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<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>