Mercurial > repos > artbio > mutational_patterns

comparison mutational_patterns.xml @ 11:7995a949189f draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"
author artbio
date Thu, 22 Oct 2020 00:18:38 +0000
parents 59c0e2a7965c
children 7954f0d3517f
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10:59c0e2a7965c 11:7995a949189f
1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy11"> 1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy12">
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>
45 --output_denovo $denovo 45 --output_denovo $denovo
46 --sigmatrix $sigmatrix 46 --sigmatrix $sigmatrix
47 #end if 47 #end if
48 48
49 #if $set_cosmic.choices == 'yes': 49 #if $set_cosmic.choices == 'yes':
50 --cosmic_version $set_cosmic.cosmic_version 50 --cosmic_version '$set_cosmic.cosmic_version'
51 --signum '$set_cosmic.signum' 51 --signum '$set_cosmic.signum'
52 --output_cosmic $cosmic 52 --output_cosmic $cosmic
53 #if $set_cosmic.contrib_matrix_out
54 --sig_contrib_matrix $sig_contrib_matrix
55 #end if
53 #end if 56 #end if
54 57
55 #if $rdata_out 58 #if $rdata_out
56 --rdata '$rdata' 59 --rdata '$rdata'
57 #end if 60 #end if
127 help="an integer between 2 and 30 signature types from cosmic"/> 130 help="an integer between 2 and 30 signature types from cosmic"/>
128 <param name="cosmic_version" type="select" label="Version of the Cosmic signature set"> 131 <param name="cosmic_version" type="select" label="Version of the Cosmic signature set">
129 <option value="v2" selected="true">Cosmic v2, March 2015</option> 132 <option value="v2" selected="true">Cosmic v2, March 2015</option>
130 <option value="v3">Cosmic v3, May 2019</option> 133 <option value="v3">Cosmic v3, May 2019</option>
131 </param> 134 </param>
135 <param name="contrib_matrix_out" type="boolean" checked="false" label="Output Signature Contribution table ?"
136 help="Output the normalized signatures contributions for further visualization" />
132 </when> 137 </when>
133 <when value="no" /> 138 <when value="no" />
134 </conditional> 139 </conditional>
135 <param name="rdata_out" type="boolean" checked="false" label="Output RData file?" help="Output all the data used by R to construct the tables and plots, can be loaded into R" /> 140 <param name="rdata_out" type="boolean" checked="false" label="Output RData file?" help="Output all the data used by R to construct the tables and plots, can be loaded into R" />
136 </inputs> 141 </inputs>
145 <filter>set_denovo['choices'] == "yes"</filter> 150 <filter>set_denovo['choices'] == "yes"</filter>
146 </data> 151 </data>
147 <data name="cosmic" format="pdf" label="Cosmic signatures"> 152 <data name="cosmic" format="pdf" label="Cosmic signatures">
148 <filter>set_cosmic['choices'] == "yes"</filter> 153 <filter>set_cosmic['choices'] == "yes"</filter>
149 </data> 154 </data>
155 <data name="sig_contrib_matrix" format="tabular" label="${tool.name}: Signature contribution table">
156 <filter>set_cosmic['contrib_matrix_out']</filter>
157 </data>
158
150 <data name="rdata" format="rdata" label="${tool.name}: RData file"> 159 <data name="rdata" format="rdata" label="${tool.name}: RData file">
151 <filter>rdata_out</filter> 160 <filter>rdata_out</filter>
152 </data> 161 </data>
153 162
154 </outputs> 163 </outputs>
173 <param name="choices" value="no"/> 182 <param name="choices" value="no"/>
174 </conditional> 183 </conditional>
175 <conditional name="set_cosmic"> 184 <conditional name="set_cosmic">
176 <param name="choices" value="no"/> 185 <param name="choices" value="no"/>
177 </conditional> 186 </conditional>
178 <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size" ftype="pdf"/> 187 <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size"/>
179 </test> 188 </test>
180 189
181 <!-- de novo signatures --> 190 <!-- de novo signatures -->
182 <test> 191 <test>
183 <param name="vcfs"> 192 <param name="vcfs">
200 </conditional> 209 </conditional>
201 <param name="nrun" value="10" /> 210 <param name="nrun" value="10" />
202 <param name="rank" value="4" /> 211 <param name="rank" value="4" />
203 <param name="newsignum" value="4" /> 212 <param name="newsignum" value="4" />
204 <param name="rdata_out" value="true" /> 213 <param name="rdata_out" value="true" />
205 <output name="denovo" file="denovo_output1.pdf" compare="sim_size" ftype="pdf"/> 214 <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/>
206 <output name="sigmatrix" file="sigmatrix.tab" ftype="tabular" compare="sim_size"/> 215 <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/>
207 <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!-- delta="170000" --> 216 <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!-- delta="170000" -->
208 </test> 217 </test>
209 218
210 <!-- cosmic signatures --> 219 <!-- cosmic signatures -->
211 <test> 220 <test>
225 <conditional name="set_denovo"> 234 <conditional name="set_denovo">
226 <param name="choices" value="no"/> 235 <param name="choices" value="no"/>
227 </conditional> 236 </conditional>
228 <conditional name="set_cosmic"> 237 <conditional name="set_cosmic">
229 <param name="choices" value="yes"/> 238 <param name="choices" value="yes"/>
239 <param name="contrib_matrix_out" value="true" />
230 </conditional> 240 </conditional>
231 <param name="signum" value="3" /> 241 <param name="signum" value="3" />
232 <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size" ftype="pdf"/> 242 <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size"/>
243 <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/>
233 </test> 244 </test>
234 <!-- cosmic signature on single sample --> 245 <!-- cosmic signature on single sample -->
235 <test> 246 <test>
236 <param name="vcfs"> 247 <param name="vcfs">
237 <collection type="list"> 248 <collection type="list">
247 </conditional> 258 </conditional>
248 <conditional name="set_cosmic"> 259 <conditional name="set_cosmic">
249 <param name="choices" value="yes"/> 260 <param name="choices" value="yes"/>
250 </conditional> 261 </conditional>
251 <param name="signum" value="5" /> 262 <param name="signum" value="5" />
252 <output name="cosmic" file="cosmic_output2.pdf" compare="sim_size" delta="50000" ftype="pdf"/> 263 <output name="cosmic" file="cosmic_output2.pdf" compare="sim_size" delta="50000"/>
253 </test> 264 </test>
254 </tests> 265 </tests>
255 <help> 266 <help>
256 267
257 **What it does** 268 **What it does**