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1 <tool id="mutsigcv" name="MutsigCV" version="1.4">
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2 <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>
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3 <requirements>
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4 <requirement type="package" version="8.1">mcr</requirement>
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5 <requirement type="package" version="1.4">mutsigcv</requirement>
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6 <requirement type="set_environment">MCR_ROOT</requirement>
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7 <requirement type="set_environment">MUTSIGCV_DIR</requirement>
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8 </requirements>
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9 <command>
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10 <!-- MutSig commands based on mode selection -->
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11
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12 #if $modes.mode_select == "morincoverage"
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13
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14 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;
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15
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16 #elif $modes.mode_select == "custom"
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17
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18 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;
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19
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20 #elif $modes.mode_select == "old"
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21
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22 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;
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23
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24 #end if
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25
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26 <!-- produce galaxy output add output selection of other files later -->
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27 cat output.txt.sig_genes.txt >> $output;
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28
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29 </command>
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30 <inputs>
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31 <conditional name="modes">
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32 <param name="mode_select" type="select" label="Select mode to run MutSig with preferred file set.">
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33 <option value="morincoverage" selected="True">1) Assume full exome coverage with updated file. </option>
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34 <option value="custom" >2) Use custom files from history. </option>
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35 <option value="old" >3) Use original MutsigCV file set. </option>
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36 </param>
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37 <when value="morincoverage">
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38 <!-- Input parameters needed -->
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39 <param name="maf_file" type="data" format="tabular" label="Mutations.maf file." />
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40 </when>
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41 <when value="custom">
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42 <param name="mutations_maf" type="data" format="tabular" label="Mutations.maf file." />
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43 <param name="coverage_txt" type="data" format="tabular" label="Coverage.txt file." />
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44 <param name="gene_covariates_txt" type="data" format="tabular" label="Gene_covariates.txt file." />
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45 </when>
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46 <when value="old">
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47 <!-- Input parameters needed -->
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48 <param name="tcga_maf" type="data" format="tabular" label="Mutations.maf file." />
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49 </when>
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50 </conditional>
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51 </inputs>
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52 <outputs>
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53 <data name="output" label="MutsigCV significant genes" format="txt"/>
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54 </outputs>
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55 <help>
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56 Reference:
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57 -----------------
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58
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59 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
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60
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61 For More Information:
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62 ----------------------------------
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63 Files used by MutsigCV can be downloaded at: http://www.broadinstitute.org/cancer/cga/mutsig_run#reference_files
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64
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65 More detailed information about these files can be found at:
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66 http://www.broadinstitute.org/cancer/software/genepattern/modules/docs/MutSigCV/1?print=yes
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67
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68 </help>
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69 <citations>
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70 <citation type="bibtex">
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71 @article {Albuquerque089631,
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72 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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73 title = {Enhancing Knowledge Discovery from Cancer Genomics Data with Galaxy},
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74 year = {2016},
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75 doi = {10.1101/089631},
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76 publisher = {Cold Spring Harbor Labs Journals},
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77 URL = {http://biorxiv.org/content/early/2016/11/26/089631},
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78 eprint = {http://biorxiv.org/content/early/2016/11/26/089631.full.pdf},
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79 journal = {bioRxiv}
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80 }
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81 </citation>
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82
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83 <citation type="bibtex">
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84 @article{
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85 goecks2010galaxy,
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86 title={Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
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87 author={Goecks, Jeremy and Nekrutenko, Anton and Taylor, James and others},
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88 journal={Genome Biol},
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89 volume={11},
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90 number={8},
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91 pages={R86},
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92 year={2010}
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93 }
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94 </citation>
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95
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96
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97 <citation type="bibtex">
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98
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99 @ARTICLE{Lawrence2014-wp,
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100 title = "Discovery and saturation analysis of cancer genes across 21
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101 tumour types",
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102 author = "Lawrence, Michael S and Stojanov, Petar and Mermel, Craig H and
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103 Robinson, James T and Garraway, Levi A and Golub, Todd R and
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104 Meyerson, Matthew and Gabriel, Stacey B and Lander, Eric S and
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105 Getz, Gad",
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106 journal = "Nature",
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107 publisher = "Nature Research",
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108 volume = 505,
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109 number = 7484,
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110 pages = "495--501",
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111 month = "5~" # jan,
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112 year = 2014,
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113 language = "en"
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114 }
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115
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116
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117 </citation>
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118 </citations>
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119 </tool>
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120
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121
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