comparison 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

4:fa6c08064fc1

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy3">
  <description>based on counts and numbers of cells expressed</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

#if $parameters
    #set pars = ' '.join(['--param g:{name} {min} {max}'.format(**$p) for $p in $parameters])
    ${pars}
#end if
#if $categories
    #set cats = ' '.join(['--category g:{name} {values}'.format(**$c) for $c in $categories])
    ${cats}
#end if
#if $subsets
    #set subs = ' '.join(['--subset g:{name} {subset}'.format(**$s) for $s in $subsets])
    ${subs}

      <param name="max" type="float" min="0" value="1e9" label="Max value"/>
    </repeat>

    <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"/>
    </repeat>

    <repeat name="subsets" title="Subsets used to filter genes" min="0">
      <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
      <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/>

5:f1e4de78d768

<?xml version="1.0" encoding="utf-8"?>
<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>
  </macros>
  <expand macro="requirements"/>

#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}

      <param name="max" type="float" min="0" value="1e9" label="Max value"/>
    </repeat>

    <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 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">
      <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
      <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/>