Mercurial > repos > vijay > pancancer_alternative_genes_pathwaymapper

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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
author vijay
date Wed, 16 Dec 2020 23:31:32 +0000
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1 <tool id="pancancer_alternative_genes_pathwaymapper" name="PAPAA: PanCancer alternative genes pathwaymapper" version="@VERSION@">
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2 <description>alternative genes pathwaymapper</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_alternative_genes_pathwaymapper.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_alternative_genes_pathwaymapper.py
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13 --classifier_decisions 'classifier'
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14 #if $genes and str($genes):
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15 --genes '$genes'
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16 #end if
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17 #if $path_genes and str($path_genes):
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18 --path_genes '$path_genes'
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19 #end if
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20 #if $filename_mut and $filename_mut is not None:
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21 --filename_mut '$filename_mut'
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22 #end if
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23 #if $filename_sample and $filename_sample is not None:
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24 --filename_sample '$filename_sample'
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25 #end if
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26 @INPUTS_COPY_NUMBER_FILE_CONDITIONAL@
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27 > '${log}'
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28 ]]>
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29 </command>
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30 <inputs>
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31 <param argument="--classifier_decisions" label="pancancer decisions" name="classifier_decisions" optional="false" type="data" format="tabular" help="classifier_decisions.tsv"/>
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32 <param argument="--genes" label="Comma separated string of HUGO gene symbols" name="genes" optional="False" type="text" value="ERBB2,PIK3CA,KRAS,AKT1"/>
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33 <param argument="--path_genes" label="string of the genes to extract or genelist file" name="path_genes" optional="true" type= "data" format="txt"/>
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34 <param argument="--filename_mut" label="Filename mutations" name="filename_mut" optional="true" type="data" format="tabular" help="data/pancan_mutation_freeze.tsv"/>
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35 <param argument="--filename_sample" label="Filename of sample" name="filename_sample" optional="true" type="data" format="tabular" help="data/sample_freeze.tsv"/>
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36 <expand macro="inputs_copy_number_file_conditional" />
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37 </inputs>
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38 <outputs>
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39 <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/>
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40 <data format="txt" name="pathway_metrics_pathwaymapper" label="${tool.name} on ${on_string} (pathway_metrics_pathwaymapper.txt)" from_work_dir="classifier/tables/pathway_metrics_pathwaymapper.txt"/>
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41 <data format="tabular" name="all_gene_metric_ranks" label="${tool.name} on ${on_string} (all_gene_metric_ranks.tsv)" from_work_dir="classifier/tables/all_gene_metric_ranks.tsv"/>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="classifier_decisions" value="classifier_decisions.tsv" ftype="tabular"/>
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46 <param name="genes" value="ERBB2,PIK3CA,KRAS,AKT1"/>
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47 <param name="path_genes" value="path_genes.txt" ftype="txt"/>
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48 <param name="filename_mut" value="pancan_mutation_freeze_t1p.tsv.gz" ftype="tabular"/>
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49 <param name="filename_sample" value="sample_freeze.tsv" ftype="tabular"/>
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50 <param name="copy_number" value="yes"/>
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51 <param name="filename_copy_loss" value="copy_number_loss_status_t10p.tsv.gz" ftype="tabular"/>
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52 <param name="filename_copy_gain" value="copy_number_gain_status_t10p.tsv.gz" ftype="tabular"/>
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53 <param name="filename_raw_mut" value="mc3.v0.2.8.PUBLIC_t1p.maf.gz" ftype="tabular"/>
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54 <output name="log" file="alternative_genes_pathwaymapper_Log.txt"/>
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55 <output name="pathway_metrics_pathwaymapper" file="pathway_metrics_pathwaymapper.txt" />
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56 <output name="all_gene_metric_ranks" file="all_gene_metric_ranks.tsv" />
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60
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61 **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_alternative_genes_pathwaymapper.py:**
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62
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63 **Inputs:**
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64 --gene Comma separated string of HUGO symbols for target genes or targenes_list.csv file
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65 --path_genes Comma separated string of HUGO symbols for all genes in the target pathway or path_genes.txt file
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66 --classifier_decisions String of the location of classifier decisions with predictions or scores
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67 --filename_mut Filename of sample/gene mutations to use in model
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68 --filename_mut_burden Filename of sample mutation burden to use in model
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69 --filename_sample Filename of patient/samples to use in model
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70 --filename_copy_loss Filename of copy number loss
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71 --filename_copy_gain Filename of copy number gain
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72
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73 **Outputs:**
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74 Calculate and display metrics for targene classification
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75
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76 Calculate and display pathway metrics ("pathway_metrics_pathwaymapper.txt")
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77
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78 Visualize Distribution of AUROC and AUPRC for all genes and Get Metrics for All Genes ("all_gene_metric_ranks.tsv) ]]>
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79 </help>
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80 <expand macro="citations" />
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81 </tool>