# HG changeset patch
# User iuc
# Date 1697464888 0
# Node ID aa4a6f0916b4b5062cfd6bfa1d0501dce2a666d3
# Parent  c29e7bb492bfd0e80a8b56b9f110ba137badb40b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 576069ce2296ef58daa8a4e03c993d5900608c4c

diff -r c29e7bb492bf -r aa4a6f0916b4 baredsc_2d.xml
--- a/baredsc_2d.xml	Mon Oct 02 13:25:17 2023 +0000
+++ b/baredsc_2d.xml	Mon Oct 16 14:01:28 2023 +0000
@@ -67,28 +67,28 @@
         </section>
     </inputs>
     <outputs>
-        <data format="npz" name="output" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: Numpy archive" from_work_dir="output.npz"/>
-        <data format="txt" name="neff" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: Neff" from_work_dir="output/baredSC_neff.txt"/>
-        <collection type="list" name="qc_plots" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: QC plots">
+        <data format="npz" name="output" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: Numpy archive" from_work_dir="output.npz"/>
+        <data format="txt" name="neff" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: Neff" from_work_dir="output/baredSC_neff.txt"/>
+        <collection type="list" name="qc_plots" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: QC plots">
             <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)" directory="QC"/>
         </collection>
-        <data format="tabular" name="pdf2d" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: mean PDF in matrix format" from_work_dir="output/baredSC_pdf2d.txt"/>
-        <data format="tabular" name="pdf2d_flat" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: PDF with error bar, one bin per line" from_work_dir="output/baredSC_pdf2d_flat.txt">
+        <data format="tabular" name="pdf2d" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: mean PDF in matrix format" from_work_dir="output/baredSC_pdf2d.txt"/>
+        <data format="tabular" name="pdf2d_flat" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: PDF with error bar, one bin per line" from_work_dir="output/baredSC_pdf2d_flat.txt">
             <actions>
                 <action name="column_names" type="metadata" default="x,y,low,mean,high,median" />
             </actions>
         </data>
-        <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: plot" from_work_dir="baredSC">
+        <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: plot" from_work_dir="baredSC">
             <change_format>
                 <when input="plots.image_file_format" value="png" format="png" />
                 <when input="plots.image_file_format" value="svg" format="svg" />
                 <when input="plots.image_file_format" value="pdf" format="pdf" />
             </change_format>
         </data>
-        <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: plots and txt">
+        <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: plots and txt">
             <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)"/>
         </collection>
-        <data format="txt" name="logevidence" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneXColName} and ${geneYColName}: Log evidence" from_work_dir="logevidence.txt"/>
+        <data format="txt" name="logevidence" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: Log evidence" from_work_dir="logevidence.txt"/>
     </outputs>
     <tests>
         <!-- First test I decreased the number of samples and bins to make it quicker-->
diff -r c29e7bb492bf -r aa4a6f0916b4 macros.xml
--- a/macros.xml	Mon Oct 02 13:25:17 2023 +0000
+++ b/macros.xml	Mon Oct 16 14:01:28 2023 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.1.1</token>
+    <token name="@TOOL_VERSION@">1.1.2</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
@@ -49,7 +49,7 @@
                 <param argument="--input" type="data" format="tabular" label="Input table (with header)" help="Expected format is one line per cell, columns with raw counts and one column 'nCount_RNA' with the total number of UMI per cell (optionally other meta data to filter)" />
             </when>
             <when value="anndata">
-                <param argument="--inputAnnData" type="data" format="anndata" label="AnnData containing raw counts" />
+                <param argument="--inputAnnData" type="data" format="h5ad" label="AnnData containing raw counts" />
             </when>
         </conditional>
     </xml>