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comparison mutational_patterns.xml @ 25:b00fef2b1c2c draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit eeb46055822c6805c209af0c450ae941100960bd
author artbio
date Wed, 06 Jul 2022 11:43:09 +0000
parents ca6c19ee7da0
children af5c65ad5317
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24:ca6c19ee7da0 25:b00fef2b1c2c
1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.4.0+galaxy0"> 1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.4.0+galaxy1">
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="3.4.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement> 4 <requirement type="package" version="3.4.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
5 <!--requirement type="package" version="1.1.1l=h7f98852_0">openssl</requirement> --> 5 <!--requirement type="package" version="1.1.1l=h7f98852_0">openssl</requirement> -->
6 <requirement type="package" version="3.3.6=r41hc72bb7e_0">r-ggplot2</requirement> 6 <requirement type="package" version="3.3.6=r41hc72bb7e_0">r-ggplot2</requirement>
44 --nrun '$set_denovo.nrun' 44 --nrun '$set_denovo.nrun'
45 --rank '$set_denovo.rank' 45 --rank '$set_denovo.rank'
46 --newsignum '$set_denovo.newsignum' 46 --newsignum '$set_denovo.newsignum'
47 --output_denovo '$denovo' 47 --output_denovo '$denovo'
48 --sigmatrix '$sigmatrix' 48 --sigmatrix '$sigmatrix'
49 --cosmic_id_threshold '$set_denovo.cosmic_id_threshold'
49 #end if 50 #end if
50 51
51 #if $set_preset.choices == 'yes': 52 #if $set_preset.choices == 'yes':
52 53
53 #if $set_preset.set_signature_input.input_signature_choices == 'cosmic' 54 #if $set_preset.set_signature_input.input_signature_choices == 'cosmic'
125 label="Number of ranks to be displayed for control of optimal number of signature" 126 label="Number of ranks to be displayed for control of optimal number of signature"
126 help="High values extend the computational time. In addition the number of ranks cannot be greater than the number of available samples in the study"/> 127 help="High values extend the computational time. In addition the number of ranks cannot be greater than the number of available samples in the study"/>
127 <param name="newsignum" type="integer" value="4" min="2" max="30" 128 <param name="newsignum" type="integer" value="4" min="2" max="30"
128 label="Number of de novo signatures to capture" 129 label="Number of de novo signatures to capture"
129 help="High values extend the computational time. Note also that you cannot extract more signature than the number of available samples in the study"/> 130 help="High values extend the computational time. Note also that you cannot extract more signature than the number of available samples in the study"/>
131 <param name="cosmic_id_threshold" type="float" value="0.85" min="0" max="1"
132 label="Minimum cosine similarity to rename a signature"
133 help="If a signature has a cosine similarity higher than this value with a cosmic v3.2 signature, it will renamed accordingly, with a -like suffix"/>
130 </when> 134 </when>
131 <when value="no" /> 135 <when value="no" />
132 </conditional> 136 </conditional>
133 137
134 <conditional name="set_preset"> 138 <conditional name="set_preset">
218 <param name="choices" value="yes"/> 222 <param name="choices" value="yes"/>
219 </conditional> 223 </conditional>
220 <conditional name="set_preset"> 224 <conditional name="set_preset">
221 <param name="choices" value="no"/> 225 <param name="choices" value="no"/>
222 </conditional> 226 </conditional>
223 <param name="nrun" value="10" /> 227 <param name="nrun" value="30" />
224 <param name="rank" value="4" /> 228 <param name="rank" value="4" />
225 <param name="newsignum" value="4" /> 229 <param name="newsignum" value="2" />
230 <param name="cosmic_id_threshold" value="0.84" />
226 <param name="rdata_out" value="true" /> 231 <param name="rdata_out" value="true" />
227 <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/> 232 <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/>
228 <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/> 233 <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/>
229 <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!-- delta="170000" --> 234 <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!-- delta="170000" -->
230 </test> 235 </test>
365 370
366 **Inputs** 371 **Inputs**
367 372
368 * a collection of VCF files with somatic mutations calls from analysis of samples. 373 * a collection of VCF files with somatic mutations calls from analysis of samples.
369 * a tabular table describing the correspondance of sample names to levels of a factor 374 * a tabular table describing the correspondance of sample names to levels of a factor
370 (tissues, ages, sexes, etc.) 375 (tissues, ages, sexes, etc.)
371 376
372 **Outputs** 377 **Outputs**
373 378
374 This tool returns pdf files with various visualisations of : 379 This tool returns pdf files with various visualisations of :
375 380