--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/visualize_decisions.xml	Wed Dec 16 23:30:56 2020 +0000
@@ -0,0 +1,64 @@
+<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>