view visualize_decisions.xml @ 0:f6dd27775d28 draft default tip

"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"

<tool id="pancancer_visualize_decisions" name="PAPAA: PanCancer visualize decisions" version="@VERSION@">
  <description>visualize decisions</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <version_command><![CDATA['papaa_visualize_decisions.py' --version]]></version_command>
  <command><![CDATA[
    mkdir 'classifier' &&
    ln -s '${classifier_decisions}' 'classifier/classifier_decisions.tsv' &&
    papaa_visualize_decisions.py
    --classifier_decisions 'classifier'
    #if str($custom):
    --custom '$custom'
    #end if
    > '${log}'
    ]]>
  </command>
  <inputs>
    <param argument="--classifier_decisions" label="pancancer decisions" name="classifier_decisions" optional="false" type="data" format="tabular" help="classifier_decisions.tsv"/>
    <param area="false" argument="--custom" label="comma separated list of columns to plot" name="custom" optional="true" type="text"/>
  </inputs>
  <outputs>
    <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/>
    <collection name="classifier_decisions_figures" type="list" label="Disease classifier decisions figures">
      <discover_datasets pattern="decision_plot_(?P&lt;identifier_0&gt;.+)\.pdf" format="pdf" directory="classifier/figures" visible="false" />
    </collection>
    <data format="pdf" name="total_decisions" label="${tool.name} on ${on_string} (total_decisions.pdf)" from_work_dir="classifier/figures/total_decisions.pdf"/>
    <data format="pdf" name="hyper_mutated" label="${tool.name} on ${on_string} (hyper_mutated.pdf)" from_work_dir="classifier/figures/hyper_mutated.pdf" />
    <collection name="custom_classifier_decisions_figures" type="list" label="custom classifier decisions figures">
      <filter>custom != ""</filter>
      <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_decision_plot\.pdf" format="pdf" directory="classifier" visible="false" />
    </collection>
  </outputs>
  <tests>
      <test>
          <param name="classifier_decisions" value="classifier_decisions.tsv" ftype="tabular"/>
          <output_collection name="classifier_decisions_figures" type="list">
                <element name="OV" file="OV.pdf" compare="sim_size" delta="50"/>
                <element name="LUAD" file="LUAD.pdf" compare="sim_size" delta="50"/>
                <element name="GBM" file="GBM.pdf" compare="sim_size" delta="50"/>
          </output_collection>    
          <output name="log" file="visualize_decisions_Log.txt"/>
          <output name="total_decisions" file="total_decisions.pdf" compare="sim_size" delta="30"/>
          <output name="hyper_mutated" file="hyper_mutated.pdf" compare="sim_size" delta="30"/>
      </test>
  </tests>
  <help><![CDATA[
    **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_visualize_decisions.py:**

      **Inputs:**
          --classifier_decisions  String of the folder location of classifier_decisions.tsv
          --custom  comma separated list of columns to plot (optional: True)
      
      **Outputs:**
          Visualize decision function for all samples ("total_decisions.pdf")  

          Plot disease type specific decision functions ("decision_plot_{}.pdf")  

          Visualize decision function for hyper mutated tumors ("hyper_mutated.pdf") ]]>
  </help>
  <expand macro="citations" />
</tool>