linter fixes for galaxy_sequence_utils (galaxyproject#6392)

* linter fixes for galaxy_sequence_utils * profile and version suffix
bernt-matthias · Oct 4, 2024 · bb5df9e · bb5df9e
1 parent d7e29bd
commit bb5df9e
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Showing 29 changed files with 43 additions and 54 deletions.
diff --git a/tool_collections/galaxy_sequence_utils/fastq_combiner/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_combiner/.lint_skip
diff --git a/tool_collections/galaxy_sequence_utils/fastq_combiner/fastq_combiner.xml b/tool_collections/galaxy_sequence_utils/fastq_combiner/fastq_combiner.xml
@@ -1,15 +1,15 @@
-<tool id="fastq_combiner" name="Combine FASTA and QUAL" version="@TOOL_VERSION@">
+<tool id="fastq_combiner" name="Combine FASTA and QUAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>into FASTQ</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <edam_topics>
         <edam_topic>topic_0622</edam_topic>
     </edam_topics>
     <edam_operations>
         <edam_operation>operation_3436</edam_operation>
     </edam_operations>
+    <expand macro="requirements"/>
     <command><![CDATA[
 gx-fastq-combiner '$fasta_file' '${fasta_file.extension}' '$qual_file' '${qual_file.extension}' '$output_file' $force_quality_encoding
     ]]></command>

diff --git a/tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip
diff --git a/tool_collections/galaxy_sequence_utils/fastq_filter/fastq_filter.xml b/tool_collections/galaxy_sequence_utils/fastq_filter/fastq_filter.xml
@@ -1,15 +1,15 @@
-<tool id="fastq_filter" name="Filter FASTQ" version="@TOOL_VERSION@">
+<tool id="fastq_filter" name="Filter FASTQ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>reads by quality score and length</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <edam_topics>
         <edam_topic>topic_0622</edam_topic>
     </edam_topics>
     <edam_operations>
         <edam_operation>operation_3695</edam_operation>
     </edam_operations>
+    <expand macro="requirements"/>
     <command><![CDATA[
 gx-fastq-filter '$input_file' '$fastq_filter_file' '$output_file' '$output_file.files_path' '${input_file.extension[len( 'fastq' ):]}'
     ]]></command>

diff --git a/tool_collections/galaxy_sequence_utils/fastq_groomer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_groomer/.lint_skip
diff --git a/tool_collections/galaxy_sequence_utils/fastq_groomer/fastq_groomer.xml b/tool_collections/galaxy_sequence_utils/fastq_groomer/fastq_groomer.xml
@@ -1,15 +1,15 @@
-<tool id="fastq_groomer" name="FASTQ Groomer" version="@TOOL_VERSION@">
+<tool id="fastq_groomer" name="FASTQ Groomer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>convert between various FASTQ quality formats</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <edam_topics>
         <edam_topic>topic_0622</edam_topic>
     </edam_topics>
     <edam_operations>
         <edam_operation>operation_0233</edam_operation>
     </edam_operations>
+    <expand macro="requirements"/>
     <command><![CDATA[
 gx-fastq-groomer '$input_file'
 #if $input_file.extension.endswith(".gz"):

diff --git a/tool_collections/galaxy_sequence_utils/fastq_manipulation/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_manipulation/.lint_skip
diff --git a/tool_collections/galaxy_sequence_utils/fastq_manipulation/fastq_manipulation.xml b/tool_collections/galaxy_sequence_utils/fastq_manipulation/fastq_manipulation.xml
@@ -1,17 +1,17 @@
-<tool id="fastq_manipulation" name="Manipulate FASTQ" version="@TOOL_VERSION@">
-    <options sanitize="false" />
+<tool id="fastq_manipulation" name="Manipulate FASTQ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <!-- This tool uses a file to rely all parameter information (actually a dynamically generated python module), we can safely not sanitize any parameters -->
     <description>reads on various attributes</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
+    <options sanitize="false" />
     <edam_topics>
         <edam_topic>topic_0622</edam_topic>
     </edam_topics>
     <edam_operations>
         <edam_operation>operation_0233</edam_operation>
     </edam_operations>
+    <expand macro="requirements"/>
     <command><![CDATA[
 gx-fastq-manipulation '$input_file' '$fastq_manipulation_file' '$output_file' '$output_file.files_path' '${input_file.extension[len('fastq'):]}'
     ]]></command>

diff --git a/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality/.lint_skip
diff --git a/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality/fastq_masker_by_quality.xml b/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality/fastq_masker_by_quality.xml
@@ -1,15 +1,15 @@
-<tool id="fastq_masker_by_quality" name="FASTQ Masker" version="@TOOL_VERSION@">
+<tool id="fastq_masker_by_quality" name="FASTQ Masker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>by quality score</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <edam_topics>
         <edam_topic>topic_0622</edam_topic>
     </edam_topics>
     <edam_operations>
         <edam_operation>operation_0368</edam_operation>
     </edam_operations>
+    <expand macro="requirements"/>
     <command><![CDATA[
 gx-fastq-masker-by-quality '$input_file' '$output_file' -f '${input_file.extension[len('fastq'):]}' -s ${quality_score} -c ${score_comparison}
 #if $mask_type == 'lowercase'

diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer/.lint_skip
diff --git a/...ons/galaxy_sequence_utils/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer.xml b/...ons/galaxy_sequence_utils/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer.xml
@@ -1,15 +1,15 @@
-<tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="@TOOL_VERSION@">
+<tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>on paired end reads</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <edam_topics>
         <edam_topic>topic_0622</edam_topic>
     </edam_topics>
     <edam_operations>
         <edam_operation>operation_3359</edam_operation>
     </edam_operations>
+    <expand macro="requirements"/>
     <command><![CDATA[
 gx-fastq-paired-end-deinterlacer '$input_file' '${input_file.extension[len('fastq'):]}' '$output1_pairs_file' '$output2_pairs_file' '$output1_singles_file' '$output2_singles_file'
     ]]></command>

diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.lint_skip
@@ -1,3 +1,2 @@
-OutputsLabelDuplicatedFilter
-TestsExpectNumOutputs
-XMLOrder
+# Allow duplicated labels (since filters are disjoint)
+OutputsLabelDuplicatedFilter
diff --git a/...ections/galaxy_sequence_utils/fastq_paired_end_interlacer/fastq_paired_end_interlacer.xml b/...ections/galaxy_sequence_utils/fastq_paired_end_interlacer/fastq_paired_end_interlacer.xml
@@ -1,14 +1,14 @@
-<tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="1.2.0.1+galaxy0">
+<tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>on paired end reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <edam_topics>
         <edam_topic>topic_0622</edam_topic>
     </edam_topics>
     <edam_operations>
         <edam_operation>operation_3436</edam_operation>
     </edam_operations>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
     <expand macro="requirements"/>
     <command><![CDATA[
 gx-fastq-paired-end-interlacer
@@ -53,35 +53,35 @@ gx-fastq-paired-end-interlacer
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="reads_selector" value="paired" />
             <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
             <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
             <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" />
             <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="reads_selector" value="paired" />
             <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" />
             <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" />
             <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger" />
             <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="reads_selector" value="paired" />
             <param name="input1_file" value="paired_end_1_errors.fastqsanger.gz" ftype="fastqsanger.gz" />
             <param name="input2_file" value="paired_end_2_errors.fastqsanger.gz" ftype="fastqsanger.gz" />
             <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
             <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="reads_selector" value="paired" />
             <param name="input1_file" value="paired_end_1_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" />
             <param name="input2_file" value="paired_end_2_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" />
             <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
             <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="reads_selector" value="paired_collection" />
             <param name="reads_coll">
                 <collection type="paired">

diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner/.lint_skip
diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner/fastq_paired_end_joiner.xml b/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner/fastq_paired_end_joiner.xml
@@ -1,15 +1,16 @@
-<tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.1.1+galaxy0">
+<!-- TODO as soon as possible adapt the TOOL VERSION macro token .. so far only bump minor versions -->
+<tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.1.1+galaxy1" profile="@PROFILE@">
     <description>on paired end reads</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <edam_topics>
         <edam_topic>topic_0622</edam_topic>
     </edam_topics>
     <edam_operations>
         <edam_operation>operation_3436</edam_operation>
     </edam_operations>
+    <expand macro="requirements"/>
     <command><![CDATA[
 gx-fastq-paired-end-joiner '$input1_file' '${input1_file.extension[len('fastq'):]}' '$input2_file' '${input2_file.extension[len('fastq'):]}' '$output_file' $style '${paste_sequence}'
     ]]></command>

diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter/.lint_skip
diff --git a/...collections/galaxy_sequence_utils/fastq_paired_end_splitter/fastq_paired_end_splitter.xml b/...collections/galaxy_sequence_utils/fastq_paired_end_splitter/fastq_paired_end_splitter.xml
@@ -1,15 +1,15 @@
-<tool id="fastq_paired_end_splitter" name="FASTQ splitter" version="@TOOL_VERSION@+galaxy1">
+<tool id="fastq_paired_end_splitter" name="FASTQ splitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>on joined paired end reads</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <edam_topics>
         <edam_topic>topic_0622</edam_topic>
     </edam_topics>
     <edam_operations>
         <edam_operation>operation_3359</edam_operation>
     </edam_operations>
+    <expand macro="requirements"/>
     <command><![CDATA[
 gx-fastq-paired-end-splitter '$input1_file' '${input1_file.extension[len('fastq'):]}' '$output1_file' '$output2_file'
     ]]></command>

diff --git a/tool_collections/galaxy_sequence_utils/fastq_stats/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_stats/.lint_skip
diff --git a/tool_collections/galaxy_sequence_utils/fastq_stats/fastq_stats.xml b/tool_collections/galaxy_sequence_utils/fastq_stats/fastq_stats.xml
@@ -1,15 +1,15 @@
-<tool id="fastq_stats" name="FASTQ Summary Statistics" version="@TOOL_VERSION@">
+<tool id="fastq_stats" name="FASTQ Summary Statistics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>by column</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <edam_topics>
         <edam_topic>topic_0622</edam_topic>
     </edam_topics>
     <edam_operations>
         <edam_operation>operation_3180</edam_operation>
     </edam_operations>
+    <expand macro="requirements"/>
     <command><![CDATA[
 gx-fastq-stats '$input_file' '$output_file' '${input_file.extension[len('fastq'):]}'
     ]]></command>

diff --git a/tool_collections/galaxy_sequence_utils/fastq_to_tabular/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_to_tabular/.lint_skip
diff --git a/tool_collections/galaxy_sequence_utils/fastq_to_tabular/fastq_to_tabular.xml b/tool_collections/galaxy_sequence_utils/fastq_to_tabular/fastq_to_tabular.xml
@@ -1,15 +1,15 @@
-<tool id="fastq_to_tabular" name="FASTQ to Tabular" version="@TOOL_VERSION@">
+<tool id="fastq_to_tabular" name="FASTQ to Tabular" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <edam_topics>
         <edam_topic>topic_0622</edam_topic>
     </edam_topics>
     <edam_operations>
         <edam_operation>operation_0233</edam_operation>
     </edam_operations>
+    <expand macro="requirements"/>
     <command><![CDATA[
 gx-fastq-to-tabular '$input_file' '$output_file' $descr_columns '${input_file.extension[len('fastq'):]}'
     ]]></command>

diff --git a/tool_collections/galaxy_sequence_utils/fastq_trimmer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_trimmer/.lint_skip
diff --git a/tool_collections/galaxy_sequence_utils/fastq_trimmer/fastq_trimmer.xml b/tool_collections/galaxy_sequence_utils/fastq_trimmer/fastq_trimmer.xml
@@ -1,15 +1,15 @@
-<tool id="fastq_trimmer" name="FASTQ Trimmer" version="@TOOL_VERSION@">
+<tool id="fastq_trimmer" name="FASTQ Trimmer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>by column</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <edam_topics>
         <edam_topic>topic_0622</edam_topic>
     </edam_topics>
     <edam_operations>
         <edam_operation>operation_3192</edam_operation>
     </edam_operations>
+    <expand macro="requirements"/>
     <command><![CDATA[
 gx-fastq-trimmer '$input_file' '$output_file' ${offset_type.left_column_offset} ${offset_type.right_column_offset} ${offset_type.base_offset_type} '${input_file.extension[len('fastq'):]}' $keep_zero_length
     ]]></command>

diff --git a/tool_collections/galaxy_sequence_utils/fastqtofasta/.lint_skip b/tool_collections/galaxy_sequence_utils/fastqtofasta/.lint_skip
diff --git a/tool_collections/galaxy_sequence_utils/fastqtofasta/fastq_to_fasta.xml b/tool_collections/galaxy_sequence_utils/fastqtofasta/fastq_to_fasta.xml
@@ -1,15 +1,15 @@
-<tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="@TOOL_VERSION@">
+<tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <edam_topics>
         <edam_topic>topic_0622</edam_topic>
     </edam_topics>
     <edam_operations>
         <edam_operation>operation_3434</edam_operation>
     </edam_operations>
+    <expand macro="requirements"/>
     <command><![CDATA[
 gx-fastq-to-fasta '$input_file' '$output_file' '${input_file.extension[len('fastq'):]}'
     ]]></command>

diff --git a/tool_collections/galaxy_sequence_utils/macros.xml b/tool_collections/galaxy_sequence_utils/macros.xml
@@ -1,5 +1,7 @@
 <macros>
     <token name="@TOOL_VERSION@">1.1.5</token>
+    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@PROFILE@">23.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">galaxy_sequence_utils</requirement>

diff --git a/tool_collections/galaxy_sequence_utils/tabular_to_fastq/.lint_skip b/tool_collections/galaxy_sequence_utils/tabular_to_fastq/.lint_skip
diff --git a/tool_collections/galaxy_sequence_utils/tabular_to_fastq/tabular_to_fastq.xml b/tool_collections/galaxy_sequence_utils/tabular_to_fastq/tabular_to_fastq.xml
@@ -1,14 +1,14 @@
-<tool id="tabular_to_fastq" name="Tabular to FASTQ" version="@TOOL_VERSION@">
+<tool id="tabular_to_fastq" name="Tabular to FASTQ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>converter</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <edam_topics>
         <edam_topic>topic_0622</edam_topic>
     </edam_topics>
     <edam_operations>
         <edam_operation>operation_3434</edam_operation>
     </edam_operations>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
     <requirements>
         <requirement  type="package" version="3.7">python</requirement>
     </requirements>