comparison scanpy-filter-genes.xml @ 7:0bba942e0869 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 0a162684a5859a53eefb14af11ba8ec64d42b213-dirty

6:cb55f68ea1d7

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy4">
  <description>based on counts and numbers of cells expressed</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-filter-genes
#if $parameters
    #set pars = ' '.join(['--param g:{name} {min} {max}'.format(**$p) for $p in $parameters])
    ${pars}
#end if
#if $categories
    #set cats = ' '.join(["--category g:{name} '{negate}{values}'".format(**$c) for $c in $categories])
    ${cats}
#end if
#if $subsets
    #set subs = ' '.join(['--subset g:{name} {subset}'.format(**$s) for $s in $subsets])
    ${subs}
#end if
    @INPUT_OPTS@
    @OUTPUT_OPTS@
    @EXPORT_MTX_OPTS@

7:0bba942e0869

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy5">
  <description>based on counts and numbers of cells expressed</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-filter-genes
#if $parameters
    #set pars = ' '.join(["--param 'g:{name}' {min} {max}".format(**$p) for $p in $parameters])
    ${pars}
#end if
#if $categories
    #set cats = ' '.join(["--category 'g:{name}' '{negate}{values}'".format(**$c) for $c in $categories])
    ${cats}
#end if
#if $subsets
    #set subs = ' '.join(["--subset 'g:{name}' '{subset}'".format(**$s) for $s in $subsets])
    ${subs}
#end if
    @INPUT_OPTS@
    @OUTPUT_OPTS@
    @EXPORT_MTX_OPTS@