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comparison mutational_patterns.xml @ 20:a2cb7dc9250a draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit b07cf2662a36d88f80dc08ef4f46454dbc133094"
author artbio
date Tue, 19 Oct 2021 06:16:32 +0000
parents 69f09dff98f9
children 8a5aaa97dbd6
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19:69f09dff98f9 20:a2cb7dc9250a
1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy4"> 1 <tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy5">
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>
35 #if $set_levels.choices == 'yes': 35 #if $set_levels.choices == 'yes':
36 --levels '$set_levels.levels' 36 --levels '$set_levels.levels'
37 #end if 37 #end if
38 38
39 #if $set_spectrum.choices == 'yes': 39 #if $set_spectrum.choices == 'yes':
40 --output_spectrum $spectrum 40 --output_spectrum '$spectrum'
41 #end if 41 #end if
42 42
43 #if $set_denovo.choices == 'yes': 43 #if $set_denovo.choices == 'yes':
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 #end if 49 #end if
50 50
51 #if $set_preset.choices == 'yes': 51 #if $set_preset.choices == 'yes':
52 52
53 #if $set_preset.set_signature_input.input_signature_choices == 'cosmic' 53 #if $set_preset.set_signature_input.input_signature_choices == 'cosmic'
57 #if $set_preset.set_signature_input.input_signature_choices == 'user_signatures' 57 #if $set_preset.set_signature_input.input_signature_choices == 'user_signatures'
58 --own_signatures '$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 --output_sigpattern $sig_contrib 62 --colors '$set_preset.colors'
63 --output_sigpattern '$sig_contrib'
63 64
64 #if $set_preset.contrib_matrix_out == 'yes' 65 #if $set_preset.contrib_matrix_out == 'yes'
65 --sig_contrib_matrix $sig_contrib_matrix 66 --sig_contrib_matrix '$sig_contrib_matrix'
66 #end if 67 #end if
67 68
68 #end if 69 #end if
69 70
70 #if $rdata_out 71 #if $rdata_out
160 <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?" 161 <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?"
161 help="Output the normalized signatures contributions for further visualization" > 162 help="Output the normalized signatures contributions for further visualization" >
162 <option value="no" selected="true">No</option> 163 <option value="no" selected="true">No</option>
163 <option value="yes">Yes</option> 164 <option value="yes">Yes</option>
164 </param> 165 </param>
166 <param name="colors" type="select" label="Color set" display="radio">
167 <option value="brewer">RColorBrewer</option>
168 <option value="intense" selected="true">Intense</option>
169 </param>
165 </when> 170 </when>
166 <when value="no" /> 171 <when value="no" />
167 </conditional> 172 </conditional>
168 <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" /> 173 <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" />
169 </inputs> 174 </inputs>