diff scanpy-filter-genes.xml @ 5:f1e4de78d768 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604

--- a/scanpy-filter-genes.xml	Mon Oct 28 05:24:17 2019 -0400
+++ b/scanpy-filter-genes.xml	Wed Nov 20 05:15:47 2019 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy3">
+<tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy0">
   <description>based on counts and numbers of cells expressed</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -13,7 +13,7 @@
     ${pars}
 #end if
 #if $categories
-    #set cats = ' '.join(['--category g:{name} {values}'.format(**$c) for $c in $categories])
+    #set cats = ' '.join(["--category g:{name} '{negate}{values}'".format(**$c) for $c in $categories])
     ${cats}
 #end if
 #if $subsets
@@ -40,7 +40,8 @@
 
     <repeat name="categories" title="Categories used to filter genes" min="0">
       <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
-      <param name="values" type="text" value="" label="Comma-separated values to keep"/>
+      <param name="values" type="text" value="" label="Comma-separated list of categories"/>
+      <param name="negate" type="boolean" truevalue="!" falsevalue="" checked="false" label="Apply as negative filter" help="If enabled, specified categories will be removed rather than retained."/>
     </repeat>
 
     <repeat name="subsets" title="Subsets used to filter genes" min="0">