Mercurial > repos > artbio > mutational_patterns
comparison mutational_patterns.xml @ 20:a2cb7dc9250a draft
"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> |