# HG changeset patch
# User iuc
# Date 1697464868 0
# Node ID 4fff5a2930135317d2d76a6b2c3926d0f770f1ef
# Parent  02b1fe7aed76203d47e80362c6518fc4d02aa424
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 576069ce2296ef58daa8a4e03c993d5900608c4c

diff -r 02b1fe7aed76 -r 4fff5a293013 baredsc_1d.xml
--- a/baredsc_1d.xml	Mon Oct 02 13:24:52 2023 +0000
+++ b/baredsc_1d.xml	Mon Oct 16 14:01:08 2023 +0000
@@ -58,27 +58,27 @@
         </section>
     </inputs>
     <outputs>
-        <data format="npz" name="output" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: Numpy archive" from_work_dir="output.npz"/>
-        <data format="txt" name="neff" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: Neff" from_work_dir="output/baredSC_neff.txt"/>
-        <collection type="list" name="qc_plots" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: QC plots">
+        <data format="npz" name="output" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: Numpy archive" from_work_dir="output.npz"/>
+        <data format="txt" name="neff" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: Neff" from_work_dir="output/baredSC_neff.txt"/>
+        <collection type="list" name="qc_plots" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: QC plots">
             <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)" directory="QC"/>
         </collection>
-        <data format="tabular" name="pdf" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: PDF with error bar" from_work_dir="output/baredSC_pdf.txt">
+        <data format="tabular" name="pdf" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: PDF with error bar" from_work_dir="output/baredSC_pdf.txt">
             <actions>
                 <action name="column_names" type="metadata" default="x,low,mean,high,median" />
             </actions>
         </data>
-        <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: plot" from_work_dir="baredSC">
+        <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: plot" from_work_dir="baredSC">
             <change_format>
                 <when input="plots.image_file_format" value="png" format="png" />
                 <when input="plots.image_file_format" value="svg" format="svg" />
                 <when input="plots.image_file_format" value="pdf" format="pdf" />
             </change_format>
         </data>
-        <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: plots and txt">
+        <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: plots and txt">
             <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)"/>
         </collection>
-        <data format="txt" name="logevidence" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: Log evidence" from_work_dir="logevidence.txt"/>
+        <data format="txt" name="logevidence" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: Log evidence" from_work_dir="logevidence.txt"/>
     </outputs>
     <tests>
         <!-- First test -->
diff -r 02b1fe7aed76 -r 4fff5a293013 macros.xml
--- a/macros.xml	Mon Oct 02 13:24:52 2023 +0000
+++ b/macros.xml	Mon Oct 16 14:01:08 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>