Mercurial > repos > artbio > mutational_patterns

comparison mutational_patterns.xml @ 23:83f8c93c34b4 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 3c4d96db0a3c54ed68bf782f08b89b6959255d58"
author artbio
date Wed, 27 Oct 2021 00:46:47 +0000
parents 00be8f0b2c89
children ca6c19ee7da0
comparison
equal deleted inserted replaced
22:00be8f0b2c89 23:83f8c93c34b4
1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy7"> 1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy8">
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="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement> 4 <requirement type="package" version="3.2.0=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="3.3.5=r41hc72bb7e_0">r-ggplot2</requirement> 6 <requirement type="package" version="3.3.5=r41hc72bb7e_0">r-ggplot2</requirement>
58 --own_signatures '$set_preset.set_signature_input.own_matrix' 58 --own_signatures '$set_preset.set_signature_input.own_matrix'
59 #end if 59 #end if
60 60
61 --signum '$set_preset.signum' 61 --signum '$set_preset.signum'
62 --colors '$set_preset.colors' 62 --colors '$set_preset.colors'
63 --display_signatures '$set_preset.display_signatures'
63 --output_sigpattern '$sig_contrib' 64 --output_sigpattern '$sig_contrib'
64 65
65 #if $set_preset.contrib_matrix_out == 'yes' 66 #if $set_preset.contrib_matrix_out == 'yes'
66 --sig_contrib_matrix '$sig_contrib_matrix' 67 --sig_contrib_matrix '$sig_contrib_matrix'
67 #end if 68 #end if
156 </when> 157 </when>
157 </conditional> 158 </conditional>
158 <param name="signum" type="integer" value="3" min="2" max="30" 159 <param name="signum" type="integer" value="3" min="2" max="30"
159 label="selects the N most significant signatures in samples to express mutational patterns" 160 label="selects the N most significant signatures in samples to express mutational patterns"
160 help="an integer between 2 and the number of elementary signatures in your signature matrix"/> 161 help="an integer between 2 and the number of elementary signatures in your signature matrix"/>
161 <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?" 162 <param name="display_signatures" type="select" display="radio" label="Output profiles of input signatures ?">
163 <option value="no">No</option>
164 <option value="yes" selected="true">Yes</option>
165 </param>
166 <param name="contrib_matrix_out" type="select" display="radio" label="Output Signature Contribution table ?"
162 help="Output the normalized signatures contributions for further visualization" > 167 help="Output the normalized signatures contributions for further visualization" >
163 <option value="no" selected="true">No</option> 168 <option value="no" selected="true">No</option>
164 <option value="yes">Yes</option> 169 <option value="yes">Yes</option>
165 </param> 170 </param>
166 <param name="colors" type="select" label="Color set" display="radio"> 171 <param name="colors" type="select" label="Color set" display="radio">
193 <filter>rdata_out</filter> 198 <filter>rdata_out</filter>
194 </data> 199 </data>
195 200
196 </outputs> 201 </outputs>
197 <tests> 202 <tests>
198 <!-- user defined (v3.2 restricted 30 minus 27) --> 203 <!-- user defined (v3.2 restricted 30 minus 27 renamed to test nomenclature effect) -->
199 <test> 204 <test>
200 <param name="vcfs"> 205 <param name="vcfs">
201 <collection type="list"> 206 <collection type="list">
202 <element name="6" value="F.vcf"/> 207 <element name="6" value="F.vcf"/>
203 <element name="7" value="G.vcf"/> 208 <element name="7" value="G.vcf"/>
247 <param name="choices" value="yes"/> 252 <param name="choices" value="yes"/>
248 <conditional name="set_signature_input"> 253 <conditional name="set_signature_input">
249 <param name="input_signature_choices" value="cosmic" /> 254 <param name="input_signature_choices" value="cosmic" />
250 <param name="cosmic_version" value="v3.2"/> 255 <param name="cosmic_version" value="v3.2"/>
251 </conditional> 256 </conditional>
257 <param name="display_signatures" value="no" />
252 <param name="contrib_matrix_out" value="yes" /> 258 <param name="contrib_matrix_out" value="yes" />
253 </conditional> 259 </conditional>
254 <param name="signum" value="3" /> 260 <param name="signum" value="3" />
255 <output name="sig_contrib" file="cosmic_output_v3.pdf" compare="sim_size"/> 261 <output name="sig_contrib" file="cosmic_output_v3.pdf" compare="sim_size"/>
256 <output name="sig_contrib_matrix" file="sig_contrib_table_v3.tsv" compare="sim_size"/> 262 <output name="sig_contrib_matrix" file="sig_contrib_table_v3.tsv" compare="sim_size"/>