# HG changeset patch
# User morinlab
# Date 1488492217 18000
# Node ID 4f6c1fa0d60b4e0da61b29ffc349c1d5e832dac4
# Parent  b78c81a7ebaf8e9392cbd6a1d78b985c6cb256b9
Deleted selected files

diff -r b78c81a7ebaf -r 4f6c1fa0d60b oncostrip.xml
--- a/oncostrip.xml	Thu Mar 02 17:03:18 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,116 +0,0 @@
-<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>