annotate monocle3-diffExp.xml @ 2:a7d4f80d1265 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"

<?xml version="1.0" encoding="utf-8"?>
<tool id="monocle3_diffExp" name="Monocle3 diffExp" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
  <description> of genes along a trajectory</description>
  <macros>
    <import>monocle3-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
LANG=en_US.UTF-8 monocle3 diffExp
    --neighbor-graph '$(neighbor_graph)'
    --reduction-method '$(reduction_method)'
#if $knn
    --knn '$(knn)'
#end if
    --method '$(method)'
    --alternative '$(alternative)'

    @INPUT_OPTS@
    output.tsv

    @VERBOSE@
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <param name="neighbor_graph" argument="--neighbor-graph" type="select" label="What neighbor graph to use, principal graph recommended for trajectory analysis.">
      <option value="knn" selected="true">KNN</option>
      <option value="principal_graph">Principal graph</option>
    </param>
    <param name="reduction_method" argument="--reduction-method" type="select" label="The reduction method to base the analysis on.">
      <option value="UMAP" selected="true">UMAP</option>
    </param>
    <param name="knn" argument="--knn" optional="true" type="integer" value="20" label="Number of nearest neighbors used for building the kNN graph which is passed to knn2nb function during the Moran's I (Geary's C) test procedure."/>
    <param name="method" argument="--method" type="select" label="A character string specifying the method for detecting significant genes showing correlated expression along the principal graph embedded in the low dimensional space.">
      <option value="Moran_I" selected="true">Moran_I</option>
    </param>
    <param name="alternative" argument="--alternative" type="select" label="A character string specifying the alternative hypothesis.">
      <option value="greater" selected="true">greater</option>
      <option value="less">less</option>
      <option value="two.sided">two-sided</option>
    </param>
    <expand macro="verbose_flag"/>
  </inputs>

  <outputs>
    <data name="output_tsv" format="tsv" from_work_dir="output.tsv" label="${tool.name} on ${on_string}: tsv"/>
  </outputs>

  <tests>
    <test>
      <param name="input_object_file" value="input.RDS"/>
      <param name="input_object_format" value="cds3"/>
      <param name="neighbor_graph" value="knn"/>
      <param name="reduction_method" value="UMAP"/>
      <param name="knn" value="20"/>
      <param name="method" value="Moran_I"/>
      <param name="alternative" value="greater"/>
      <output name="output_tsv" file="output.tsv" ftype="tsv" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
========================================================================
Monocle3 differential expression testing along trajectory (`graph_test`)
========================================================================

Identify differentially expressed genes along the inferred trajectory.

@HELP@

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