diff scanpy-plot-embedding.xml @ 4:109cfa259d8b draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003

--- a/scanpy-plot-embedding.xml	Wed Nov 20 05:17:27 2019 -0500
+++ b/scanpy-plot-embedding.xml	Mon Nov 25 14:40:15 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy1">
+<tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy6">
   <description>visualise cell embeddings</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -17,6 +17,9 @@
 #if $point_size
     --size ${point_size}
 #end if
+#if $gene_symbols_field
+    --gene-symbols ${gene_symbols_field}
+#end if
     @PLOT_OPTS@
 ]]></command>
 
@@ -28,6 +31,7 @@
         <valid initial="string.printable"/>
       </sanitizer>
     </param>
+    <param name="gene_symbols_field" argument="--gene-symbols" type="text" optional="true" label="Field for gene symbols" help="The field used in the AnnData object to store gene symbols, leave blank for the default (index), else a common value is 'gene_symbols'"/>
     <param name="use_raw" argument="--use-raw" type="boolean" checked="true" truevalue="--use-raw" falsevalue="--no-raw" label="Use raw attributes if present"/>
     <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend">
       <option value="right margin" selected="true">Right margin</option>
@@ -40,7 +44,7 @@
   </inputs>
 
   <outputs>
-    <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: embedding plot"/>
+    <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: ${basis} embedding plot"/>
   </outputs>
 
   <tests>