# HG changeset patch
# User morinlab
# Date 1488492198 18000
# Node ID b78c81a7ebaf8e9392cbd6a1d78b985c6cb256b9
# Parent  8263ddfcd202d1b60f954e8e9d504e848ae4985c
Uploaded

diff -r 8263ddfcd202 -r b78c81a7ebaf oncostrip.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/oncostrip.xml	Thu Mar 02 17:03:18 2017 -0500
@@ -0,0 +1,116 @@
+<tool id="oncostrip" name="Oncostrip Plot" version="0.9.30">
+
+  <description>
+    Cohort-wide mutation oncostrip from MAF and (optionally) GISTIC data
+  </description>
+
+  <command detect_errors="aggressive">
+
+      mkdir outputs;
+      touch gene_list.txt;
+      #if $gene_input_type.gene_input_type_selector.value == "other":
+        echo $gene_input_type.gene > gene_list.txt;
+      #else:
+        cat $gene_input_type.gene_file > gene_list.txt;
+      #end if
+
+      Rscript $__tool_directory__/oncostrip_gistic.R
+        --input_maf $input_maf
+        --gene_list gene_list.txt
+        --output_plot $output_plot
+      #if $include_anno.anno == "use_anno":
+        --anno $include_anno.anno_file
+      #end if
+      #if $sort_by == "anno":
+        --sort_by anno
+      #elif $sort_by == "gene":
+        --sort_by gene
+      #else:
+        --sort_by $sort_by 
+      #end if
+      #if $include_gistic.gistic == "use_gistic":
+      -gal $include_gistic.file1
+      -ga $include_gistic.file2
+      -gd $include_gistic.file3
+      #end if
+      ;
+      
+  </command>
+
+  <inputs>
+    <param type="data" format="maf" name="input_maf" label="MAF File"/>
+    <conditional name="gene_input_type">
+      <param name="gene_input_type_selector" type="select" label="Choose how to input genes">
+        <option value="file" selected="True">Gene File</option>
+        <option value="other">Other</option>
+      </param>
+      <when value="file">
+        <param name="gene_file" type="data" format="txt" label="Gene File"  help="list of genes separated by newlines" />
+      </when>
+      <when value="other">
+        <param name="gene" type="text" value="TP53" label="Gene" help="type the single gene" />
+      </when>
+    </conditional>
+
+    <param name="sort_by" type="select" label="Sort samples and genes in output?">
+      <option value="none">No sorting</option>
+      <option value="gene">Sort genes and patients using mutation frequency</option>
+      <option value="anno">Sort on annotation, then mutation frequency</option>
+    </param>
+
+    <conditional name="include_anno">
+    <param name="anno" type="select" display="radio" label="Optional: include annotation information for each sample">
+	<option value="use_anno" checked="false">Include</option>
+        <option value="no_anno" checked="true">Do not include</option>
+    </param>
+    <when value="use_anno">
+      <param name="anno_file" type="data" format="txt" optional="true" label="Annotation file"  help="text file with the first column listing each sample and remaining columns reserved for annotation" />
+
+      
+    </when>
+    </conditional>
+    <conditional name="include_gistic">
+      <param name="gistic" type="select" display="radio" label="Optional: include GISTIC output in display">
+	<option value="use_gistic" checked="false">Include</option>
+	<option value="no_gistic" checked="true">Do not include</option>
+      </param>
+      <when value="use_gistic">
+	<param name="file1" type="data" format="txt" label="all_lesions"  help="all_lesions output from GISTIC" />
+	<param name="file2" type="data" format="txt" label="amp_genes"  help="amp_genes output from GISTIC" />
+	<param name="file3" type="data" format="txt" label="del_genes"  help="del_genes output from GISTIC" />
+      </when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data format="pdf" name="output_plot"/>
+  </outputs>
+  <citations>
+    <citation type="bibtex">
+      @article {Albuquerque089631,
+      author = {Albuquerque, Marco A and Grande, Bruno M and Ritch, Elie and Jessa, Selin and Krzywinski, Martin I and Grewal, Jasleen and Shah, Sohrab and Boutros, Paul and Morin, Ryan},
+      title = {Enhancing Knowledge Discovery from Cancer Genomics Data with Galaxy},
+      year = {2016},
+      doi = {10.1101/089631},
+      publisher = {Cold Spring Harbor Labs Journals},
+      URL = {http://biorxiv.org/content/early/2016/11/26/089631},
+      eprint = {http://biorxiv.org/content/early/2016/11/26/089631.full.pdf},
+      journal = {bioRxiv}
+      }
+
+    </citation>
+    <citation type="bibtex">
+      @misc{
+      goecks2010galaxy,
+      title={Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
+      author={Goecks, Jeremy and Nekrutenko, Anton and Taylor, James and others},
+      journal={Genome Biol},
+      volume={11},
+      number={8},
+      pages={R86},
+      year={2010}
+      }
+    </citation>
+    <citation type="doi">10.1101/052662</citation>
+    </citations>
+</tool>