diff --git a/tools/anndata/export.xml b/tools/anndata/export.xml
index aab4d7cc26f..52d8896e572 100644
--- a/tools/anndata/export.xml
+++ b/tools/anndata/export.xml
@@ -1,90 +1,33 @@
-<tool id="anndata_export" name="Export AnnData and loom files" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>Interconvert AnnData and Loom formats</description>
+<tool id="anndata_export" name="Export AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>matrix and annotations</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
-#if $hd5_format.filetype == 'anndata':
-    @CMD@
-#else:
-    @LOOMCMD@
-#end if
+@CMD@
       ]]></command>
     <configfiles>
         <configfile name="script_file"><![CDATA[
 @CMD_imports@
-#if $hd5_format.filetype == 'anndata':
-adata = ad.read_h5ad('$hd5_format.input')
-    #if $hd5_format.output_format == 'loom':
-adata.write_loom('anndata.loom')
-    #else if $hd5_format.output_format == 'tabular':
+adata = ad.read_h5ad('$input')
 adata.write_csvs('.', sep="\t", skip_data = False)
-    #end if
-#end if
     ]]></configfile>
 </configfiles>
     <inputs>
-        <conditional name="hd5_format">
-            <param name="filetype" type="select" label="hd5 format">
-                <option value="anndata" selected="true">Anndata file</option>
-                <option value="loom">Loom file</option>
-            </param>
-            <when value="anndata">
-                <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
-                <param name="output_format" type="select" label="Format to write the annotated data matrix">
-                    <option value="loom">loom</option>
-                    <option value="tabular">Tabular</option>
-                </param>
-            </when>
-            <when value="loom">
-                <param name="input" type="data" format="loom" label="Loom file to be exported to a series of tabular files."/>
-            </when>
-        </conditional>
+        <param name="input" type="data" format="h5ad" label="Annotated data matrix to export" help="Create individual tabular files for matrix, obs, obsm, var and varm annotations"/>
     </inputs>
     <outputs>
-        <data name="loom_output" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix">
-            <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'loom'</filter>
-        </data>
-        <data name="tabular_x" format="tabular" from_work_dir="X.csv" label="${tool.name} on ${on_string}: Matrix table (X)">
-            <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
-        </data>
-        <data name="tabular_obs" format="tabular" from_work_dir="obs.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional observations annotation (obs)">
-            <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
-        </data>
-        <data name="tabular_obsm" format="tabular" from_work_dir="obsm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional observations annotation (obsm)">
-            <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
-        </data>
-        <data name="tabular_var" format="tabular" from_work_dir="var.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional variables annotation (var)">
-            <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
-        </data>
-        <data name="tabular_varm" format="tabular" from_work_dir="varm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional variables annotation (varm)">
-            <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
-        </data>
-        <collection name="layer_tsvs" type="list" label="Layer matrices" >
-            <filter>hd5_format['filetype'] == 'loom'</filter>
-            <discover_datasets pattern="__designation__" format="tabular" directory="output" visible="false" />
-        </collection>
-        <collection name="attribute_tsvs" type="list" label="Attribute matrices" >
-            <filter>hd5_format['filetype'] == 'loom'</filter>
-            <discover_datasets pattern="__designation__" format="tabular" directory="attributes" visible="false" />
-        </collection>
+        <data name="tabular_x" format="tabular" from_work_dir="X.csv" label="${tool.name} on ${on_string}: Matrix table (X)"/>
+        <data name="tabular_obs" format="tabular" from_work_dir="obs.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional observations annotation (obs)"/>
+        <data name="tabular_obsm" format="tabular" from_work_dir="obsm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional observations annotation (obsm)"/>
+        <data name="tabular_var" format="tabular" from_work_dir="var.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional variables annotation (var)"/>
+        <data name="tabular_varm" format="tabular" from_work_dir="varm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional variables annotation (varm)"/>
     </outputs>
     <tests>
-        <test expect_num_outputs="1">
-            <param name="filetype" value="anndata"/>
-            <param name="input" value="krumsiek11.h5ad"/>
-            <param name="output_format" value="loom"/>
-            <assert_stdout>
-                <has_text_matching expression="adata.write_loom"/>
-            </assert_stdout>
-            <output name="loom_output" value="export.krumsiek11.loom" ftype="loom" compare="sim_size"/>
-        </test>
         <test expect_num_outputs="5">
-            <param name="filetype" value="anndata"/>
             <param name="input" value="krumsiek11.h5ad"/>
-            <param name="output_format" value="tabular"/>
             <assert_stdout>
                 <has_text_matching expression="adata.write_csvs"/>
             </assert_stdout>
@@ -94,26 +37,9 @@ adata.write_csvs('.', sep="\t", skip_data = False)
             <output name="tabular_var" value="export.krumsiek11.var.tabular" ftype="tabular"/>
             <output name="tabular_varm" value="export.krumsiek11.varm.tabular" ftype="tabular"/>
         </test>
-        <test expect_num_outputs="2">
-            <param name="filetype" value="loom"/>
-            <param name="input" value="loomtest.loom"/>
-            <output_collection name="layer_tsvs" type="list">
-                <element name="mainmatrix.tsv" value="firstlayer.tsv" ftype="tabular"/>
-                <element name="extralayer.tsv" value="secondlayer.tsv" ftype="tabular"/>
-                <element name="thirdlayer.tsv" value="finallayer.tsv" ftype="tabular"/>
-            </output_collection>
-            <output_collection name="attribute_tsvs" type="list">
-                <element name="row_attr.tsv" value="rows.tsv" ftype="tabular"/>
-                <element name="col_attr.tsv" value="cols.tsv" ftype="tabular"/>
-            </output_collection>
-        </test>
     </tests>
     <help><![CDATA[
-This tool exports an AnnData dataset to a Loom file
-(`write_loom method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_loom.html>`__)
-or a Tabular file (`write_csvs method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_csvs.html>`__)
-
-It can also create a series of tabular files from an input loom dataset.
+This tool exports an AnnData dataset to a tabular files (`write_csvs method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_csvs.html>`__)
 
 @HELP@
     ]]></help>
diff --git a/tools/anndata/import.xml b/tools/anndata/import.xml
index 8d3ce3692d4..99ab2808a68 100644
--- a/tools/anndata/import.xml
+++ b/tools/anndata/import.xml
@@ -1,9 +1,9 @@
-<tool id="anndata_import" name="Import Anndata and loom" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
-    <description>from different format</description>
+<tool id="anndata_import" name="Import Anndata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>from different formats</description>
     <macros>
         <import>macros.xml</import>
         <xml name="params_10x">
-            <param name="barcodes" type="data" format="tabular,txt" label="Barcodes"/>
+            <param name="barcodes" type="data" format="tabular,txt" label="Barcodes (whitelist) file with one barcode per line"/>
             <param name="var_names" type="select" label="Variables index">
                 <option value="gene_symbols">gene_symbols</option>
                 <option value="gene_ids">gene_ids</option>
@@ -13,164 +13,132 @@
         </xml>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.9.6">scanpy</requirement>
+        <requirement type="package" version="1.10.2">scanpy</requirement>
     </expand>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
-#if $hd5_format.filetype == 'anndata'
-    #if $hd5_format.in.adata_format == 'mtx'
-        mkdir mtx
-        #if $hd5_format.in.tenx.use == 'legacy_10x'
-            && cp '$hd5_format.in.matrix' 'mtx/matrix.mtx'
-            && cp '$hd5_format.in.tenx.genes' 'mtx/genes.tsv'
-            && cp '$hd5_format.in.tenx.barcodes' 'mtx/barcodes.tsv'
-        #else if $hd5_format.in.tenx.use == 'v3_10x'
-            && cp '$hd5_format.in.matrix' 'mtx/matrix.mtx'
-            && gzip 'mtx/matrix.mtx'
-            && cp '$hd5_format.in.tenx.features' 'mtx/features.tsv'
-            && gzip 'mtx/features.tsv'
-            && cp '$hd5_format.in.tenx.barcodes' 'mtx/barcodes.tsv'
-            && gzip 'mtx/barcodes.tsv'
-        #end if
-        &&
-    #else if $hd5_format.in.adata_format == 'umi_tools'
-        ## avoid gzipping in the inputdir
-        gzip -c '$hd5_format.in.input' > umi_tools_input.gz
-        &&
+#if $in.adata_format == 'mtx'
+    mkdir mtx
+    #if $in.tenx.use == 'legacy_10x'
+        && cp '$in.matrix' 'mtx/matrix.mtx'
+        && cp '$in.tenx.genes' 'mtx/genes.tsv'
+        && cp '$in.tenx.barcodes' 'mtx/barcodes.tsv'
+    #else if $in.tenx.use == 'v3_10x'
+        && cp '$in.matrix' 'mtx/matrix.mtx'
+        && gzip 'mtx/matrix.mtx'
+        && cp '$in.tenx.features' 'mtx/features.tsv'
+        && gzip 'mtx/features.tsv'
+        && cp '$in.tenx.barcodes' 'mtx/barcodes.tsv'
+        && gzip 'mtx/barcodes.tsv'
     #end if
-
-    @CMD@
-
-    #if $hd5_format.in.adata_format == 'mtx'
-        && rm -rf mtx
-    #end if
-
-#else:
-        python '$__tool_directory__/tsv_to_loompy.py'
-        -c '${hd5_format.coldata}'
-        -r '${hd5_format.rowdata}'
-        -f '${hd5_format.mainmatrix}'
-        #if $hd5_format.other_files:
-            '${hd5_format.other_files}'
-        #end if
+    &&
+#else if $in.adata_format == 'umi_tools'
+    ## avoid gzipping in the inputdir
+    gzip -c '$in.input' > umi_tools_input.gz
+    &&
 #end if
+
+@CMD@
       ]]></command>
     <configfiles>
         <configfile name="script_file"><![CDATA[
 @CMD_imports@
-#if $hd5_format.filetype == 'anndata'
-    #if $hd5_format.in.adata_format == 'loom'
+#if $in.adata_format == 'loom'
 adata = ad.read_loom(
-    '$hd5_format.in.input',
-    sparse=$hd5_format.in.sparse,
-    cleanup=$hd5_format.in.cleanup,
-    X_name='$hd5_format.in.x_name',
-    obs_names='$hd5_format.in.obs_names',
-    var_names='$hd5_format.in.var_names')
+    '$in.input',
+    sparse=$in.sparse,
+    cleanup=$in.cleanup,
+    X_name='$in.x_name',
+    obs_names='$in.obs_names',
+    var_names='$in.var_names')
 
-    #else if $hd5_format.in.adata_format == 'tabular'
-        #set delimiter=$hd5_format.in.input.metadata.delimiter
-        #if $delimiter != ','
-            #set delimiter='\\t'
-        #end if
+#else if $in.adata_format == 'tabular'
+    #set delimiter=$in.input.metadata.delimiter
+    #if $delimiter != ','
+        #set delimiter='\\t'
+    #end if
 adata = ad.read_csv(
-    '$hd5_format.in.input',
+    '$in.input',
     delimiter='$delimiter',
-    first_column_names=$hd5_format.in.first_column_names)
+    first_column_names=$in.first_column_names)
+## convert into sparse matrix. Dense matrix needs large disk space and higher access times
+from scipy.sparse import csr_matrix
+adata.X = csr_matrix(adata.X)
 
-    #else if $hd5_format.in.adata_format == '10x_h5'
+#else if $in.adata_format == '10x_h5'
 import scanpy as sc
-adata = sc.read_10x_h5('$hd5_format.in.input')
+adata = sc.read_10x_h5('$in.input')
 
-    #else if $hd5_format.in.adata_format == 'mtx'
-        #if $hd5_format.in.tenx.use == 'no'
-adata = ad.read_mtx(filename='$hd5_format.in.matrix')
-        #else
+#else if $in.adata_format == 'mtx'
+    #if $in.tenx.use == 'no'
+adata = ad.read_mtx(filename='$in.matrix')
+    #else
 import scanpy as sc
 adata = sc.read_10x_mtx(
     'mtx',
-    var_names='$hd5_format.in.tenx.var_names',
-    make_unique=$hd5_format.in.tenx.make_unique,
+    var_names='$in.tenx.var_names',
+    make_unique=$in.tenx.make_unique,
     cache=False,
-    gex_only=$hd5_format.in.tenx.gex_only)
-        #end if
+    gex_only=$in.tenx.gex_only)
+    #end if
 
-    #else if $hd5_format.in.adata_format == 'umi_tools'
+#else if $in.adata_format == 'umi_tools'
 adata = ad.read_umi_tools('umi_tools_input.gz')
-    #end if
-adata.write('anndata.h5ad')
 #end if
+adata.write('anndata.h5ad', compression='gzip')
+print(adata)
 ]]></configfile>
     </configfiles>
     <inputs>
-        <conditional name="hd5_format">
-            <param name="filetype" type="select" label="hd5 format to be created">
-                <option value="anndata" selected="true">Anndata file</option>
-                <option value="loom">Loom file</option>
+        <conditional name="in">
+            <param name="adata_format" type="select" label="Create annadata from">
+                <option value="loom">Loom data</option>
+                <option value="tabular">Tabular, CSV, TSV</option>
+                <option value="10x_h5">H5 format from Cell ranger or not</option>
+                <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option>
+                <option value="umi_tools">UMI tools count matrix</option>
             </param>
-            <when value="anndata">
-                <conditional name="in">
-                    <param name="adata_format" type="select" label="Format for the annotated data matrix">
-                        <option value="loom">Loom</option>
-                        <option value="tabular">Tabular, CSV, TSV</option>
-                        <option value="10x_h5">H5 format from Cell ranger or not</option>
-                        <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option>
-                        <option value="umi_tools">UMI tools</option>
+            <when value="loom">
+                <param name="input" type="data" format="loom" label="Annotated data matrix"/>
+                <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/>
+                <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/>
+                <param name="x_name" type="text" value="spliced" label="X_name"/>
+                <param name="obs_names" type="text" value="CellID" label="obs_names"/>
+                <param name="var_names" type="text" value="Gene" label="var_names"/>
+            </when>
+            <when value="tabular">
+                <param name="input" type="data" format="tabular,csv,tsv" label="Annotated data matrix"/>
+                <param name="first_column_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Does the first column store the row names?"/>
+            </when>
+            <when value="10x_h5" >
+                <param name="input" type="data" format="h5" label="Data matrix"/>
+            </when>
+            <when value="mtx">
+                <param name="matrix" type="data" format="mtx" label="Matrix in Matrix Market format"/>
+                <conditional name="tenx">
+                    <param name="use" type="select" label="Use 10x Genomics formatted mtx">
+                        <option value="no">No</option>
+                        <option value="legacy_10x">Output from Cell Ranger v2 or earlier versions</option>
+                        <option value="v3_10x">Output from Cell Ranger v3 or later versions</option>
                     </param>
-                    <when value="loom">
-                        <param name="input" type="data" format="loom" label="Annotated data matrix"/>
-                        <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/>
-                        <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/>
-                        <param name="x_name" type="text" value="spliced" label="X_name"/>
-                        <param name="obs_names" type="text" value="CellID" label="obs_names"/>
-                        <param name="var_names" type="text" value="Gene" label="var_names"/>
-                    </when>
-                    <when value="tabular">
-                        <param name="input" type="data" format="tabular,csv,tsv" label="Annotated data matrix"/>
-                        <param name="first_column_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Does the first column store the row names?"/>
-                    </when>
-                    <when value="10x_h5" >
-                        <param name="input" type="data" format="h5" label="Data matrix"/>
+                    <when value="no"/>
+                    <when value="legacy_10x">
+                        <param name="genes" type="data" format="tabular" label="2-column genes file with gene id and gene name"/>
+                        <expand macro="params_10x"/>
                     </when>
-                    <when value="mtx">
-                        <param name="matrix" type="data" format="mtx" label="Matrix"/>
-                        <conditional name="tenx">
-                            <param name="use" type="select" label="Use 10x Genomics formatted mtx">
-                                <option value="no">No</option>
-                                <option value="legacy_10x">Output from Cell Ranger v2 or earlier versions</option>
-                                <option value="v3_10x">Output from Cell Ranger v3 or later versions</option>
-                            </param>
-                            <when value="no"/>
-                            <when value="legacy_10x">
-                                <param name="genes" type="data" format="tabular" label="Genes"/>
-                                <expand macro="params_10x"/>
-                            </when>
-                            <when value="v3_10x">
-                                <param name="features" type="data" format="tabular" label="Features"/>
-                                <expand macro="params_10x"/>
-                            </when>
-                        </conditional>
-                    </when>
-                    <when value="umi_tools">
-                        <param name="input" type="data" format="tabular" label="condensed count matrix from UMI tools"/>
+                    <when value="v3_10x">
+                        <param name="features" type="data" format="tabular" label="3-column features file with feature id, feature name and feature type" help="For scRNA-seq, features are genes. The 3rd column typically contains the word 'Gene Expression'"/>
+                        <expand macro="params_10x"/>
                     </when>
                 </conditional>
             </when>
-            <when value="loom">
-                <param name="mainmatrix" type="data" format="tabular" label="File for main layer of loom file." help="All subsequent tsv must be the same dimensions as this file. When converted back to tsv using hd5 export, this will be labeled as 'mainmatrix.tsv'"/>
-                <param name="other_files" type="data" format="tabular" multiple="true" optional="true" label="Add layers" help="Adds layers of same dimension to the loom file. When converted to tsv using hd5 export, these layers will retain their names."/>
-                <param name="coldata" type="data" format="tabular" label="Tsv of column data." help="First row is column attributes, subsequent are values."/>
-                <param name="rowdata" type="data" format="tabular" label="Tsv of row data." help="First row is row attributes, subsequent are values."/>
+            <when value="umi_tools">
+                <param name="input" type="data" format="tabular" label="condensed count matrix from UMI tools"/>
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="Anndata import on ${on_string}">
-            <filter>hd5_format['filetype'] == 'anndata'</filter>
-        </data>
-        <data name="loomdata" format="loom" from_work_dir="converted.loom" label="Loom import on ${on_string}">
-            <filter>hd5_format['filetype'] == 'loom'</filter>
-        </data>
+        <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="Anndata import on ${on_string}"/>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
@@ -191,7 +159,13 @@ adata.write('anndata.h5ad')
                 <has_text_matching expression="obs_names='CellID'"/>
                 <has_text_matching expression="var_names='Gene'"/>
             </assert_stdout>
-            <output name="anndata" value="import.loom.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/cell_type"/>
+                    <has_h5_keys keys="obs/obs_names"/>
+                    <has_h5_keys keys="var/var_names"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <conditional name="in">
@@ -203,8 +177,8 @@ adata.write('anndata.h5ad')
                 <has_text_matching expression="ad.read_csv"/>
                 <has_text_matching expression="delimiter=','"/>
                 <has_text_matching expression="first_column_names=True"/>
+                <has_text_matching expression="3 × 2"/>
             </assert_stdout>
-            <output name="anndata" value="import.csv.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test expect_num_outputs="1">
             <conditional name="in">
@@ -216,8 +190,8 @@ adata.write('anndata.h5ad')
                 <has_text_matching expression="ad.read_csv"/>
                 <has_text_matching expression="delimiter='\\t'"/>
                 <has_text_matching expression="first_column_names=True"/>
+                <has_text_matching expression="3 × 2"/>
             </assert_stdout>
-            <output name="anndata" value="import.tsv.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
         <test expect_num_outputs="1">
             <conditional name="in">
@@ -226,8 +200,10 @@ adata.write('anndata.h5ad')
                 <conditional name="tenx">
                     <param name="use" value="no"/>
                 </conditional>
-                </conditional>
-            <output name="anndata" value="import.mtx.no_10x.h5ad" ftype="h5ad" compare="sim_size"/>
+            </conditional>
+            <assert_stdout>
+                <has_text_matching expression="343 × 12"/>
+            </assert_stdout>
         </test>
         <test expect_num_outputs="1">
             <conditional name="in">
@@ -242,7 +218,14 @@ adata.write('anndata.h5ad')
                     <param name="gex_only" value="true"/>
                 </conditional>
             </conditional>
-            <output name="anndata" value="import.mtx.legacy_10x.h5ad" ftype="h5ad" compare="sim_size"/>
+            <assert_stdout>
+                <has_text_matching expression="12 × 343"/>
+            </assert_stdout>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="var/gene_ids"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <conditional name="in">
@@ -257,31 +240,29 @@ adata.write('anndata.h5ad')
                     <param name="gex_only" value="true"/>
                 </conditional>
             </conditional>
-            <output name="anndata" value="import.mtx.v3_10x.h5ad" ftype="h5ad" compare="sim_size"/>
+            <assert_stdout>
+                <has_text_matching expression="1107 × 507"/>
+            </assert_stdout>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="var/gene_ids"/>
+                    <has_h5_keys keys="var/feature_types"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="1">
-            <param name="filetype" value="anndata"/>
             <conditional name="in">
                 <param name="adata_format" value="umi_tools"/>
                 <param name="input" value="umi_tools.tsv"/>
             </conditional>
-            <output name="anndata" value="import.umi_tools.h5ad" ftype="h5ad" compare="sim_size"/>
-        </test>
-        <test expect_num_outputs="1">
-            <param name="filetype" value="loom"/>
-            <param name="mainmatrix" value="firstlayer.tsv"/>
-            <param name="other_files" value="secondlayer.tsv"/>
-            <param name="coldata" value="cols.tsv"/>
-            <param name="rowdata" value="rows.tsv"/>
-            <output name="loomdata" value="converted.loom.test" ftype="loom" compare="sim_size"/>
+            <assert_stdout>
+                <has_text_matching expression="2 × 13"/>
+            </assert_stdout>
         </test>
         <test expect_num_outputs="1"><!-- 10x h5 test -->
-            <conditional name="hd5_format">
-                <param name="filetype" value="anndata"/>
-                <conditional name="in">
-                    <param name="adata_format" value="10x_h5"/>
-                    <param name="input" value="dropletutils_input.h5"/>
-                </conditional>
+            <conditional name="in">
+                <param name="adata_format" value="10x_h5"/>
+                <param name="input" value="dropletutils_input.h5"/>
             </conditional>
             <output name="anndata">
                 <assert_contents>
@@ -296,7 +277,7 @@ adata.write('anndata.h5ad')
 
 **What it does**
 
-This tool creates an AnnData or loom dataset from several input types:
+This tool creates an AnnData from several input types:
 
 - Loom (`read_loom method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_loom.html>`__)
 - Tabular (`read_csv method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_csv.html>`__)
diff --git a/tools/anndata/inspect.xml b/tools/anndata/inspect.xml
index 5b4b700ec72..87fed9e8a35 100644
--- a/tools/anndata/inspect.xml
+++ b/tools/anndata/inspect.xml
@@ -1,4 +1,4 @@
-<tool id="anndata_inspect" name="Inspect AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="anndata_inspect" name="Inspect AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>object</description>
     <macros>
         <import>macros.xml</import>
@@ -283,7 +283,7 @@ pd.DataFrame(adata.varm['PCs']).to_csv("$varm_PCs", sep="\t", index = False)
             </conditional>
             <output name="uns_neighbors_connectivities" ftype="mtx">
                 <assert_contents>
-                    <has_text_matching expression="100	100	1248" />
+                    <has_text_matching expression="100	100	2496" />
                     <has_text_matching expression="4.880" />
                 </assert_contents>
             </output>
@@ -305,14 +305,14 @@ pd.DataFrame(adata.varm['PCs']).to_csv("$varm_PCs", sep="\t", index = False)
             <output name="uns_paga_connectivities" ftype="mtx">
                 <assert_contents>
                     <has_text_matching expression="16	16	97" />
-                    <has_text_matching expression="1.000" />
+                    <has_text_matching expression="2 1 1" />
                     <has_text_matching expression="8.839" />
                 </assert_contents>
             </output>
             <output name="uns_paga_connectivities_tree" ftype="mtx">
                 <assert_contents>
                     <has_text_matching expression="16	16	15" />
-                    <has_text_matching expression="1.000" />
+                    <has_text_matching expression="1 2 1" />
                 </assert_contents>
             </output>
         </test>
diff --git a/tools/anndata/macros.xml b/tools/anndata/macros.xml
index 69494861dcd..fdeef099049 100644
--- a/tools/anndata/macros.xml
+++ b/tools/anndata/macros.xml
@@ -1,6 +1,7 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.10.3</token>
+    <token name="@TOOL_VERSION@">0.10.9</token>
     <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.09</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">anndata</requirement>
@@ -19,12 +20,6 @@
     <token name="@CMD@"><![CDATA[
 cat '$script_file' &&
 python '$script_file'
-    ]]>
-    </token>
-    <token name="@LOOMCMD@"><![CDATA[
-mkdir ./output &&
-mkdir ./attributes &&
-python '$__tool_directory__/loompy_to_tsv.py' -f '${hd5_format.input}'
     ]]>
     </token>
     <token name="@CMD_imports@"><![CDATA[
@@ -76,4 +71,11 @@ and cells, such as Name, Chromosome, Position (for genes), and Strain, Sex, Age
             </when>
         </conditional>
     </xml>
+    <xml name="sanitize_query" token_validinitial="string.printable">
+        <sanitizer>
+            <valid initial="@VALIDINITIAL@">
+                <remove value="&apos;" />
+            </valid>
+       </sanitizer>
+    </xml>
 </macros>
diff --git a/tools/anndata/manipulate.xml b/tools/anndata/manipulate.xml
index 0534748c3b4..0f8d9153018 100644
--- a/tools/anndata/manipulate.xml
+++ b/tools/anndata/manipulate.xml
@@ -1,4 +1,4 @@
-<tool id="anndata_manipulate" name="Manipulate AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="anndata_manipulate" name="Manipulate AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>object</description>
     <macros>
         <import>macros.xml</import>
@@ -50,6 +50,27 @@ adata.rename_categories(
     key='$manipulate.key',
     categories=$categories)
 
+#else if $manipulate.function == 'remove_keys'
+    #if $manipulate.obs_keys
+        #set $keys = [x.strip() for x in str($manipulate.obs_keys).split(',')]
+adata.obs = adata.obs.drop(columns=$keys)
+    #end if
+
+    #if $manipulate.var_keys
+        #set $keys = [x.strip() for x in str($manipulate.var_keys).split(',')]
+adata.var = adata.vars.drop(columns=$keys)
+    #end if
+
+#else if $manipulate.function == 'flag_genes'
+## adapted from anndata operations
+    #for $flag in $manipulate.gene_flags
+k_cat = adata.var_names.str.startswith('${flag.startswith}')
+if k_cat.sum() > 0:
+    adata.var['${flag.col_name}'] = k_cat
+else:
+    print(f'No genes starting with {'${flag.startswith}'} found.')
+#end for
+
 #else if $manipulate.function == 'strings_to_categoricals'
 adata.strings_to_categoricals()
 
@@ -71,6 +92,14 @@ obs.index = obs_index
 adata.obs = obs
     #end if
 
+#else if $manipulate.function == 'split_on_obs'
+import os
+res_dir = "output_split"
+os.makedirs(res_dir, exist_ok=True)
+for s,field_value in enumerate(adata.obs["${manipulate.key}"].unique()):
+    ad_s = adata[adata.obs.${manipulate.key} == field_value]
+    ad_s.write(f"{res_dir}/${manipulate.key}_{s}.h5ad", compression='gzip')
+
 #else if $manipulate.function == 'filter'
     #if $manipulate.filter.filter == 'key'
         #if $manipulate.var_obs == 'var'
@@ -126,7 +155,11 @@ adata.raw = adata
 
 #end if
 
-adata.write('anndata.h5ad')
+#if $manipulate.function != 'split_on_obs'
+adata.write('anndata.h5ad', compression='gzip')
+print(adata)
+#end if
+
 ]]></configfile>
     </configfiles>
     <inputs>
@@ -137,9 +170,12 @@ adata.write('anndata.h5ad')
                 <option value="obs_names_make_unique">Makes the obs index unique by appending '1', '2', etc</option>
                 <option value="var_names_make_unique">Makes the var index unique by appending '1', '2', etc</option>
                 <option value="rename_categories">Rename categories of annotation</option>
+                <option value="remove_keys">Remove keys from obs or var annotations</option>
+                <option value="flag_genes">Flag genes start with a pattern</option><!--adapted from EBI anndata operations tool -->
                 <option value="strings_to_categoricals">Transform string annotations to categoricals</option>
                 <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option>
                 <option value="add_annotation">Add new annotation(s) for observations or variables</option>
+                <option value="split_on_obs">Split the AnnData object into multiple AnnData objects based on the values of a given obs key</option><!--adapted from EBI anndata operations tool-->
                 <option value="filter">Filter observations or variables</option>
                 <option value="save_raw">Freeze the current state into the 'raw' attribute</option>
             </param>
@@ -167,6 +203,26 @@ adata.write('anndata.h5ad')
                 <param name="key" type="text" value="" label="Key for observations or variables annotation" help="Annotation key in obs or var"/>
                 <param name="categories" type="text" value="" label="Comma-separated list of new categories" help="It should be the same number as the old categories"/>
             </when>
+            <when value="remove_keys">
+                <param name="obs_keys" type="text" value="" optional="true" label="Keys/fields to remove from observations (obs)">
+                    <expand macro="sanitize_query"/>
+                </param>
+                <param name="var_keys" type="text" value="" optional="true" label="Keys/fields to remove from variables (var)">
+                    <expand macro="sanitize_query"/>
+                </param>
+            </when>
+            <when value="flag_genes">
+                <repeat name="gene_flags" title="Flag genes that start with these names">
+                    <param name="startswith" type="text" label="Text that you expect the genes to be flagged to start with" help="For example, 'MT-' for mito genes">
+                        <sanitizer invalid_char="">
+                            <valid initial="string.ascii_letters,string.digits,string.punctuation">
+                                <remove value="&apos;" />
+                            </valid>
+                        </sanitizer>
+                    </param>
+                    <param name="col_name" type="text" label="Name of the column in var.names where this boolean flag is stored" help="For example, name this column as 'mito' for mitochondrial genes."/>
+                </repeat>
+            </when>
             <when value="strings_to_categoricals" ></when>
             <when value="transpose" ></when>
             <when value="add_annotation">
@@ -177,6 +233,15 @@ adata.write('anndata.h5ad')
                 <param name="new_annot" type="data" format="tabular" label="Table with new annotations"
                     help="The new table should have the same number of rows and same order than obs or var. The key names should be in the header (1st line)"/>
             </when>
+            <when value="split_on_obs">
+                <param name="key" type="text" label="The obs key to split on" help="For example, if you want to split on cluster annotation, you can use the key 'louvain'. The output will be a collection of anndata objects">
+                    <sanitizer invalid_char="">
+                        <valid initial="string.ascii_letters,string.digits,string.punctuation">
+                            <remove value="&apos;" />
+                        </valid>
+                    </sanitizer>
+                </param>
+            </when>
             <when value="filter">
                 <param name="var_obs" type="select" label="What to filter?">
                     <option value="var">Variables (var)</option>
@@ -237,10 +302,16 @@ adata.write('anndata.h5ad')
         </conditional>
     </inputs>
     <outputs>
-        <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${manipulate.function}) on ${on_string}"/>
+        <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${manipulate.function}) on ${on_string}">
+            <filter>manipulate['function'] != 'split_on_obs'</filter>
+        </data>
+        <collection name="output_h5ad_split" type="list" label="${tool.name} (${manipulate.function}) on ${on_string} Collection">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.h5" directory="output_split" format="h5ad" visible="true"/>
+            <filter>manipulate['function'] == 'split_on_obs'</filter>
+        </collection>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 1 -->
             <param name="input" value="import.csv.h5ad"/>
             <conditional name="manipulate">
@@ -256,10 +327,15 @@ adata.write('anndata.h5ad')
                 <has_text_matching expression="join='inner'"/>
                 <has_text_matching expression="index_unique='-'"/>
                 <has_text_matching expression="batch_key='batch'"/>
+                <has_text_matching expression="6 × 2"/>
             </assert_stdout>
-            <output name="anndata" value="manipulate.concatenate.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/batch"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 2 -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="manipulate">
@@ -268,10 +344,17 @@ adata.write('anndata.h5ad')
             </conditional>
             <assert_stdout>
                 <has_text_matching expression="adata.obs_names_make_unique\(join='-'\)"/>
+                <has_text_matching expression="500 × 11"/>
             </assert_stdout>
-            <output name="anndata" value="manipulate.obs_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/cell_type"/>
+                    <has_h5_keys keys="uns/highlights"/>
+                    <has_h5_keys keys="uns/iroot"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 3 -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="manipulate">
@@ -280,25 +363,39 @@ adata.write('anndata.h5ad')
             </conditional>
             <assert_stdout>
                 <has_text_matching expression="adata.var_names_make_unique\(join='-'\)"/>
+                <has_text_matching expression="500 × 11"/>
             </assert_stdout>
-            <output name="anndata" value="manipulate.var_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/cell_type"/>
+                    <has_h5_keys keys="uns/highlights"/>
+                    <has_h5_keys keys="uns/iroot"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 4 -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="manipulate">
                 <param name="function" value="rename_categories"/>
                 <param name="key" value="cell_type"/>
-                <param name="categories" value="Ery, Mk, Mo, progenitor"/>
+                <param name="categories" value="ery, mk, mo, progenitor"/>
             </conditional>
             <assert_stdout>
                 <has_text_matching expression="adata.rename_categories"/>
                 <has_text_matching expression="key='cell_type'"/>
-                <has_text_matching expression="categories=\['Ery', 'Mk', 'Mo', 'progenitor'\]"/>
+                <has_text_matching expression="categories=\['ery', 'mk', 'mo', 'progenitor'\]"/>
+                <has_text_matching expression="500 × 11"/>
             </assert_stdout>
-            <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/cell_type"/>
+                    <has_h5_keys keys="uns/highlights"/>
+                    <has_h5_keys keys="uns/iroot"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 5 -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="manipulate">
@@ -306,10 +403,17 @@ adata.write('anndata.h5ad')
             </conditional>
             <assert_stdout>
                 <has_text_matching expression="adata.strings_to_categoricals"/>
+                <has_text_matching expression="500 × 11"/>
             </assert_stdout>
-            <output name="anndata" value="manipulate.strings_to_categoricals.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/cell_type"/>
+                    <has_h5_keys keys="uns/highlights"/>
+                    <has_h5_keys keys="uns/iroot"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 6 -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="manipulate">
@@ -317,10 +421,17 @@ adata.write('anndata.h5ad')
             </conditional>
             <assert_stdout>
                 <has_text_matching expression="adata.transpose"/>
+                <has_text_matching expression="11 × 500"/>
             </assert_stdout>
-            <output name="anndata" value="manipulate.transpose.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="var/cell_type"/>
+                    <has_h5_keys keys="uns/highlights"/>
+                    <has_h5_keys keys="uns/iroot"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 7 -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="manipulate">
@@ -328,9 +439,20 @@ adata.write('anndata.h5ad')
                 <param name="var_obs" value="var"/>
                 <param name="new_annot" value="var_add_annotation.tabular"/>
             </conditional>
-            <output name="anndata" value="manipulate.add_annotation_var.h5ad" ftype="h5ad" compare="sim_size"/>
+            <assert_stdout>
+                <has_text_matching expression="500 × 11"/>
+            </assert_stdout>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/cell_type"/>
+                    <has_h5_keys keys="var/annot1"/>
+                    <has_h5_keys keys="var/annot2"/>
+                    <has_h5_keys keys="uns/highlights"/>
+                    <has_h5_keys keys="uns/iroot"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 8 -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="manipulate">
@@ -338,9 +460,20 @@ adata.write('anndata.h5ad')
                 <param name="var_obs" value="obs"/>
                 <param name="new_annot" value="obs_add_annotation.tabular"/>
             </conditional>
-            <output name="anndata" value="manipulate.add_annotation_obs.h5ad" ftype="h5ad" compare="sim_size"/>
+            <assert_stdout>
+                <has_text_matching expression="500 × 11"/>
+            </assert_stdout>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/cell_type"/>
+                    <has_h5_keys keys="obs/annot1"/>
+                    <has_h5_keys keys="obs/annot2"/>
+                    <has_h5_keys keys="uns/highlights"/>
+                    <has_h5_keys keys="uns/iroot"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 9 -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="manipulate">
@@ -354,9 +487,18 @@ adata.write('anndata.h5ad')
                     </conditional>
                 </conditional>
             </conditional>
-            <output name="anndata" value="manipulate.filter_var_index.h5ad" ftype="h5ad" compare="sim_size"/>
+            <assert_stdout>
+                <has_text_matching expression="500 × 2"/>
+            </assert_stdout>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/cell_type"/>
+                    <has_h5_keys keys="uns/highlights"/>
+                    <has_h5_keys keys="uns/iroot"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 10 -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="manipulate">
@@ -372,23 +514,120 @@ adata.write('anndata.h5ad')
                     </conditional>
                 </conditional>
             </conditional>
-            <output name="anndata" value="manipulate.filter_obs_key.h5ad" ftype="h5ad" compare="sim_size"/>
+            <assert_stdout>
+                <has_text_matching expression="260 × 11"/>
+            </assert_stdout>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/cell_type"/>
+                    <has_h5_keys keys="uns/highlights"/>
+                    <has_h5_keys keys="uns/iroot"/>
+                </assert_contents>
+            </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <!-- test 11 -->
             <param name="input" value="krumsiek11.h5ad"/>
             <conditional name="manipulate">
                 <param name="function" value="save_raw"/>
             </conditional>
-            <output name="anndata" value="manipulate.save_raw.h5ad" ftype="h5ad" compare="sim_size" delta="20000" />
+            <assert_stdout>
+                <has_text_matching expression="500 × 11"/>
+            </assert_stdout>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/cell_type"/>
+                    <has_h5_keys keys="uns/highlights"/>
+                    <has_h5_keys keys="uns/iroot"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- test 12 remove_keys -->
+            <param name="input" value="krumsiek11.h5ad"/>
+            <conditional name="manipulate">
+                <param name="function" value="remove_keys"/>
+                <param name="obs_keys" value="cell_type"/>
+            </conditional>
+            <assert_stdout>
+                <has_text_matching expression="500 × 11"/>
+            </assert_stdout>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="uns/highlights"/>
+                    <has_h5_keys keys="uns/iroot"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- test 13 flag_genes -->
+            <param name="input" value="krumsiek11.h5ad"/>
+            <conditional name="manipulate">
+                <param name="function" value="flag_genes"/>
+                <repeat name="gene_flags">
+                    <param name="startswith" value="Gata"/>
+                    <param name="col_name" value="Gata_TF"/>
+                </repeat>
+                <repeat name="gene_flags">
+                    <param name="startswith" value="Gf"/>
+                    <param name="col_name" value="GF"/>
+                </repeat>
+            </conditional>
+            <assert_stdout>
+                <has_text_matching expression="500 × 11"/>
+            </assert_stdout>
+            <output name="anndata" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="var/Gata_TF"/>
+                    <has_h5_keys keys="var/GF"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- test 14 split_on_obs -->
+            <param name="input" value="krumsiek11.h5ad"/>
+            <conditional name="manipulate">
+                <param name="function" value="split_on_obs"/>
+                <param name="key" value="cell_type"/>
+            </conditional>
+            <output_collection name="output_h5ad_split" type="list">
+                <element name="cell_type_0">
+                    <assert_contents>
+                        <has_h5_keys keys="obs/cell_type"/>
+                        <has_h5_keys keys="uns/highlights"/>
+                        <has_h5_keys keys="uns/iroot"/>
+                    </assert_contents>
+                </element>
+                <element name="cell_type_1">
+                    <assert_contents>
+                        <has_h5_keys keys="obs/cell_type"/>
+                        <has_h5_keys keys="uns/highlights"/>
+                        <has_h5_keys keys="uns/iroot"/>
+                    </assert_contents>
+                </element>
+                <element name="cell_type_2">
+                    <assert_contents>
+                        <has_h5_keys keys="obs/cell_type"/>
+                        <has_h5_keys keys="uns/highlights"/>
+                        <has_h5_keys keys="uns/iroot"/>
+                    </assert_contents>
+                </element>
+                <element name="cell_type_3">
+                    <assert_contents>
+                        <has_h5_keys keys="obs/cell_type"/>
+                        <has_h5_keys keys="uns/highlights"/>
+                        <has_h5_keys keys="uns/iroot"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
         </test>
     </tests>
     <help><![CDATA[
 **What it does**
 
-This tool takes a AnnData dataset, manipulates it and returns it. 
+This tool takes a AnnData dataset, manipulates it and returns it.
 
-The possible manipulations are: 
+The possible manipulations are:
 
 - Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.concatenate.html>`__)
 
@@ -408,6 +647,14 @@ The possible manipulations are:
 
     Besides calling `self.obs[key].cat.categories = categories` - similar for `var` - this also renames categories in unstructured annotation that uses the categorical annotation `key`
 
+- Remove keys from obs or var annotations
+
+    Helps in cleaning up andata with many annotations. For example, helps in removing qc metrics calculated during the preprocesing or already existing cluster annotations.
+
+- Flag genes start with a pattern
+
+    Useful for flagging the mitochoncdrial or ribosomal protein genes
+
 - Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.strings_to_categoricals.html>`__)
 
     Only affects string annotations that lead to less categories than the total number of observations.
@@ -416,7 +663,11 @@ The possible manipulations are:
 
     Data matrix is transposed, observations and variables are interchanged.
 
-- Add annotation for variables or observations 
+- Add annotation for variables or
+
+- Split the AnnData object into multiple AnnData objects based on the values of a given obs key
+
+    For example, helps in splitting an anndata objects based on cluster annotation. This function generates a collection with number of elements equal to the number of categories in the input obs key.
 
 - Filter data variables or observations, by index or key
 
diff --git a/tools/anndata/modify_loom.xml b/tools/anndata/modify_loom.xml
index 776e890d74b..96e654836d0 100644
--- a/tools/anndata/modify_loom.xml
+++ b/tools/anndata/modify_loom.xml
@@ -1,62 +1,191 @@
-<tool id="modify_loom" name="Manipulate loom object" version="@TOOL_VERSION@+galaxy1">
-    <description>Add layers, or row/column attributes to a loom file</description>
+<tool id="modify_loom" name="Loom operations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Manipulate, export and import loom data</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="1.26.4">numpy</requirement><!-- loompy seems to adapt to numpy 2.x. Remove this in the next update -->
+    </expand>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
-cp '${input}' loom_add_out.loom &&
-python '$__tool_directory__/modify_loom.py' -f 'loom_add_out.loom'
-#if $which_add.add_type == "cols":
-    -a cols -c '${which_add.cols}'
-#else if $which_add.add_type == "cols":
-    -a rows -r '${which_add.rows}'
-#else if $which_add.add_type == "layers":
-    -a layers -l '${which_add.layers}'
+#if $operation.to_perform == 'manipulate'
+cp '${operation.loom}' converted.loom &&
+python '$__tool_directory__/modify_loom.py' -f 'converted.loom'
+    #if $operation.which_add.add_type == "cols":
+    -a cols -c '${operation.which_add.cols}'
+    #else if $operation.which_add.add_type == "rows":
+    -a rows -r '${operation.which_add.rows}'
+    #else if $operation.which_add.add_type == "layers":
+    -a layers -l '${operation.which_add.layers}'
+    #end if
+
+#else if $operation.to_perform == 'export'
+mkdir ./output &&
+mkdir ./attributes &&
+python '$__tool_directory__/loompy_to_tsv.py' -f '$operation.loom'
+
+#else if $operation.to_perform == 'import'
+    #if $operation.from.file_type == 'ad'
+@CMD@
+    #else if $operation.from.file_type == 'tab'
+python '$__tool_directory__/tsv_to_loompy.py'
+    -c '${operation.coldata}'
+    -r '${operation.rowdata}'
+    -f '${operation.mainmatrix}'
+        #if $operation.other_files
+    '${operation.other_files}'
+        #end if
+    #end if
 #end if
       ]]></command>
+    <configfiles>
+    <configfile name="script_file"><![CDATA[
+@CMD_imports@
+#if $operation.to_perform == 'import'
+    #if $operation.from.file_type == 'ad'
+adata = ad.read_h5ad('$operation.anndata')
+adata.write_loom('converted.loom')
+    #end if
+#end if
+      ]]></configfile>
+    </configfiles>
     <inputs>
-        <param name="input" type="data" format="loom" label="Loom file"/>
-        <conditional name="which_add">
-            <param name="add_type" type="select" label="Select data attribute to add to loom">
-                <option value="cols">Columns</option>
-                <option value="rows">Rows</option>
-                <option value="layers">Layers</option>
+        <conditional name="operation">
+            <param name="to_perform" type="select" label="Operation to perform on loom data">
+                <option value="manipulate">Manipulate loom data</option>
+                <option value="export">Export loom layers and attributes</option>
+                <option value="import">Import loom from an anndata or tabular files</option>
             </param>
-            <when value="cols">
-                <param name="cols" type="data" format="tabular" label="Column file of same dimensions as existing file"/>
+            <when value="manipulate">
+                <param name="loom" type="data" format="loom" label="Loom file"/>
+                <conditional name="which_add">
+                    <param name="add_type" type="select" label="Select data attribute to add to loom">
+                        <option value="cols">Columns</option>
+                        <option value="rows">Rows</option>
+                        <option value="layers">Layers</option>
+                    </param>
+                    <when value="cols">
+                        <param name="cols" type="data" format="tabular" label="Column file of same dimensions as existing file"/>
+                    </when>
+                    <when value="rows">
+                        <param name="rows" type="data" format="tabular" label="Row file of same dimensions as existing file"/>
+                    </when>
+                    <when value="layers">
+                        <param name="layers" type="data" multiple="true" format="tabular" label="Layer file(s) of same dimensions as existing file"/>
+                    </when>
+                </conditional>
             </when>
-            <when value="rows">
-                <param name="rows" type="data" format="tabular" label="Row file of same dimensions as existing file"/>
+            <when value="export">
+                <param name="loom" type="data" format="loom" label="Loom file"/>
             </when>
-            <when value="layers">
-                <param name="layers" type="data" multiple="true" format="tabular" label="Layer file(s) of same dimensions as existing file"/>
+            <when value="import">
+                <conditional name="from">
+                    <param name="file_type" type="select" label="Create loom file from">
+                        <option value="ad">an anndata object</option>
+                        <option value="tab">from tabular files of matrix and row and column attributes</option>
+                    </param>
+                    <when value="ad">
+                        <param name="anndata" type="data" format="h5ad" label="Anndata file"/>
+                    </when>
+                    <when value="tab">
+                        <param name="mainmatrix" type="data" format="tabular" label="File for main layer of loom file." help="All subsequent tsv must be the same dimensions as this file. When converted back to tsv using hd5 export, this will be labeled as 'mainmatrix.tsv'"/>
+                        <param name="other_files" type="data" format="tabular" multiple="true" optional="true" label="Add layers" help="Adds layers of same dimension to the loom file. When converted to tsv using hd5 export, these layers will retain their names."/>
+                        <param name="coldata" type="data" format="tabular" label="Tsv of column data." help="First row is column attributes, subsequent are values."/>
+                        <param name="rowdata" type="data" format="tabular" label="Tsv of row data." help="First row is row attributes, subsequent are values."/>
+                    </when>
+                </conditional>
+
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data name="loomout" format="loom" from_work_dir='loom_add_out.loom' label="Expanded loom file from '${on_string}'"/>
+        <data name="loomout" format="loom" from_work_dir='converted.loom' label="${tool.name} (${operation.to_perform}) on ${on_string} Loom file">
+            <filter>operation['to_perform'] == 'manipulate' or operation['to_perform'] == 'import'</filter>
+        </data>
+        <collection name="layer_tsvs" type="list" label="Layer matrices" >
+            <filter>operation['to_perform'] == 'export'</filter>
+            <discover_datasets pattern="__designation__" format="tabular" directory="output" visible="false" />
+        </collection>
+        <collection name="attribute_tsvs" type="list" label="Attribute matrices" >
+            <filter>operation['to_perform'] == 'export'</filter>
+            <discover_datasets pattern="__designation__" format="tabular" directory="attributes" visible="false" />
+        </collection>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="input" value="addtest.loom"/>
-            <param name="add_type" value="cols"/>
-            <param name="cols" value="cols.tsv"/>
+            <conditional name="operation">
+                <param name="to_perform" value="manipulate"/>
+                <param name="loom" value="addtest.loom"/>
+                <conditional name="which_add">
+                    <param name="add_type" value="cols"/>
+                    <param name="cols" value="cols.tsv"/>
+                </conditional>
+            </conditional>
             <output name="loomout" value="addloomout1.loom" ftype="loom" compare="sim_size"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="input" value="addtest.loom"/>
-            <param name="add_type" value="rows"/>
-            <param name="rows" value="rows.tsv"/>
+            <conditional name="operation">
+                <param name="to_perform" value="manipulate"/>
+                <param name="loom" value="addtest.loom"/>
+                <conditional name="which_add">
+                    <param name="add_type" value="rows"/>
+                    <param name="rows" value="rows.tsv"/>
+                </conditional>
+            </conditional>
             <output name="loomout" value="addloomout2.loom" ftype="loom" compare="sim_size"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="input" value="addtest.loom"/>
-            <param name="add_type" value="layers"/>
-            <param name="layers" value="addlayer1.tsv"/>
+            <conditional name="operation">
+                <param name="to_perform" value="manipulate"/>
+                <param name="loom" value="addtest.loom"/>
+                <conditional name="which_add">
+                    <param name="add_type" value="layers"/>
+                    <param name="layers" value="addlayer1.tsv"/>
+                </conditional>
+            </conditional>
             <output name="loomout" value="addloomout3.loom" ftype="loom" compare="sim_size"/>
         </test>
+        <test expect_num_outputs="2">
+            <conditional name="operation">
+                <param name="to_perform" value="export"/>
+                <param name="loom" value="loomtest.loom"/>
+            </conditional>
+            <output_collection name="layer_tsvs" type="list">
+                <element name="extralayer.tsv" value="secondlayer.tsv" ftype="tabular"/>
+                <element name="mainmatrix.tsv" value="firstlayer.tsv" ftype="tabular"/>
+                <element name="thirdlayer.tsv" value="finallayer.tsv" ftype="tabular"/>
+            </output_collection>
+            <output_collection name="attribute_tsvs" type="list">
+                <element name="col_attr.tsv" value="cols.tsv" ftype="tabular"/>
+                <element name="row_attr.tsv" value="rows.tsv" ftype="tabular"/>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="operation">
+                <param name="to_perform" value="import"/>
+                <conditional name="from">
+                    <param name="file_type" value="ad"/>
+                    <param name="anndata" value="krumsiek11.h5ad"/>
+                </conditional>
+            </conditional>
+            <assert_stdout>
+                <has_text_matching expression="adata.write_loom"/>
+            </assert_stdout>
+            <output name="loomout" value="export.krumsiek11.loom" ftype="loom" compare="sim_size"/>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="operation">
+                <param name="to_perform" value="import"/>
+                <conditional name="from">
+                    <param name="file_type" value="tab"/>
+                    <param name="mainmatrix" value="firstlayer.tsv"/>
+                    <param name="other_files" value="secondlayer.tsv"/>
+                    <param name="coldata" value="cols.tsv"/>
+                    <param name="rowdata" value="rows.tsv"/>
+                </conditional>
+            </conditional>
+            <output name="loomout" value="converted.loom.test" ftype="loom" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
 This tool allows the user to modify an existing loom data file by adding column attributes, row attributes or additional layers via tsv files.
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