Mercurial > repos > vijay > pancancer_map_mutation_class

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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
author vijay
date Wed, 16 Dec 2020 23:31:49 +0000
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54c85c40dce1 "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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1 <tool id="pancancer_map_mutation_class" name="PAPAA: PanCancer map mutation class" version="@VERSION@">
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2 <description>map mutation class</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <version_command><![CDATA['papaa_map_mutation_class.py' --version]]></version_command>
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9 <command><![CDATA[
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10 mkdir 'classifier' &&
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11 ln -s '${classifier_decisions}' 'classifier/classifier_decisions.tsv' &&
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12 papaa_map_mutation_class.py
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13 --classifier_decisions 'classifier'
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14 #if $path_genes and str($path_genes):
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15 --path_genes '$path_genes'
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16 #end if
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17 @INPUTS_COPY_NUMBER_FILE_CONDITIONAL@
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18 @INPUT_FILENAME_RAW_MUT@
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19 > '${log}'
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20 ]]>
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21 </command>
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22 <inputs>
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23 <param argument="--classifier_decisions" label="pancancer decisions" name="classifier_decisions" optional="false" type="data" format="tabular" help="classifier_decisions.tsv"/>
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24 <param argument="--path_genes" label="string of the genes to extract or genelist file" name="path_genes" optional="true" type= "data" format="txt"/>
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25 <expand macro="inputs_copy_number_file_conditional" />
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26 <expand macro="input_filename_raw_mut" />
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27 </inputs>
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28 <outputs>
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29 <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/>
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30 <data format="tabular" name="mutation_classification_scores" label="${tool.name} on ${on_string} (mutation_classification_scores.tsv)" from_work_dir="classifier/tables/mutation_classification_scores.tsv"/>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="classifier_decisions" value="classifier_decisions.tsv" ftype="tabular"/>
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35 <param name="path_genes" value="path_genes.txt" ftype="txt"/>
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36 <param name="copy_number" value="yes"/>
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37 <param name="filename_copy_loss" value="copy_number_loss_status_t10p.tsv.gz" ftype="tabular"/>
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38 <param name="filename_copy_gain" value="copy_number_gain_status_t10p.tsv.gz" ftype="tabular"/>
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39 <param name="filename_raw_mut" value="mc3.v0.2.8.PUBLIC_t1p.maf.gz" ftype="tabular"/>
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40 <output name="log" file="map_mutation_class_Log.txt"/>
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41 <output name="mutation_classification_scores" file="mutation_classification_scores.tsv" />
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45
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46 **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_map_mutation_class.py:**
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47
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48 **Inputs:**
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49 --classifer_decisions String of the location of folder containing classifier_decisions.tsv
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50 --path_genes comma separated string of HUGO symbols for all genes in the pathway or Pathway genes list file
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51 --filename_copy_loss Filename of copy number loss
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52 --filename_copy_gain Filename of copy number gain
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53 --filename_raw_mut Filename of raw mut MAF
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54
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55 **Outputs:**
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56 Merge per sample classifier scores with mutation types present in each sample and generate "mutation_classification_scores.tsv" file ]]>
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57 </help>
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58 <expand macro="citations" />
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59 </tool>