Mercurial > repos > artbio > mutational_patterns
comparison mutational_patterns.xml @ 4:7ba08c826888 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
author | artbio |
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date | Mon, 05 Oct 2020 19:29:42 +0000 |
parents | e332cf9dfa06 |
children | fe31d059a482 |
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3:e332cf9dfa06 | 4:7ba08c826888 |
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1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy4"> | 1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy5"> |
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> |
216 <element name="8" value="H.vcf"/> | 216 <element name="8" value="H.vcf"/> |
217 <element name="9" value="I.vcf"/> | 217 <element name="9" value="I.vcf"/> |
218 </collection> | 218 </collection> |
219 </param> | 219 </param> |
220 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> | 220 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> |
221 <param name="levels" value="GH_levels.tab" ftype="tabular"/> | 221 <param name="levels" value="FGHI_levels.tab" ftype="tabular"/> |
222 <conditional name="set_spectrum"> | 222 <conditional name="set_spectrum"> |
223 <param name="choices" value="no"/> | 223 <param name="choices" value="no"/> |
224 </conditional> | 224 </conditional> |
225 <conditional name="set_denovo"> | 225 <conditional name="set_denovo"> |
226 <param name="choices" value="no"/> | 226 <param name="choices" value="no"/> |
228 <conditional name="set_cosmic"> | 228 <conditional name="set_cosmic"> |
229 <param name="choices" value="yes"/> | 229 <param name="choices" value="yes"/> |
230 </conditional> | 230 </conditional> |
231 <param name="signum" value="3" /> | 231 <param name="signum" value="3" /> |
232 <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size" ftype="pdf"/> | 232 <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size" ftype="pdf"/> |
233 </test> | |
234 <test> | |
235 <param name="vcfs"> | |
236 <collection type="list"> | |
237 <element name="1" value="G.vcf"/> | |
238 </collection> | |
239 </param> | |
240 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> | |
241 <conditional name="set_spectrum"> | |
242 <param name="choices" value="no"/> | |
243 </conditional> | |
244 <conditional name="set_denovo"> | |
245 <param name="choices" value="no"/> | |
246 </conditional> | |
247 <conditional name="set_cosmic"> | |
248 <param name="choices" value="yes"/> | |
249 </conditional> | |
250 <param name="signum" value="5" /> | |
251 <output name="cosmic" file="cosmic_output2.pdf" compare="sim_size" delta="50000" ftype="pdf"/> | |
233 </test> | 252 </test> |
234 </tests> | 253 </tests> |
235 <help> | 254 <help> |
236 | 255 |
237 **What it does** | 256 **What it does** |