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comparison mutational_patterns.xml @ 2:aea952be68cb draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit cd8f633245d53cf47eaf860a4e0ae8d806c34419"
author artbio
date Wed, 16 Sep 2020 22:58:28 +0000
parents 921c1f55481d
children e332cf9dfa06
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1:921c1f55481d 2:aea952be68cb
1 <tool id="mutational_patterns" name="Analyse Mutational Patters/Signatures" version="2.0.0_galaxy_2"> 1 <tool id="mutational_patterns" name="Analyse Mutational Patters/Signatures" version="2.0.0+galaxy3">
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>
7 <requirement type="package" version="0.21.0=r40h0357c0b_1004">r-nmf</requirement> 7 <requirement type="package" version="0.21.0=r40h0357c0b_1004">r-nmf</requirement>
8 <requirement type="package" version="2.3=r40h6115d3f_1003">r-gridextra</requirement>
8 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement> 9 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
9 <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement> 10 <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement>
10 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement> 11 <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
11 <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement> 12 <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement>
12 <!-- install bioconda genomes 13 <!-- install bioconda genomes
26 #for $sample in $vcfs: 27 #for $sample in $vcfs:
27 $filename_to_element_identifiers.__setitem__(str($sample), $sample.element_identifier) 28 $filename_to_element_identifiers.__setitem__(str($sample), $sample.element_identifier)
28 #end for 29 #end for
29 '#echo json.dumps(filename_to_element_identifiers)#' 30 '#echo json.dumps(filename_to_element_identifiers)#'
30 --genome '$genome' 31 --genome '$genome'
31 --levels '$levels' 32
32 --signum '$signum' 33 #if $set_levels.choices == 'yes':
33 --output '$output' 34 --levels '$set_levels.levels'
35 #end if
36
37 #if $set_spectrum.choices == 'yes':
38 --output_spectrum $spectrum
39 #end if
40
41 #if $set_denovo.choices == 'yes':
42 --nrun $set_denovo.nrun
43 --rank $set_denovo.rank
44 --newsignum $set_denovo.newsignum
45 --output_denovo $denovo
46 #end if
47
48 #if $set_cosmic.choices == 'yes':
49 --signum '$set_cosmic.signum'
50 --output_cosmic $cosmic
51 #end if
34 52
35 ]]></command> 53 ]]></command>
36 <inputs> 54 <inputs>
37 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/> 55 <param name="vcfs" type="data_collection" format="vcf" label="VCF file(s) collection" multiple="true"/>
38 <param name="genome" type="select" label="Reference Genome"> 56 <param name="genome" type="select" label="Reference Genome">
41 <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option> 59 <option value="BSgenome.Hsapiens.UCSC.hg19">BSgenome.Hsapiens.UCSC.hg19</option>
42 <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option> 60 <option value="BSgenome.Hsapiens.UCSC.hg38" selected="true">BSgenome.Hsapiens.UCSC.hg38</option>
43 <!--<option value="BSgenome.Mmusculus.UCSC.mm10">BSgenome.Mmusculus.UCSC.mm10</option> 61 <!--<option value="BSgenome.Mmusculus.UCSC.mm10">BSgenome.Mmusculus.UCSC.mm10</option>
44 <option value="BSgenome.Mmusculus.UCSC.mm9">BSgenome.Mmusculus.UCSC.mm9</option>--> 62 <option value="BSgenome.Mmusculus.UCSC.mm9">BSgenome.Mmusculus.UCSC.mm9</option>-->
45 </param> 63 </param>
46 <param name="levels" type="data" format="tabular" 64 <conditional name="set_levels">
47 label="A two-column tab-separated file describing levels attributed to each sample name" 65 <param name="choices" type="select" label="samples have levels/labels for grouping them in the analysis" display="radio"
48 help="Tip: the sample name list in the vcf collection can be obtained using 66 help="for instance, female/male or genotype-1/genotype-2/genotype-3, etc.">
49 the IUC Galaxy tool 'Extract element identifiers of a list collection' &lt;br&gt; 67 <option value="no" selected="true">No</option>
50 example:&lt;br&gt; 68 <option value="yes">Yes</option>
51 sample1 female&lt;br&gt; 69 </param>
52 sample2 female&lt;br&gt; 70 <when value="yes">
53 sample3 male&lt;br&gt; 71 <param name="levels" type="data" format="tabular"
54 sample4 female&lt;br&gt; 72 label="A two-column tab-separated file describing levels attributed to each sample name"
55 sample5 male&lt;br&gt; 73 help="Tip: the sample name list in the vcf collection can be obtained using
56 sample5 male" /> 74 the IUC Galaxy tool 'Extract element identifiers of a list collection' &lt;br&gt;
57 <param name="signum" type="integer" value="2" min="2" max="30" 75 example:&lt;br&gt;
58 label="selects the N most significant signatures in samples to express mutational patterns" 76 sample1 female&lt;br&gt;
59 help="an integer between 2 and 30 signature types from cosmic"/> 77 sample2 female&lt;br&gt;
60 78 sample3 male&lt;br&gt;
79 sample4 female&lt;br&gt;
80 sample5 male&lt;br&gt;
81 sample5 male" />
82 </when>
83 <when value="no" />
84 </conditional>
85 <conditional name="set_spectrum">
86 <param name="choices" type="select" label="Analyse Mutational Spectrum" display="radio">
87 <option value="yes" selected="true">Yes</option>
88 <option value="no">No</option>
89 </param>
90 <when value="yes" />
91 <when value="no" />
92 </conditional>
93 <conditional name="set_denovo">
94 <param name="choices" type="select" label="Extract de novo signatures with MutationalPatterns" display="radio">
95 <option value="yes" selected="true">Yes</option>
96 <option value="no">No</option>
97 </param>
98 <when value="yes">
99 <param name="nrun" type="integer" value="10" min="10" max="200"
100 label="Number of cycles to find best fitting of signatures"
101 help="High values extend the computational time"/>
102 <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"
104 help="High values extend the computational time"/>
105 <param name="newsignum" type="integer" value="4" min="2" max="30"
106 label="Number of de novo signatures to capture"
107 help="High values extend the computational time"/>
108 </when>
109 <when value="no" />
110 </conditional>
111
112 <conditional name="set_cosmic">
113 <param name="choices" type="select" label="Decompose with Cosmic signature v2" display="radio">
114 <option value="yes" selected="true">Yes</option>
115 <option value="no">No</option>
116 </param>
117 <when value="yes">
118 <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"
120 help="an integer between 2 and 30 signature types from cosmic"/>
121 </when>
122 <when value="no" />
123 </conditional>
61 </inputs> 124 </inputs>
62 <outputs> 125 <outputs>
63 <data name="output" format="pdf" label="Mutational Patterns/Signatures" /> 126 <data name="spectrum" format="pdf" label="Mutational Spectrum">
127 <filter>set_spectrum['choices'] == "yes"</filter>
128 </data>
129 <data name="denovo" format="pdf" label="De novo signatures">
130 <filter>set_denovo['choices'] == "yes"</filter>
131 </data>
132 <data name="cosmic" format="pdf" label="Cosmic signatures">
133 <filter>set_cosmic['choices'] == "yes"</filter>
134 </data>
64 </outputs> 135 </outputs>
65 <tests> 136 <tests>
66 <test> 137 <test>
67 <param name="vcfs"> 138 <param name="vcfs">
68 <collection type="list"> 139 <collection type="list">
69 <element name="1" value="EGF167.vcf"/> 140 <element name="1" ftype="vcf" value="G.vcf"/>
70 <element name="2" value="EGF089.vcf"/> 141 <element name="2" ftype="vcf" value="H.vcf"/>
71 <element name="3" value="EGF037F.vcf"/>
72 </collection> 142 </collection>
73 </param> 143 </param>
74 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/> 144 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
75 <param name="levels" value="levels.tab" ftype="tabular"/> 145 <param name="levels" value="GH_levels.tab" ftype="tabular"/>
146 <conditional name="set_spectrum">
147 <param name="choices" value="no"/>
148 </conditional>
149 <conditional name="set_denovo">
150 <param name="choices" value="no"/>
151 </conditional>
152 <conditional name="set_cosmic">
153 <param name="choices" value="yes"/>
154 </conditional>
76 <param name="signum" value="3" /> 155 <param name="signum" value="3" />
77 <output name="output" file="output.pdf" compare="sim_size" ftype="pdf"/> 156 <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size" ftype="pdf"/>
157 </test>
158 <test>
159 <param name="vcfs">
160 <collection type="list">
161 <element name="6" value="F.vcf"/>
162 <element name="7" value="G.vcf"/>
163 <element name="8" value="H.vcf"/>
164 <element name="9" value="I.vcf"/>
165 </collection>
166 </param>
167 <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
168 <conditional name="set_spectrum">
169 <param name="choices" value="no"/>
170 </conditional>
171 <conditional name="set_denovo">
172 <param name="choices" value="yes"/>
173 </conditional>
174 <conditional name="set_cosmic">
175 <param name="choices" value="no"/>
176 </conditional>
177 <output name="denovo" file="denovo_output1.pdf" compare="sim_size" ftype="pdf"/>
178 </test>
179 <test>
180 <param name="vcfs">
181 <collection type="list">
182 <element name="1" ftype="vcf" value="G.vcf"/>
183 <element name="2" ftype="vcf" value="H.vcf"/>
184 </collection>
185 </param>
186 <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"/>
191 <conditional name="set_spectrum">
192 <param name="choices" value="yes"/>
193 </conditional>
194 <conditional name="set_denovo">
195 <param name="choices" value="no"/>
196 </conditional>
197 <conditional name="set_cosmic">
198 <param name="choices" value="no"/>
199 </conditional>
200 <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size" ftype="pdf"/>
78 </test> 201 </test>
79 </tests> 202 </tests>
80 <help> 203 <help>
81 204
82 **What it does** 205 **What it does**