comparison oncodrivefm.xml @ 1:fe65a4d95e7a draft

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0:a9c4c014fc47

    #elif $advancedsettings.mapoption.mapfile=="included_file":   
      -m $__tool_directory__/ensg_kegg.tsv
    #end if
    ./odfm;
    
  cat ./out/odfm-pathways.tsv >> $out_file2;
  cat ./out/odfm-genes.tsv >> $out_file1;

  pwd >> $out_file2;
  ls ./out/* >> $out_file2;
  
  </command>
  <inputs>
    <param name="input_maf" format="tabular" type="data" label="Input MAF File" />
    <section name="advancedsettings" title="Advanced Settings" expanded="false">

        <option value="median" selected="true">Median</option>
        <option value="mean">Mean</option>
      </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"/>
      <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>
          <option value="custom">Use a mapping file from the history</option>
          <option value="no_file">Use no mapping file</option>

	See url for more information: http://bg.upf.edu/group/projects/oncodrive-fm.php
      
        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>
</tool>

1:fe65a4d95e7a

    #elif $advancedsettings.mapoption.mapfile=="included_file":   
      -m $__tool_directory__/ensg_kegg.tsv
    #end if
    ./odfm;
    
  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>
    <param name="input_maf" format="tabular" type="data" label="Input MAF File" />
    <section name="advancedsettings" title="Advanced Settings" expanded="false">

        <option value="median" selected="true">Median</option>
        <option value="mean">Mean</option>
      </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="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>
          <option value="custom">Use a mapping file from the history</option>
          <option value="no_file">Use no mapping file</option>

	See url for more information: http://bg.upf.edu/group/projects/oncodrive-fm.php
      
        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>