--- a/export.xml	Sun Nov 12 16:43:28 2023 +0000
+++ b/export.xml	Sat Sep 14 19:57:36 2024 +0000
@@ -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"/>
+        <test expect_num_outputs="5">
             <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 @@
             <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>