" from_work_dir="${accession_code}/10x_data/genes.tsv" label="${tool.name} on ${on_string} ${accession} genes.tsv (${matrix_type.value_label})" />
-        <data name="sdrf" format="txt" from_work_dir="${accession_code}/sdrf.txt" label="${tool.name} on ${on_string} ${accession} sdrf.txt (${matrix_type.value_label})" >
+        <data name="expr_mtx" format="txt" from_work_dir="${accession_code}/10x_data/matrix.mtx" label="${tool.name} on ${on_string} ${accession_code} matrix.mtx (${matrix_type.value_label})" />
+        <data name="barcodes" format="txt" from_work_dir="${accession_code}/10x_data/barcodes.tsv" label="${tool.name} on ${on_string} ${accession_code} barcodes.tsv (${matrix_type.value_label})" />
+        <data name="genes" format="txt" from_work_dir="${accession_code}/10x_data/genes.tsv" label="${tool.name} on ${on_string} ${accession_code} genes.tsv (${matrix_type.value_label})" />
+        <data name="sdrf" format="txt" from_work_dir="${accession_code}/sdrf.txt" label="${tool.name} on ${on_string} ${accession_code} sdrf.txt (${matrix_type.value_label})" >
             <filter>get_sdrf</filter>
         </data>
-        <data name="condensed_sdrf" format="txt" from_work_dir="${accession_code}/condensed-sdrf.tsv" label="${tool.name} on ${on_string} ${accession} condensed-sdrf.tsv (${matrix_type.value_label})" >
+        <data name="condensed_sdrf" format="txt" from_work_dir="${accession_code}/condensed-sdrf.tsv" label="${tool.name} on ${on_string} ${accession_code} condensed-sdrf.tsv (${matrix_type.value_label})" >
             <filter>get_condensed_sdrf</filter>
         </data>
-        <data name="idf" format="txt" from_work_dir="${accession_code}/idf.txt" label="${tool.name} on ${on_string} ${accession} idf.txt (${matrix_type.value_label})">
+        <data name="idf" format="txt" from_work_dir="${accession_code}/idf.txt" label="${tool.name} on ${on_string} ${accession_code} idf.txt (${matrix_type.value_label})">
             <filter>get_idf</filter>
         </data>
-        <data name="marker_genes" format="txt" from_work_dir="${accession_code}/marker_genes_${number_of_clusters}.tsv" >
+        <data name="marker_genes" from_work_dir="${accession_code}/marker_genes_${number_of_clusters}.tsv" format="txt"  >
             <filter>get_marker_genes</filter>
         </data>
-        <data name="exp_design" format="txt" from_work_dir="${accession_code}/exp_design.tsv" >
+        <data name="exp_design" from_work_dir="${accession_code}/exp_design.tsv" format="txt"  >
             <filter>get_exp_design</filter>
         </data>
     </outputs>

From 1125531a7a9ffab4e40d4e1099559f64cd43acea Mon Sep 17 00:00:00 2001
From: Andrey Solovyev <a.solovyev39@gmail.com>
Date: Wed, 8 Jul 2020 12:23:05 +0100
Subject: [PATCH 09/11] update cli tool version

---
 tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml b/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml
index 36d480c9..e6717338 100644
--- a/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml
+++ b/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml
@@ -4,7 +4,7 @@
     <token name="@PROFILE@">18.01</token>
     <xml name="requirements">
       <requirements>
-        <requirement type="package" version="0.0.9">atlas-data-import</requirement>
+        <requirement type="package" version="0.0.10">atlas-data-import</requirement>
             <yield/>
       </requirements>
     </xml>

From ec3ffc272544cb6d27e2c3acf3db4ecbebe832bc Mon Sep 17 00:00:00 2001
From: Andrey Solovyev <a.solovyev39@gmail.com>
Date: Thu, 9 Jul 2020 15:00:38 +0100
Subject: [PATCH 10/11] add symlinks for output files

---
 .../data-scxa/retrieve-scxa.xml               | 41 +++++++++++--------
 1 file changed, 25 insertions(+), 16 deletions(-)

diff --git a/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml b/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
index 4473966f..9d01eb66 100644
--- a/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
+++ b/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
@@ -5,13 +5,22 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        get_experiment_data.R --accesssion-code "${accession_code}" --matrix-type "${matrix_type}" --get-sdrf "${get_sdrf}" --get-condensed-sdrf "${get_condensed_sdrf}" --get-marker-genes "${get_marker_genes}" 
+        ln -s "${accession_code}_${matrix_type}/10x_data/matrix.mtx" matrix.mtx &&
+        ln -s "${accession_code}_${matrix_type}/10x_data/genes.tsv" genes.tsv &&
+        ln -s "${accession_code}_${matrix_type}/10x_data/barcodes.tsv" barcodes.tsv &&
+        ln -s "${accession_code}_${matrix_type}/sdrf.txt" sdrf.txt &&
+        ln -s "${accession_code}_${matrix_type}/condensed-sdrf.tsv" condensed-sdrf.tsv &&
+        ln -s "${accession_code}_${matrix_type}/idf.txt" idf.txt &&
+        ln -s "${accession_code}_${matrix_type}/marker_genes_${number_of_clusters}.tsv" marker_genes_${number_of_clusters}.tsv &&
+        ln -s "${accession_code}_${matrix_type}/exp_design.tsv" exp_design.tsv &&
+
+        get_experiment_data.R --accesssion-code "${accession_code}" --matrix-type "${matrix_type}" --get-sdrf "${get_sdrf}" --get-condensed-sdrf "${get_condensed_sdrf}" --get-marker-genes "${get_marker_genes}"
 
         #if $config_file 
-        --config-file "${config_file}" 
-        #end if
+        --config-file "${config_file}"
+        #end if        
         #if $get_exp_design
-        --get-exp-design "${get_exp_design}"
+        --get-exp-design "${get_exp_design}" 
         #end if 
         #if $decorated_rows 
         --decorated-rows "${decorated_rows}" 
@@ -29,10 +38,10 @@
     <inputs>
         <param type="text" name="accession_code" label="SC-Atlas experiment accession" value="E-GEOD-100058" help="EBI Single Cell Atlas accession for the experiment that you want to retrieve." />
         <param type="select" name="matrix_type" label="Choose the type of matrix to download" help="Type of matrix to be imported">
-            <option value="raw">Raw</option>
-            <option value="filtered">Filtered Counts</option>
-            <option value="tpm">TPM-normalised</option>
-            <option value="cpm">CPM-normalised</option>
+            <option value="RAW">Raw</option>
+            <option value="FILTERED">Filtered Counts</option>
+            <option value="TPM">TPM-normalised</option>
+            <option value="CPM">CPM-normalised</option>
         </param>
         <param type="boolean" name="get_sdrf" checked="false" label="Import SDRF file" help="Boolean indicating whether SDRF file needs to be imported" />
         <param type="boolean" name="get_exp_design" checked="false" label="Import experiment design file" help="Boolean indicating whether experiment design file needs to be imported" />
@@ -45,22 +54,22 @@
         <param type="integer" name="number_of_clusters" value="0" label="Number of clusters" help="Number of clusters in marker genes file" />
     </inputs>
     <outputs>
-        <data name="expr_mtx" format="txt" from_work_dir="${accession_code}/10x_data/matrix.mtx" label="${tool.name} on ${on_string} ${accession_code} matrix.mtx (${matrix_type.value_label})" />
-        <data name="barcodes" format="txt" from_work_dir="${accession_code}/10x_data/barcodes.tsv" label="${tool.name} on ${on_string} ${accession_code} barcodes.tsv (${matrix_type.value_label})" />
-        <data name="genes" format="txt" from_work_dir="${accession_code}/10x_data/genes.tsv" label="${tool.name} on ${on_string} ${accession_code} genes.tsv (${matrix_type.value_label})" />
-        <data name="sdrf" format="txt" from_work_dir="${accession_code}/sdrf.txt" label="${tool.name} on ${on_string} ${accession_code} sdrf.txt (${matrix_type.value_label})" >
+        <data name="expr_mtx" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string} ${accession_code} matrix.mtx (${matrix_type.value_label})" />
+        <data name="barcodes" format="txt" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string} ${accession_code} barcodes.tsv (${matrix_type.value_label})" />
+        <data name="genes" format="txt" from_work_dir="genes.tsv" label="${tool.name} on ${on_string} ${accession_code} genes.tsv (${matrix_type.value_label})" />
+        <data name="sdrf" format="txt" from_work_dir="sdrf.txt" label="${tool.name} on ${on_string} ${accession_code} sdrf.txt (${matrix_type.value_label})" >
             <filter>get_sdrf</filter>
         </data>
-        <data name="condensed_sdrf" format="txt" from_work_dir="${accession_code}/condensed-sdrf.tsv" label="${tool.name} on ${on_string} ${accession_code} condensed-sdrf.tsv (${matrix_type.value_label})" >
+        <data name="condensed_sdrf" format="txt" from_work_dir="condensed-sdrf.tsv" label="${tool.name} on ${on_string} ${accession_code} condensed-sdrf.tsv (${matrix_type.value_label})" >
             <filter>get_condensed_sdrf</filter>
         </data>
-        <data name="idf" format="txt" from_work_dir="${accession_code}/idf.txt" label="${tool.name} on ${on_string} ${accession_code} idf.txt (${matrix_type.value_label})">
+        <data name="idf" format="txt" from_work_dir="idf.txt" label="${tool.name} on ${on_string} ${accession_code} idf.txt (${matrix_type.value_label})">
             <filter>get_idf</filter>
         </data>
-        <data name="marker_genes" from_work_dir="${accession_code}/marker_genes_${number_of_clusters}.tsv" format="txt"  >
+        <data name="marker_genes" from_work_dir="marker_genes_${number_of_clusters}.tsv" format="txt"  >
             <filter>get_marker_genes</filter>
         </data>
-        <data name="exp_design" from_work_dir="${accession_code}/exp_design.tsv" format="txt"  >
+        <data name="exp_design" from_work_dir="exp_design.tsv" format="txt"  >
             <filter>get_exp_design</filter>
         </data>
     </outputs>

From 125cf464c48f83a6594961a86f4ec2492fc2e538 Mon Sep 17 00:00:00 2001
From: Andrey Solovyev <a.solovyev39@gmail.com>
Date: Thu, 3 Sep 2020 10:14:15 +0100
Subject: [PATCH 11/11] update atlas-data-import to 0.0.11 (#189)

* add optional inputs to scmap-cell (#182)

* add optional inputs to scmap-cell

* increment version number

* update tool versions (#183)

* add default values to parameters (#184)

* add default values to parameters

* bump wrapper version

* update scmap-cli to 0.0.10 (#185)

* update scmap-cli to 0.0.10

* Switch to the conda version of planemo in .travis.yml

* Revert "Switch to the conda version of planemo in .travis.yml"

This reverts commit 1693b3ed0015d163230d2269f2bee2b74e7a5caa.

* pin planemo=0.70.0 and bioblend=0.13.0

* pin planemo=0.62.1

* pin planemo=0.70.0 and bioblend=0.14.0

* pin planemo=0.70.0 and bioblend=0.12.0

* specify python3

* check python version

* add pip upgrade; remove package versions

* add pip upgrade

* specify python3 when installing planemo

* Revert "specify python3 when installing planemo"

This reverts commit c02ec7b5a34431201e70c6037c505c43659e9569.

* specify pip3 version of packages

* specify pip3 version of packages

* Revert "specify pip3 version of packages"

This reverts commit 28d7f355acf44ca3b2789d449890f842b579d0df.

* Revert "specify pip3 version of packages"

This reverts commit 215630c425cfaa28cd7b6c8c01d9d454b9e68f08.

* Revert "Revert "specify python3 when installing planemo""

This reverts commit 0cdf27af84ccc030a884a138979d2e73dfe914a5.

* Revert "specify python3 when installing planemo"

This reverts commit c02ec7b5a34431201e70c6037c505c43659e9569.

* Revert "add pip upgrade"

This reverts commit d75c05a8d345e45376600bb25db5d1fb7fdd3a00.

* Revert "add pip upgrade; remove package versions"

This reverts commit f595c7df4c0eb21029cd48c53c91f4bf607e3119.

* Revert "check python version"

This reverts commit d095f1efcb4a35b0d4adce3fe52364399295920f.

* Revert "specify python3"

This reverts commit 7c6de29292cf7e54ff1d580e4b4d256fee01c9b2.

* Revert "pin planemo=0.70.0 and bioblend=0.12.0"

This reverts commit 784945d1e418c062d0fa8f2ddcdb91f116a9691c.

* Revert "pin planemo=0.70.0 and bioblend=0.14.0"

This reverts commit e4e8fe0114fc8d074b889e80543d4f47976fb608.

* Revert "pin planemo=0.62.1"

This reverts commit 81da51626dbf95636c36f6d39284afc2f2b49da5.

* Revert "pin planemo=0.70.0 and bioblend=0.13.0"

This reverts commit 7c78b390fc43c2e940a05e14686df02c7f27630b.

* Revert "Revert "Switch to the conda version of planemo in .travis.yml""

This reverts commit 8312aaadeaa1cc339fd46baf9a9ea2cb035ba39f.

* Revert "Switch to the conda version of planemo in .travis.yml"

This reverts commit 1693b3ed0015d163230d2269f2bee2b74e7a5caa.

* Specify gxformat2=0.11.1 when installing planemo

* specify package version using ==

* make sure pip3 is installed

* pin planemo==0.70

* update scmap and scpred wrappers to provide correct output format (#186)

* update scmap and scpred wrappers to provide correct output format

* switch to 'tabular'

* bump tool version

* Feature/update scmap and scpred (#187)

* update scmap and scpred wrappers to provide correct output format

* switch to 'tabular'

* bump tool version

* bump the tool version (for real)

* update atlas-data-import to 0.0.11

* Revert "Merge branch 'develop' of https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary into feature/add_import_retries"

This reverts commit b9119124b38f78b8899d055bebbc977a89498fbc, reversing
changes made to 251045ee847d90ed6e8d4a0da1eeb1f0fb1710e4.
---
 tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml b/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml
index e6717338..5058faf0 100644
--- a/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml
+++ b/tools/tertiary-analysis/data-scxa/atlas-retrieve-macros.xml
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.0.0</token>
+    <token name="@TOOL_VERSION@">1.0.1</token>
     <token name="@HELP@">More information can be found at https://github.com/ebi-gene-expression-group/atlas-data-import</token>
     <token name="@PROFILE@">18.01</token>
     <xml name="requirements">
       <requirements>
-        <requirement type="package" version="0.0.10">atlas-data-import</requirement>
+        <requirement type="package" version="0.0.11">atlas-data-import</requirement>
             <yield/>
       </requirements>
     </xml>