# HG changeset patch
# User morinlab
# Date 1480880782 18000
# Node ID 5004e63b170cb7a16258bb33019028f0b755cc08

Uploaded

diff -r 000000000000 -r 5004e63b170c MutsigCV.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MutsigCV.xml	Sun Dec 04 14:46:22 2016 -0500
@@ -0,0 +1,121 @@
+<tool id="mutsigcv" name="MutsigCV" version="1.4">
+  <description>MutSigCV analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.</description>
+  <requirements>
+    <requirement type="package" version="8.1">mcr</requirement>
+    <requirement type="package" version="1.4">mutsigcv</requirement>
+    <requirement type="set_environment">MCR_ROOT</requirement>
+    <requirement type="set_environment">MUTSIGCV_DIR</requirement>
+  </requirements>
+  <command>
+  <!-- MutSig commands based on mode selection -->	
+
+  #if $modes.mode_select == "morincoverage"
+			
+    sh \$MUTSIGCV_DIR/run_MutSigCV.sh \$MCR_ROOT/v81 $modes.maf_file $__tool_directory__/updated_coverage.txt $__tool_directory__/updated_covariate.txt output.txt  $__tool_directory__/mutation_type_dictionary_file.txt \$MUTSIGCV_DIR/chr_files_hg19;
+		
+  #elif $modes.mode_select == "custom"
+		
+    sh \$MUTSIGCV_DIR/run_MutSigCV.sh \$MCR_ROOT/v81 $modes.mutations_maf  $modes.coverage_txt $modes.gene_covariates_txt output.txt \$FILE_PATH/mutation_type_dictionary_file.txt \$MUTSIGCV_DIR/chr_files_hg19;
+		
+  #elif $modes.mode_select == "old"
+
+    sh \$MUTSIG_DIR/run_MutSigCV.sh \$MCR_ROOT/v81 $modes.tcga_maf  \$MUTSIG_DIR/exome_full192.coverage.txt \$MUTSIG_DIR/gene.covariates.txt output.txt \$MUTSIG_DIR/mutation_type_dictionary_file.txt \$MUTSIG_DIR/chr_files_hg19;
+		
+  #end if
+		
+  <!-- produce galaxy output add output selection of other files later -->
+  cat output.txt.sig_genes.txt >> $output;
+
+  </command>  
+  <inputs>
+    <conditional name="modes">
+      <param name="mode_select" type="select" label="Select mode to run MutSig with preferred file set.">
+        <option value="morincoverage" selected="True">1) Assume full exome  coverage with updated file. </option>
+        <option value="custom" >2) Use custom files from history. </option>
+        <option value="old" >3) Use original MutsigCV file set. </option>
+      </param>
+      <when value="morincoverage">
+        <!-- Input parameters needed -->
+        <param name="maf_file" type="data" format="tabular" label="Mutations.maf file." />
+      </when>	
+      <when value="custom">
+        <param name="mutations_maf" type="data" format="tabular" label="Mutations.maf file." />		
+        <param name="coverage_txt" type="data" format="tabular"  label="Coverage.txt file." />
+        <param name="gene_covariates_txt" type="data" format="tabular" label="Gene_covariates.txt file." />
+      </when>
+      <when value="old">
+        <!-- Input parameters needed -->
+        <param name="tcga_maf" type="data" format="tabular" label="Mutations.maf file." />
+      </when>	
+    </conditional>
+  </inputs>
+  <outputs>
+    <data name="output" label="MutsigCV significant genes" format="txt"/>
+  </outputs>
+  <help>
+Reference:
+-----------------
+
+Lawrence MS, Stojanov P, Polak P, Kryukov GV, et al. Mutational heterogenieity in cancer and the search for new cancer genes.  Nature. 2013 Jun 16. doi: 10.1038/nature12213
+
+For More Information:
+----------------------------------
+Files used by MutsigCV can be downloaded at: http://www.broadinstitute.org/cancer/cga/mutsig_run#reference_files
+
+More detailed information about these files can be found at:
+http://www.broadinstitute.org/cancer/software/genepattern/modules/docs/MutSigCV/1?print=yes
+
+  </help>
+  <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">
+      @article{
+      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="bibtex">
+
+      @ARTICLE{Lawrence2014-wp,
+      title     = "Discovery and saturation analysis of cancer genes across 21
+      tumour types",
+      author    = "Lawrence, Michael S and Stojanov, Petar and Mermel, Craig H and
+      Robinson, James T and Garraway, Levi A and Golub, Todd R and
+      Meyerson, Matthew and Gabriel, Stacey B and Lander, Eric S and
+      Getz, Gad",
+      journal   = "Nature",
+      publisher = "Nature Research",
+      volume    =  505,
+      number    =  7484,
+      pages     = "495--501",
+      month     =  "5~" # jan,
+      year      =  2014,
+      language  = "en"
+      }
+
+      
+    </citation>
+  </citations>
+</tool>
+
+