comparison scanpy-find-markers.xml @ 1:71668dd2d47b draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"

0:c608fd80ec15

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy1">
  <description>to find differentially expressed genes between groups</description>
  <macros>
    <import>scanpy_macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-find-markers.py
    -i input.h5
    -f '${input_format}'
    -o output.h5
    -F '${output_format}'
    -n '${n_genes}'
    #if $output_markers
        --output-text-file output.csv
    #end if
    #if $settings.default == "false"
        -g '${settings.groupby}'
        --reference '${settings.reference}'
        --method '${settings.method}'
        #if $settings.use_raw == "false"
            --no-raw
        #end if
        #if $settings.rankby_abs
            --rankby_abs
        #end if
        #if $settings.groups
            --groups '${settings.groups}'
        #end if
#end if
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>
    <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/>
    <param name="output_markers" type="boolean" checked="true" label="Output markers table in csv format"/>
    <conditional name="settings">
      <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
      <when value="true"/>
      <when value="false">
        <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/>
        <param name="use_raw" type="boolean" checked="true" label="Use raw attribute if present"/>
        <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="method" argument="--method" type="select" label="Method for testing differentially expressed genes">
          <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option>
          <option value="t-test">t-test</option>
          <option value="wilcoxon">wilcoxon test, currently broken don't use</option>
          <option value="logreg">logistic regression</option>
        </param>
        <param name="rankby_abs" argument="--rankby_abs" type="boolean" 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."/>
      </when>
    </conditional>
  </inputs>

  <outputs>

1:71668dd2d47b

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy1">
  <description>to find differentially expressed genes between groups</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-find-markers
#if $output_markers
    --save output.csv
#end if
    --n-genes '${n_genes}'
    --groupby '${groupby}'
#if $settings.default == "false"
    --method '${settings.method}'
    ${settings.use_raw}
    ${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}'
#end if
    @INPUT_OPTS@
    @OUTPUT_OPTS@
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>
    <param name="output_markers" type="boolean" checked="true" label="Output markers table in csv format"/>
    <param name="n_genes" argument="--n-genes" type="integer" value="50" label="Number of top genes to show per group/cluster"/>
    <param name="groupby" argument="--groupby" type="text" value="louvain" label="The sample grouping/clustering to use."/>
    <conditional name="settings">
      <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
      <when value="true"/>
      <when value="false">
        <param name="method" argument="--method" type="select" label="Method for testing differentially expressed genes">
          <option value="t-test_overestim_var" selected="true">t-test with over-estimated variance</option>
          <option value="t-test">t-test</option>
          <option value="wilcoxon">wilcoxon test, currently broken don't use</option>
          <option value="logreg">logistic regression</option>
        </param>
        <param name="use_raw" type="boolean" truevalue="--use-raw" falsevalue="--no-raw" checked="true"
               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."/>
      </when>
    </conditional>
  </inputs>

  <outputs>