--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/map_mutation_class.xml	Wed Dec 16 23:31:49 2020 +0000
@@ -0,0 +1,59 @@
+<tool id="pancancer_map_mutation_class" name="PAPAA: PanCancer map mutation class" version="@VERSION@">
+  <description>map mutation class</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <version_command><![CDATA['papaa_map_mutation_class.py' --version]]></version_command>
+  <command><![CDATA[
+      mkdir 'classifier' &&
+      ln -s '${classifier_decisions}' 'classifier/classifier_decisions.tsv' && 
+      papaa_map_mutation_class.py
+      --classifier_decisions 'classifier'
+      #if $path_genes and str($path_genes):
+      --path_genes '$path_genes'
+      #end if
+      @INPUTS_COPY_NUMBER_FILE_CONDITIONAL@
+      @INPUT_FILENAME_RAW_MUT@
+      > '${log}'
+    ]]> 
+  </command>
+  <inputs>
+    <param argument="--classifier_decisions" label="pancancer decisions" name="classifier_decisions" optional="false" type="data" format="tabular" help="classifier_decisions.tsv"/>
+    <param argument="--path_genes" label="string of the genes to extract or genelist file" name="path_genes" optional="true" type= "data" format="txt"/>
+    <expand macro="inputs_copy_number_file_conditional" />
+    <expand macro="input_filename_raw_mut" />
+  </inputs>
+  <outputs>
+    <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/>
+    <data format="tabular" name="mutation_classification_scores" label="${tool.name} on ${on_string} (mutation_classification_scores.tsv)" from_work_dir="classifier/tables/mutation_classification_scores.tsv"/>
+  </outputs>
+  <tests>
+        <test>
+          <param name="classifier_decisions" value="classifier_decisions.tsv" ftype="tabular"/>
+          <param name="path_genes" value="path_genes.txt" ftype="txt"/>
+          <param name="copy_number" value="yes"/>
+          <param name="filename_copy_loss" value="copy_number_loss_status_t10p.tsv.gz" ftype="tabular"/>
+          <param name="filename_copy_gain" value="copy_number_gain_status_t10p.tsv.gz" ftype="tabular"/>
+          <param name="filename_raw_mut" value="mc3.v0.2.8.PUBLIC_t1p.maf.gz" ftype="tabular"/>
+          <output name="log" file="map_mutation_class_Log.txt"/>
+          <output name="mutation_classification_scores" file="mutation_classification_scores.tsv" />
+        </test>
+  </tests>
+  <help><![CDATA[
+
+    **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_map_mutation_class.py:**
+      
+      **Inputs:**
+        --classifer_decisions   String of the location of folder containing classifier_decisions.tsv
+        --path_genes  comma separated string of HUGO symbols for all genes in the pathway or Pathway genes list file
+        --filename_copy_loss  Filename of copy number loss
+        --filename_copy_gain  Filename of copy number gain
+        --filename_raw_mut  Filename of raw mut MAF
+        
+      **Outputs:**
+      Merge per sample classifier scores with mutation types present in each sample and generate "mutation_classification_scores.tsv" file  ]]>
+    </help>
+    <expand macro="citations" />
+</tool>