Mercurial > repos > artbio > mutational_patterns
comparison mutational_patterns.xml @ 1:921c1f55481d draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit ca3b3ab85c8224821c76ebd56b1be2441a28f609"
| author | artbio |
|---|---|
| date | Sun, 13 Sep 2020 22:27:03 +0000 |
| parents | 924c527fb379 |
| children | aea952be68cb |
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| 0:924c527fb379 | 1:921c1f55481d |
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| 1 <tool id="mutational_patterns" name="Analyse Mutational Patters/Signatures" version="2.0.0_galaxy_1"> | 1 <tool id="mutational_patterns" name="Analyse Mutational Patters/Signatures" version="2.0.0_galaxy_2"> |
| 2 <description>from genomic variations in vcf files</description> | 2 <description>from genomic variations in vcf files</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement> | 4 <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement> |
| 5 <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement> | 5 <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement> |
| 6 <requirement type="package" version="0.2.20=r40h0357c0b_1002">r-rjson</requirement> | 6 <requirement type="package" version="0.2.20=r40h0357c0b_1002">r-rjson</requirement> |
| 88 * the number of cosmic signatures to decompose mutational patterns of samples | 88 * the number of cosmic signatures to decompose mutational patterns of samples |
| 89 | 89 |
| 90 | 90 |
| 91 This tool returns a pdf file with the visualisation : | 91 This tool returns a pdf file with the visualisation : |
| 92 | 92 |
| 93 * the Cosine similarity of samples when decomposed over the 30 signatures of cosmic | 93 * the Cosine similarity of samples when decomposed over the 30 signatures of cosmic_ |
| 94 * the absolute contribution of the n most contributing cosmic signatures in the samples mutational patterns (to be set by the user, between 2 and 30) | 94 * the absolute contribution of the n most contributing cosmic_ signatures in the samples mutational patterns (to be set by the user, between 2 and 30) |
| 95 * the relative contribution of the n most contributing cosmic signatures in the samples mutational patterns (to be set by the user, between 2 and 30) | 95 * the relative contribution of the n most contributing cosmic_ signatures in the samples mutational patterns (to be set by the user, between 2 and 30) |
| 96 * a clustering of the samples with respect to the relative contribution of their cosmic signatures | 96 * a clustering of the samples with respect to the relative contribution of their cosmic_ signatures |
| 97 * pie charts of the samples displaying for each sample the relative contribution of the n most contributing cosmic signatures in their mutational pattern | 97 * pie charts of the samples displaying for each sample the relative contribution of the n most contributing cosmic_ signatures in their mutational pattern |
| 98 | 98 |
| 99 .. _cosmic: https://cancer.sanger.ac.uk/cosmic/signatures_v2.tt | |
| 99 | 100 |
| 100 </help> | 101 </help> |
| 101 <citations> | 102 <citations> |
| 102 <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation> | 103 <citation type="doi">10.18129/B9.bioc.MutationalPatterns</citation> |
| 103 <citation type="doi">10.1186/s13073-018-0539-0</citation> | 104 <citation type="doi">10.1186/s13073-018-0539-0</citation> |