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
date Mon, 05 Oct 2020 19:29:42 +0000
parents e332cf9dfa06
children fe31d059a482
comparison
equal deleted inserted replaced
3:e332cf9dfa06 4:7ba08c826888
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**