comparison scanpy-find-markers.xml @ 26:a57c0538e56b draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 8724e7a15bd07ee890908acc22efb826052f2ef6-dirty"

25:e2f004c3b2b3

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
  <description>to find differentially expressed genes between groups</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

    ${settings.rankby_abs}
    #if $settings.groups
        --groups '${settings.groups}'
    #end if
    --reference '${settings.reference}'
    --filter-params 'min_in_group_fraction:${settings.min_in_group_fraction},max_out_group_fraction:${settings.max_out_group_fraction},min_fold_change:${settings.min_fold_change}'
    $settings.pts $settings.tie_correct
    #end if
    @INPUT_OPTS@
    @OUTPUT_OPTS@
]]></command>

               label="Use raw attribute if present"/>
        <param name="rankby_abs" argument="--rankby_abs" type="boolean" truevalue="--rankby-abs" falsevalue="" checked="false"
               label="Rank by absolute value of the scores instead of the scores"/>
        <param name="groups" argument="--groups" optional="true" type="text" label="Subset of groups/clusters to which comparisons shell be restricted."/>
        <param name="reference" argument="--reference" type="text" value="rest" label="If 'rest', compare to the union of the rest of the group/cluster. If a group identifier, compare to that group"/>
        <param name="min_in_group_fraction" type="float" min="0.0" max="1.0" value="0.25" label="Minimum in-group fraction"
               help="Post-test filtering to only keep genes expressed in at least this fraction of cells in the test group."/>
        <param name="max_out_group_fraction" type="float" min="0.0" max="1.0" value="0.5" label="Maximum out-group fraction"
               help="Post-test filtering to only keep genes expressed in at most this fraction of cells in the reference group."/>
        <param name="min_fold_change" type="float" value="2" label="Minimum fold change"
               help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/>
        <param name="pts" argument="--pts"  type="boolean" checked="false" label="Compute the fraction of cells expressing the genes?" truevalue="--pts" falsevalue="" />
        <param name="tie_correct" argument="--tie-correct"  type="boolean" checked="false" label="Use tie correction for 'wilcoxon' scores. Used only for 'wilcoxon'." truevalue="--tie-correct" falsevalue=""/>
      </when>
    </conditional>
  </inputs>

26:a57c0538e56b

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
  <description>to find differentially expressed genes between groups</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

    ${settings.rankby_abs}
    #if $settings.groups
        --groups '${settings.groups}'
    #end if
    --reference '${settings.reference}'
    #if $settings.filter.default == "false"
      --filter-params 'min_in_group_fraction:${settings.filter.min_in_group_fraction},max_out_group_fraction:${settings.filter.max_out_group_fraction},min_fold_change:${settings.filter.min_fold_change}'
    #end if
    $settings.pts $settings.tie_correct
    #end if
    @INPUT_OPTS@
    @OUTPUT_OPTS@
]]></command>

               label="Use raw attribute if present"/>
        <param name="rankby_abs" argument="--rankby_abs" type="boolean" truevalue="--rankby-abs" falsevalue="" checked="false"
               label="Rank by absolute value of the scores instead of the scores"/>
        <param name="groups" argument="--groups" optional="true" type="text" label="Subset of groups/clusters to which comparisons shell be restricted."/>
        <param name="reference" argument="--reference" type="text" value="rest" label="If 'rest', compare to the union of the rest of the group/cluster. If a group identifier, compare to that group"/>
        <conditional name="filter">
          <param name="default" type="boolean" checked="false" label="Use filtering defaults"/>
          <when value="true"/>
          <when value="false">
            <param name="min_in_group_fraction" type="float" min="0.0" max="1.0" value="0.25" label="Minimum in-group fraction"
                   help="Post-test filtering to only keep genes expressed in at least this fraction of cells in the test group."/>
            <param name="max_out_group_fraction" type="float" min="0.0" max="1.0" value="0.5" label="Maximum out-group fraction"
                   help="Post-test filtering to only keep genes expressed in at most this fraction of cells in the reference group."/>
            <param name="min_fold_change" type="float" value="2" label="Minimum fold change"
                   help="Post-test filtering to only keep genes with at least this fold change of expression relative to the reference group."/>
          </when>
        </conditional>
        <param name="pts" argument="--pts"  type="boolean" checked="false" label="Compute the fraction of cells expressing the genes?" truevalue="--pts" falsevalue="" />
        <param name="tie_correct" argument="--tie-correct"  type="boolean" checked="false" label="Use tie correction for 'wilcoxon' scores. Used only for 'wilcoxon'." truevalue="--tie-correct" falsevalue=""/>
      </when>
    </conditional>
  </inputs>