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comparison mutational_patterns.xml @ 3:e332cf9dfa06 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 0f7593f703ba0dfd12aea1c0460e371f08b57d2f"
author artbio
date Thu, 24 Sep 2020 01:32:52 +0000
parents aea952be68cb
children 7ba08c826888
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2:aea952be68cb 3:e332cf9dfa06
1 <tool id="mutational_patterns" name="Analyse Mutational Patters/Signatures" version="2.0.0+galaxy3"> 1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy4">
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>
41 #if $set_denovo.choices == 'yes': 41 #if $set_denovo.choices == 'yes':
42 --nrun $set_denovo.nrun 42 --nrun $set_denovo.nrun
43 --rank $set_denovo.rank 43 --rank $set_denovo.rank
44 --newsignum $set_denovo.newsignum 44 --newsignum $set_denovo.newsignum
45 --output_denovo $denovo 45 --output_denovo $denovo
46 --sigmatrix $sigmatrix
46 #end if 47 #end if
47 48
48 #if $set_cosmic.choices == 'yes': 49 #if $set_cosmic.choices == 'yes':
50 --cosmic_version $set_cosmic.cosmic_version
49 --signum '$set_cosmic.signum' 51 --signum '$set_cosmic.signum'
50 --output_cosmic $cosmic 52 --output_cosmic $cosmic
51 #end if 53 #end if
52 54
55 #if $rdata_out
56 --rdata '$rdata'
57 #end if
58
53 ]]></command> 59 ]]></command>
54 <inputs> 60 <inputs>
55 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/> 61 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/>
56 <param name="genome" type="select" label="Reference Genome"> 62 <param name="genome" type="select" label="Reference Genome">
57 <option value="BSgenome.Hsapiens.1000genomes.hs37d5">BSgenome.Hsapiens.1000genomes.hs37d5</option> 63 <option value="BSgenome.Hsapiens.1000genomes.hs37d5">BSgenome.Hsapiens.1000genomes.hs37d5</option>
88 <option value="no">No</option> 94 <option value="no">No</option>
89 </param> 95 </param>
90 <when value="yes" /> 96 <when value="yes" />
91 <when value="no" /> 97 <when value="no" />
92 </conditional> 98 </conditional>
99
93 <conditional name="set_denovo"> 100 <conditional name="set_denovo">
94 <param name="choices" type="select" label="Extract de novo signatures with MutationalPatterns" display="radio"> 101 <param name="choices" type="select" label="Extract de novo signatures with MutationalPatterns" display="radio">
95 <option value="yes" selected="true">Yes</option> 102 <option value="yes" selected="true">Yes</option>
96 <option value="no">No</option> 103 <option value="no">No</option>
97 </param> 104 </param>
99 <param name="nrun" type="integer" value="10" min="10" max="200" 106 <param name="nrun" type="integer" value="10" min="10" max="200"
100 label="Number of cycles to find best fitting of signatures" 107 label="Number of cycles to find best fitting of signatures"
101 help="High values extend the computational time"/> 108 help="High values extend the computational time"/>
102 <param name="rank" type="integer" value="4" min="3" max="30" 109 <param name="rank" type="integer" value="4" min="3" max="30"
103 label="Number of ranks to be displayed for control of optimal number of signature" 110 label="Number of ranks to be displayed for control of optimal number of signature"
104 help="High values extend the computational time"/> 111 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"/>
105 <param name="newsignum" type="integer" value="4" min="2" max="30" 112 <param name="newsignum" type="integer" value="4" min="2" max="30"
106 label="Number of de novo signatures to capture" 113 label="Number of de novo signatures to capture"
107 help="High values extend the computational time"/> 114 help="High values extend the computational time. Note also that you cannot extract more signature than the number of available samples in the study"/>
108 </when> 115 </when>
109 <when value="no" /> 116 <when value="no" />
110 </conditional> 117 </conditional>
111 118
112 <conditional name="set_cosmic"> 119 <conditional name="set_cosmic">
116 </param> 123 </param>
117 <when value="yes"> 124 <when value="yes">
118 <param name="signum" type="integer" value="3" min="2" max="30" 125 <param name="signum" type="integer" value="3" min="2" max="30"
119 label="selects the N most significant signatures in samples to express mutational patterns" 126 label="selects the N most significant signatures in samples to express mutational patterns"
120 help="an integer between 2 and 30 signature types from cosmic"/> 127 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">
129 <option value="v2" selected="true">Cosmic v2, March 2015</option>
130 <option value="v3">Cosmic v3, May 2019</option>
131 </param>
121 </when> 132 </when>
122 <when value="no" /> 133 <when value="no" />
123 </conditional> 134 </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" />
124 </inputs> 136 </inputs>
125 <outputs> 137 <outputs>
126 <data name="spectrum" format="pdf" label="Mutational Spectrum"> 138 <data name="spectrum" format="pdf" label="Mutational Spectrum">
127 <filter>set_spectrum['choices'] == "yes"</filter> 139 <filter>set_spectrum['choices'] == "yes"</filter>
128 </data> 140 </data>
129 <data name="denovo" format="pdf" label="De novo signatures"> 141 <data name="denovo" format="pdf" label="De novo signatures">
130 <filter>set_denovo['choices'] == "yes"</filter> 142 <filter>set_denovo['choices'] == "yes"</filter>
131 </data> 143 </data>
144 <data name="sigmatrix" format="tabular" label="De novo signatures probability matrix">
145 <filter>set_denovo['choices'] == "yes"</filter>
146 </data>
132 <data name="cosmic" format="pdf" label="Cosmic signatures"> 147 <data name="cosmic" format="pdf" label="Cosmic signatures">
133 <filter>set_cosmic['choices'] == "yes"</filter> 148 <filter>set_cosmic['choices'] == "yes"</filter>
134 </data> 149 </data>
150 <data name="rdata" format="rdata" label="${tool.name}: RData file">
151 <filter>rdata_out</filter>
152 </data>
153
135 </outputs> 154 </outputs>
136 <tests> 155 <tests>
156 <!-- simple profile -->
137 <test> 157 <test>
138 <param name="vcfs"> 158 <param name="vcfs">
139 <collection type="list"> 159 <collection type="list">
140 <element name="1" ftype="vcf" value="G.vcf"/> 160 <element name="1" ftype="vcf" value="G.vcf"/>
141 <element name="2" ftype="vcf" value="H.vcf"/> 161 <element name="2" ftype="vcf" value="H.vcf"/>
142 </collection> 162 </collection>
143 </param> 163 </param>
144 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> 164 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
165 <conditional name="set_levels">
166 <param name="choices" value="yes"/>
167 </conditional>
145 <param name="levels" value="GH_levels.tab" ftype="tabular"/> 168 <param name="levels" value="GH_levels.tab" ftype="tabular"/>
146 <conditional name="set_spectrum"> 169 <conditional name="set_spectrum">
147 <param name="choices" value="no"/> 170 <param name="choices" value="yes"/>
148 </conditional> 171 </conditional>
149 <conditional name="set_denovo"> 172 <conditional name="set_denovo">
150 <param name="choices" value="no"/> 173 <param name="choices" value="no"/>
151 </conditional> 174 </conditional>
152 <conditional name="set_cosmic"> 175 <conditional name="set_cosmic">
153 <param name="choices" value="yes"/> 176 <param name="choices" value="no"/>
154 </conditional> 177 </conditional>
155 <param name="signum" value="3" /> 178 <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size" ftype="pdf"/>
156 <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size" ftype="pdf"/>
157 </test> 179 </test>
180
181 <!-- de novo signatures -->
158 <test> 182 <test>
159 <param name="vcfs"> 183 <param name="vcfs">
160 <collection type="list"> 184 <collection type="list">
161 <element name="6" value="F.vcf"/> 185 <element name="6" value="F.vcf"/>
162 <element name="7" value="G.vcf"/> 186 <element name="7" value="G.vcf"/>
172 <param name="choices" value="yes"/> 196 <param name="choices" value="yes"/>
173 </conditional> 197 </conditional>
174 <conditional name="set_cosmic"> 198 <conditional name="set_cosmic">
175 <param name="choices" value="no"/> 199 <param name="choices" value="no"/>
176 </conditional> 200 </conditional>
201 <param name="nrun" value="10" />
202 <param name="rank" value="4" />
203 <param name="newsignum" value="4" />
204 <param name="rdata_out" value="true" />
177 <output name="denovo" file="denovo_output1.pdf" compare="sim_size" ftype="pdf"/> 205 <output name="denovo" file="denovo_output1.pdf" compare="sim_size" ftype="pdf"/>
206 <output name="sigmatrix" file="sigmatrix.tab" ftype="tabular" compare="sim_size"/>
207 <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!-- delta="170000" -->
178 </test> 208 </test>
209
210 <!-- cosmic signatures -->
179 <test> 211 <test>
180 <param name="vcfs"> 212 <param name="vcfs">
181 <collection type="list"> 213 <collection type="list">
182 <element name="1" ftype="vcf" value="G.vcf"/> 214 <element name="6" value="F.vcf"/>
183 <element name="2" ftype="vcf" value="H.vcf"/> 215 <element name="7" value="G.vcf"/>
216 <element name="8" value="H.vcf"/>
217 <element name="9" value="I.vcf"/>
184 </collection> 218 </collection>
185 </param> 219 </param>
186 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> 220 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
187 <conditional name="set_levels">
188 <param name="choices" value="yes"/>
189 </conditional>
190 <param name="levels" value="GH_levels.tab" ftype="tabular"/> 221 <param name="levels" value="GH_levels.tab" ftype="tabular"/>
191 <conditional name="set_spectrum"> 222 <conditional name="set_spectrum">
192 <param name="choices" value="yes"/> 223 <param name="choices" value="no"/>
193 </conditional> 224 </conditional>
194 <conditional name="set_denovo"> 225 <conditional name="set_denovo">
195 <param name="choices" value="no"/> 226 <param name="choices" value="no"/>
196 </conditional> 227 </conditional>
197 <conditional name="set_cosmic"> 228 <conditional name="set_cosmic">
198 <param name="choices" value="no"/> 229 <param name="choices" value="yes"/>
199 </conditional> 230 </conditional>
200 <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size" ftype="pdf"/> 231 <param name="signum" value="3" />
232 <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size" ftype="pdf"/>
201 </test> 233 </test>
202 </tests> 234 </tests>
203 <help> 235 <help>
204 236
205 **What it does** 237 **What it does**