Mercurial > repos > morinlab > oncoprintplus
annotate oncoprintplus.xml @ 4:2877b1ba1250 draft default tip
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncoprintplus commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
| author | morinlab |
|---|---|
| date | Tue, 11 Oct 2016 14:26:04 -0400 |
| parents | 97767a410c75 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="oncoprintplus" name="OncoPrintPlus" version="1.0.0"> |
| 2 | |
| 3 <description> | |
| 4 creates a summary matrix plot of cohort wide mutations | |
| 5 </description> | |
| 6 | |
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2877b1ba1250
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncoprintplus commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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7 <macros> |
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2877b1ba1250
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncoprintplus commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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8 <import>citations.xml</import> |
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2877b1ba1250
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncoprintplus commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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9 </macros> |
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2877b1ba1250
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncoprintplus commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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10 |
| 0 | 11 <requirements> |
| 12 <requirement type="binary">Rscript</requirement> | |
| 13 <requirement type="package" version="3.2.1">R</requirement> | |
| 14 <requirement type="package" version="1.0">cancer_genomics_functions</requirement> | |
| 15 <requirement type="environment" verion="1.0">CANCER_GENOMICS_FUNCTIONS_PATH</requirement> | |
| 16 <requirement type="package" version="5.3.4">boutroslab_plotting_general</requirement> | |
| 17 </requirements> | |
| 18 | |
| 19 <command detect_errors="aggressive"> | |
| 20 | |
| 21 touch output.pdf; | |
| 22 Rscript $__tool_directory__/oncoprintplus.R | |
| 23 --input_snv $input_maf | |
| 24 --cancer_genomics_functions_path \$CANCER_GENOMICS_FUNCTIONS_PATH/ | |
| 25 | |
| 26 #if $gene.order.value == "default" | |
| 27 | |
| 28 #else | |
| 29 --gene_order $gene.order | |
| 30 #end if | |
| 31 | |
| 32 #if $gene.gene_list | |
| 33 --gene_list $gene.gene_list | |
| 34 #end if | |
| 35 | |
| 36 #if $gene.snv_counts | |
| 37 --plot_gene_snv_counts | |
| 38 #end if | |
| 39 | |
| 40 #if $gene.mutsig.plot | |
| 41 --plot_gene_mutsig | |
| 42 #end if | |
| 43 | |
| 44 #if $gene.mutsig.mutsig | |
| 45 --gene_mutsig $gene.mutsig.mutsig | |
| 46 #end if | |
| 47 | |
| 48 #if $gene.oncodrive.plot | |
| 49 --plot_gene_oncodrive | |
| 50 #end if | |
| 51 | |
| 52 #if $gene.oncodrive.oncodrive | |
| 53 --gene_oncodrive $gene.oncodrive.oncodrive | |
| 54 #end if | |
| 55 | |
| 56 #if $patient.covariates.use_covariates == "no": | |
| 57 | |
| 58 #if $patient.covariates.order.value == "default": | |
| 59 | |
| 60 #else | |
| 61 --patient_order snv_counts | |
| 62 #end if | |
| 63 | |
| 64 #else | |
| 65 | |
| 66 --patient_covariate_data $patient.covariates.covariate_data | |
| 67 | |
| 68 #for $item in $patient.covariates.plot: | |
| 69 --plot_patient_covariate $item.covariate_to_plot | |
| 70 #end for | |
| 71 | |
| 72 #for $item in $patient.covariates.order: | |
| 73 --patient_order $item.covariate_or_internal.order | |
| 74 #end for | |
| 75 | |
| 76 #end if | |
| 77 | |
| 78 #if $patient.snv_counts | |
| 79 --plot_patient_snv_counts | |
| 80 #end if | |
| 81 | |
| 82 #if $patient.snv_distribution | |
| 83 --plot_patient_snv_distribution | |
| 84 #end if | |
| 85 | |
| 86 --center_plot $center_plot | |
| 87 --output ./output.pdf; | |
| 88 | |
| 89 mv output.pdf $output; | |
| 90 | |
| 91 </command> | |
| 92 | |
| 93 <inputs> | |
| 94 | |
| 95 <param type="data" format="maf" name="input_maf" label="Cohort Wide MAF File"/> | |
| 96 | |
| 97 <param type="select" name="center_plot" label="Central Plot"> | |
| 98 <option value="impact" selected="True">VCF2MAF IMPACT</option> | |
| 99 <option value="variant_classification">Variant Classification</option> | |
| 100 </param> | |
| 101 | |
| 102 <section name="gene" title="Gene Related Inputs" expanded="False"> | |
| 103 <param type="select" name="order" label="Order of Genes"> | |
| 104 <option value="default" selected="True">Order in MAF</option> | |
| 105 <option value="snv_counts">SNV Counts</option> | |
| 106 <option value="mutsig">MutSigCV Data</option> | |
| 107 <option value="oncodrive">Oncodrive-FM Data</option> | |
| 108 </param> | |
| 109 <param type="boolean" name="snv_counts" label="Plot Gene SNV Counts" checked="true"/> | |
| 110 <param type="data" format="txt" name="gene_list" label="List of Genes Include" optional="true"/> | |
| 111 <section name="mutsig" title="MutsigCV Inputs" expanded="False"> | |
| 112 <param type="boolean" name="plot" label="Plot MutSigCV Data" checked="false"/> | |
| 113 <param type="data" format="txt" name="mutsig" label="Mutsig Input" optional="true"/> | |
| 114 </section> | |
| 115 <section name="oncodrive" title="Oncodrive-FM Inputs" expanded="False"> | |
| 116 <param type="boolean" name="plot" label="Plot Oncodrive-FM Data" checked="false"/> | |
| 117 <param type="data" format="txt" name="oncodrive" label="Oncodrive-FM Input" optional="true"/> | |
| 118 </section> | |
| 119 </section> | |
| 120 <section name="patient" title="Patient Related Inputs" expanded="False"> | |
| 121 <conditional name="covariates"> | |
| 122 <param name="use_covariates" type="select" label="Use Patient Covariates"> | |
| 123 <option value="no" selected="True">No</option> | |
| 124 <option value="yes">Yes</option> | |
| 125 </param> | |
| 126 <when value="no"> | |
| 127 <repeat name="order" title="Patient Order" default="1"> | |
| 128 <param type="select" name="order" label="Order of Patients"> | |
| 129 <option value="default" selected="True">Order in MAF</option> | |
| 130 <option value="snv_counts">SNV Counts</option> | |
| 131 </param> | |
| 132 </repeat> | |
| 133 </when> | |
| 134 <when value="yes"> | |
| 135 <param type="data" format="tabular" name="covariate_data" label="Patient Covariate File"/> | |
| 136 <repeat name="plot" title="Plot Patient Covariate" default="1"> | |
| 137 <param type="text" name="covariate_to_plot" label="Plot Patient Covariate" /> | |
| 138 </repeat> | |
| 139 <repeat name="order" title="Patient Order" default="1"> | |
| 140 <conditional name="covariate_or_internal"> | |
| 141 <param name="use_covariate_or_internal" type="select" label="Order on"> | |
| 142 <option value="cov" selected="True">Covariate</option> | |
| 143 <option value="int">Other</option> | |
| 144 </param> | |
| 145 <when value="cov"> | |
| 146 <param type="select" name="order" label="Order of Patients"> | |
| 147 <option value="default" selected="True">Order in MAF</option> | |
| 148 <option value="snv_counts">SNV Counts</option> | |
| 149 </param> | |
| 150 </when> | |
| 151 <when value="int"> | |
| 152 <param name="order" type="text" title="Order of Patients"/> | |
| 153 </when> | |
| 154 </conditional> | |
| 155 </repeat> | |
| 156 </when> | |
| 157 </conditional> | |
| 158 <param type="boolean" name="snv_counts" label="Plot Patient SNV Counts" checked="true"/> | |
| 159 <param type="boolean" name="snv_distribution" label="Plot Patient SNV Distribution" checked="true"/> | |
| 160 </section> | |
| 161 </inputs> | |
| 162 <outputs> | |
| 163 <data format="pdf" name="output"/> | |
| 164 </outputs> | |
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4
2877b1ba1250
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncoprintplus commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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165 <help> |
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2877b1ba1250
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncoprintplus commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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166 https://labs.oicr.on.ca/boutros-lab/software/bpg |
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2877b1ba1250
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncoprintplus commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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167 </help> |
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2877b1ba1250
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncoprintplus commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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168 <citations> |
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2877b1ba1250
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncoprintplus commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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169 <expand macro="morinlab_citation"/> |
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2877b1ba1250
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncoprintplus commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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170 <expand macro="galaxy_citation"/> |
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2877b1ba1250
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncoprintplus commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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171 </citations> |
| 0 | 172 </tool> |