<?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>
    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Marker object"/>
    <data name="output_csv" format="csv" from_work_dir="output.csv" label="${tool.name} on ${on_string}: Marker table">
      <filter>output_markers</filter>
    </data>
  </outputs>

  <tests>
    <test>
      <param name="input_obj_file" value="find_cluster.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="output_format" value="anndata"/>
      <param name="output_csv" value="true"/>
      <param name="n_genes" value="50"/>
      <param name="output_markers" value="false"/>
      <param name="default" value="false"/>
      <param name="groupby" value="louvain"/>
      <param name="method" value="t-test_overestim_var"/>
      <param name="rankby_abs" value="false"/>
      <output name="output_h5" file="find_markers.h5" ftype="h5" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
=============================================================
Rank genes for characterizing groups (`tl.rank_genes_groups`)
=============================================================

Rank genes for characterizing groups.

@HELP@

@VERSION_HISTORY@
]]></help>
  <expand macro="citations"/>
</tool>