<?xml version="1.0" encoding="utf-8"?>
<tool id="monocle3_topmarkers" name="Monocle3 top markers" version="0.1.5+galaxy0" profile="@PROFILE@">
  <description>for cell groups</description>
  <macros>
    <import>monocle3-macros.xml</import>
  </macros>
  <requirements>
    <requirement type="package" version="0.0.8">monocle3-cli</requirement>
  </requirements>
    <command detect_errors="exit_code"><![CDATA[
    ln -s '$input_object' input.rds;
    #if $ref_cells.source == 'file' and $ref_cells.file
    list_of_cells=\$(cat $ref_cells.file | tr '\n' ',')
    #end if
    LANG=en_US.UTF-8 monocle3 topMarkers
    --input-object-format cds3
    #if $filter_fraction_expression
    --filter-fraction-expression '$filter_fraction_expression'
    #end if
    #if $top_n_markers
    --top-n-markers '$top_n_markers'
    #end if
    #if $plot_top_markers
    --plot-top-markers top_markers.pdf
    #end if
    #if $save_full_markers
    --save-full-markers full_markers.tsv
    #end if
    #if $ref_cells.source == 'file' and $ref_cells.file
    --reference-cells \$list_of_cells
    #end if
    #if $ref_cells.source == 'number' and $ref_cells.number
    --reference-cells '$ref_cells.number'
    #end if
    #if $marker_sig_test
    --marker-sig-test
    #end if
    #if $genes_to_test_per_group
    --genes-to-test-per-group '$genes_to_test_per_group'
    #end if
    #if $group_cells_by
    --group-cells-by '$group_cells_by'
    #end if
    --cores \${GALAXY_SLOTS:-1}
    --introspective

    input.rds
    output.tsv
    ]]></command>
<inputs>
  <param label="Input Object" name="input_object" type="data" format='rdata'  help="Input file with monocle3 object cds3 in RDS"/>
  <conditional name="ref_cells">
    <param label="Reference cells source" name="source" type="select" argument="--reference-cells" help="(Optional) Set of cells to be considered as reference for marker significance test. Accelerates the marker significance test at some cost in sensitivity.">
      <option value="file">File</option>
      <option value="number">Number of cells</option>
    </param>
    <when value="file">
      <param label="Reference cells file" name="file" optional="true" argument="--reference-cells" type="data" format='txt'  help="File with cells to be used as reference cells."/>
    </when>
    <when value="number">
      <param label="Number of reference cells" name="number" optional="true" argument="--reference-cells" type="integer" help="Number of cells to be used as reference cells."/>
    </when>
  </conditional>
  <param label="Filter fraction for expression" optional='true' value="0.1" name="filter_fraction_expression" argument="--filter-fraction-expression" type="float"   help="Filters the markers test result by this fraction of expression"/>
  <param label="Top-n-markers" optional='true' value="5" name="top_n_markers" argument="--top-n-markers" type="integer"   help="The number of top marker genes to report in plots and in top markers list"/>
  <param label="Number of genes to test per group" optional='true' value="25" name="genes_to_test_per_group" argument="--genes-to-test-per-group" type="integer"   help="how many genes of the top ranked specific genes by Jenson-Shannon, to do the more expensive regression test on"/>
  <param label="Group cell by" optional='true' value='cluster' name="group_cells_by" argument="--group-cells-by" type="text"   help="Cell groups, choose from 'cluster', 'partition', or any categorical variable in `colData(cds)`"/>
  <param label="Use logistic regression to asses discriminatory power" value='false' name="marker_sig_test" argument="--marker-sig-test" type="boolean" checked='false' help="whether to assess the discriminative power of each marker through logistic regression. Can be slow, consider disabling to speed up top_markers()."/>
  <param label="Save full markers" value='false' name="save_full_markers" argument="--save-full-markers" type="boolean"  checked='false' help="whether to generate the full markers list as well."/>
  <param label="Plot top markers" value='false' name="plot_top_markers" argument="--plot-top-markers" type="boolean"  checked='true' help="whether to generate the top markers plot."/>
</inputs>

<outputs>
  <data label="${tool.name} on ${on_string}: Top markers plot" name="top_markers_plot" format='pdf' from_work_dir='top_markers.pdf'>
    <filter>plot_top_markers</filter>
  </data>
  <data label="${tool.name} on ${on_string}: Full markers" name="full_markers" from_work_dir="full_markers.tsv" format='tabular'>
    <filter>save_full_markers</filter>
  </data>
  <data label="${tool.name} on ${on_string}: Top markers" name="top_markers_table" from_work_dir="output.tsv" format='tabular' />
</outputs>

<tests>
  <test>
    <param name="input_object_file" value="input.rds"/>
    <param name="filter_fraction_expression" value="0.1"/>
    <output name="top_markers_table" file="top_markers_table.tsv" ftype="tsv" compare="sim_size"/>
  </test>
</tests>

<help><![CDATA[
==========================================================
Monocle3 top markers genes
==========================================================

Identify the genes most specifically expressed in groups of cells. See inline help for options.

@HELP@

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