Mercurial > repos > morinlab > oncodrivefm

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

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author morinlab
date Wed, 30 Nov 2016 13:10:18 -0500
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1 <tool id="oncodrivefm" name="OncodriveFM">
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2 <description>
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3 an approach to uncover driver genes or gene modules
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="2.0.1">requests</requirement>
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7 <requirement type="package" version="0.6.0">oncodrivefm</requirement>
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8 </requirements>
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9 <command detect_errors="aggressive">
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10
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11 <!-- make directory and name for multiple output -->
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12 mkdir ./out;
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13 ln -s $input_maf ./odfm;
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14
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15 <!-- run program with pathway file options -->
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16 oncodrivefm
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17 -o ./out
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18 -N $advancedsettings.samplings
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19 -e $advancedsettings.estimator
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20 --gt $advancedsettings.gthreshold
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21 --pt $advancedsettings.pthreshold
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22 -s $advancedsettings.slices
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23 #if $advancedsettings.mapoption.mapfile=="custom":
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24 -m "${mapoption.mpath}"
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25 #elif $advancedsettings.mapoption.mapfile=="included_file":
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26 -m $__tool_directory__/ensg_kegg.tsv
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27 #end if
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28 ./odfm;
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29
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30 cat ./out/odfm-genes.tsv | grep -v \\# | sort -g -k 3 | awk 'BEGIN {OFS = "\t"}{if ($advancedsettings.qcut > $3 ) print \$1, \$2, \$3; }' >> $out_file1;
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31 cat ./out/odfm-pathways.tsv | grep -v \\# | sort -g -k 4 >> $out_file2;
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32
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33 </command>
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34 <inputs>
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35 <param name="input_maf" format="tabular" type="data" label="Input MAF File" />
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36 <section name="advancedsettings" title="Advanced Settings" expanded="false">
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37 <param name="samplings" type="integer" label="Samplings" help="Number of samplings to compute the FM bias pvalue" value="10000"/>
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38 <param name="estimator" type="select" label="Estimator" help="Test estimator for computation" optional="true">
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39 <option value="median" selected="true">Median</option>
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40 <option value="mean">Mean</option>
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41 </param>
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42 <param name="gthreshold" type="integer" label="Gene Threshold" help="Minimum number of mutations per gene to compute the FM bias" value="2"/>
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43 <param name="pthreshold" type="integer" label="Pathway Threshold" help="Minimum number of mutations per pathway to compute the FM bias" value="10" />
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44 <param name="qcut" type="float" label="Q value cutoff" help="Only return genes with Q value below this threshold" value="1.0" />
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45 <param name="slices" type="text" label="Slices" help="Slices to process separated by commas(slices=SIFT,PPH2,MA)" value="SIFT,PPH2"/>
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46 <conditional name="mapoption">
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47 <param name="mapfile" type="select" label="Choose the source for the OncodriveFM Mapping File">
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48 <option value="included_file" selected="true">Use hg19 mapping file</option>
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49 <option value="custom">Use a mapping file from the history</option>
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50 <option value="no_file">Use no mapping file</option>
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51 </param>
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52 <when value="custom">
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53 <param name="mpath" type="data" format="tabular" label="OncodriveFM Mapping File"/>
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54 </when>
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55 </conditional>
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56 </section>
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57 </inputs>
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58 <outputs>
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59 <data format="tabular" name="out_file1" label="oncodrivefm-genes.tsv" />
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60 <data format="tabular" name="out_file2" label="oncodrivefm-pathways.tsv" >
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61 <filter>(mapoption['mapfile'] == "included_file") or (mapoption['mapfile'] == "custom")</filter>
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62 </data>
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63 </outputs>
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64 <help>
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65 Oncodrive-fm is an approach to uncover driver genes or gene modules.
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66 It computes a metric of functional impact using three well-known methods (SIFT, PolyPhen2 and MutationAssessor)
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67 and assesses how the functional impact of variants found in a gene across several tumor samples deviates from
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68 a null distribution. It is thus based on the assumption that any bias towards the accumulation of variants
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69 with high functional impact is an indication of positive selection and can thus be used to detect candidate
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70 driver genes or gene modules.
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71
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72 See url for more information: http://bg.upf.edu/group/projects/oncodrive-fm.php
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73
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74 If you use this Galaxy tool in work leading to a scientific publication please cite:
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75 Gonzalez-Perez A and Lopez-Bigas N. 2012. Functional impact bias reveals cancer drivers. Nucleic Acids Res., 10.1093/nar/gks743.
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76 </help>
1
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77 <citations>
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78 <citation type="bibtex">
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79 @ARTICLE{Gonzalez-Perez2012-wq,
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80 title = "Functional impact bias reveals cancer drivers",
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81 author = "Gonzalez-Perez, Abel and Lopez-Bigas, Nuria",
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82 journal = "Nucleic Acids Res.",
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83 volume = 40,
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84 number = 21,
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85 pages = "e169--e169",
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86 month = "1~" # nov,
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87 year = 2012
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88 }
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89
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90
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91 </citation>
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92 <citation type="bibtex">
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93 @article {Albuquerque089631,
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94 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},
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95 title = {Enhancing Knowledge Discovery from Cancer Genomics Data with Galaxy},
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96 year = {2016},
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97 doi = {10.1101/089631},
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98 publisher = {Cold Spring Harbor Labs Journals},
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99 URL = {http://biorxiv.org/content/early/2016/11/26/089631},
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100 eprint = {http://biorxiv.org/content/early/2016/11/26/089631.full.pdf},
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101 journal = {bioRxiv}
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102 }
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103
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104 </citation>
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105 <citation type="bibtex">
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106 @misc{
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107 goecks2010galaxy,
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108 title={Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
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109 author={Goecks, Jeremy and Nekrutenko, Anton and Taylor, James and others},
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110 journal={Genome Biol},
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111 volume={11},
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112 number={8},
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113 pages={R86},
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114 year={2010}
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115 }
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116 </citation>
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117
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118 </citations>
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119 </tool>
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120