diff scanpy-read-10x.xml @ 5:f180f7230cdb 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-read-10x.xml	Wed Nov 20 05:18:16 2019 -0500
+++ b/scanpy-read-10x.xml	Mon Nov 25 14:41:17 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy0">
+<tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy6">
   <description>into hdf5 object handled by scanpy</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -30,14 +30,14 @@
     <param name="gene_meta" type="data" format="tsv,tabular" label="Gene metadata table" optional="true"
            help="Requires a header row and index column that matches the gene table"/>
     <expand macro="output_object_params"/>
-    <param name="var_names" type="select" label="Attribute used as annotation index">
+    <param name="var_names" type="select" label="Attribute used as annotation index" help="If Gene ID is selected the index will point to the gene identifiers (first columns expected) and the gene symbols will be left in a field called 'gene_symbols'.">
       <option value="gene_ids" selected="true">Gene ID</option>
       <option value="gene_symbols">Gene symbol</option>
     </param>
   </inputs>
 
   <outputs>
-    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: ${output_format}"/>
+    <expand macro="output_data_obj" description="${output_format}"/>
   </outputs>
 
   <tests>