# HG changeset patch
# User morinlab
# Date 1480527295 18000
# Node ID fe65a4d95e7ad5878dc4a2ce8e4556333277e3a5
# Parent  a9c4c014fc4774025015925bf648bf1b8bcde14f
Uploaded

diff -r a9c4c014fc47 -r fe65a4d95e7a oncodrivefm.xml
--- a/oncodrivefm.xml	Tue Oct 11 14:24:44 2016 -0400
+++ b/oncodrivefm.xml	Wed Nov 30 12:34:55 2016 -0500
@@ -27,11 +27,8 @@
     #end if
     ./odfm;
     
-  cat ./out/odfm-pathways.tsv >> $out_file2;
-  cat ./out/odfm-genes.tsv >> $out_file1;
-
-  pwd >> $out_file2;
-  ls ./out/* >> $out_file2;
+  cat ./out/odfm-genes.tsv | grep -v \\# | sort -g -k 3  | awk 'BEGIN {OFS = "\t"}{if ($advancedsettings.qcut > $3 ) print \$1, \$2, \$3; }' >> $out_file1;
+  cat ./out/odfm-pathways.tsv | grep -v \\# | sort -g -k 4 >> $out_file2;
   
   </command>
   <inputs>
@@ -44,7 +41,8 @@
       </param>
       <param name="gthreshold" type="integer" label="Gene Threshold" help="Minimum number of mutations per gene to compute the FM bias" value="2"/>
       <param name="pthreshold" type="integer" label="Pathway Threshold" help="Minimum number of mutations per pathway to compute the FM bias" value="10" />
-      <param name="slices" type="text" label="Slices" help="Slices to process separated by commas(slices=SIFT,PolyPhen,MA)" value="SIFT,PolyPhen"/>
+      <param name="qcut" type="float" label="Q value cutoff" help="Only return genes with Q value below this threshold" value="1.0" />
+      <param name="slices" type="text" label="Slices" help="Slices to process separated by commas(slices=SIFT,PPH2,MA)" value="SIFT,PPH2"/>
       <conditional name="mapoption">
         <param name="mapfile" type="select" label="Choose the source for the OncodriveFM Mapping File">
           <option value="included_file" selected="true">Use hg19 mapping file</option>
@@ -76,5 +74,47 @@
         If you use this Galaxy tool in work leading to a scientific publication please cite:
         Gonzalez-Perez A and Lopez-Bigas N. 2012. Functional impact bias reveals cancer drivers. Nucleic Acids Res., 10.1093/nar/gks743.
   </help>
+  <citations>
+    <citation type="bibtex">
+      @ARTICLE{Gonzalez-Perez2012-wq,
+      title    = "Functional impact bias reveals cancer drivers",
+      author   = "Gonzalez-Perez, Abel and Lopez-Bigas, Nuria",
+      journal  = "Nucleic Acids Res.",
+      volume   =  40,
+      number   =  21,
+      pages    = "e169--e169",
+      month    =  "1~" # nov,
+      year     =  2012
+      }
+
+      
+    </citation>
+    <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>
+    
+  </citations>
 </tool>