view oncodrivefm.xml @ 3:97e99acadbaf draft default tip

Uploaded

<tool id="oncodrivefm" name="OncodriveFM">
  <description>
  an approach to uncover driver genes or gene modules
  </description>
  <requirements>
    <requirement type="package" version="2.0.1">requests</requirement>
    <requirement type="package" version="0.6.0">oncodrivefm</requirement>
  </requirements>
  <command detect_errors="aggressive">
  
  <!-- make directory and name for multiple output -->
  mkdir ./out;
  ln -s $input_maf ./odfm;
	
  <!-- run program with pathway file options -->
  oncodrivefm 
    -o ./out
    -N $advancedsettings.samplings 
    -e $advancedsettings.estimator 
    --gt $advancedsettings.gthreshold 
    --pt $advancedsettings.pthreshold 
    -s $advancedsettings.slices 
    #if $advancedsettings.mapoption.mapfile=="custom":
      -m "${mapoption.mpath}" 
    #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">
      <param name="samplings" type="integer" label="Samplings" help="Number of samplings to compute the FM bias pvalue" value="10000"/>
      <param name="estimator" type="select" label="Estimator" help="Test estimator for computation" optional="true">
        <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>
        </param>
        <when value="custom">
          <param name="mpath" type="data" format="tabular" label="OncodriveFM Mapping File"/>
        </when>
      </conditional>
    </section>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1" label="oncodrivefm-genes.tsv" />
    <data format="tabular" name="out_file2" label="oncodrivefm-pathways.tsv" >
      <filter>(mapoption['mapfile'] == "included_file") or (mapoption['mapfile'] == "custom")</filter>
    </data>
  </outputs>
  <help>
        Oncodrive-fm is an approach to uncover driver genes or gene modules.
        It computes a metric of functional impact using three well-known methods (SIFT, PolyPhen2 and MutationAssessor)
        and assesses how the functional impact of variants found in a gene across several tumor samples deviates from
        a null distribution. It is thus based on the assumption that any bias towards the accumulation of variants
        with high functional impact is an indication of positive selection and can thus be used to detect candidate
        driver genes or gene modules. 
		
	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>