Mercurial > repos > vijay > pancancer_alternative_genes_pathwaymapper

comparison alternative_genes_pathwaymapper.xml @ 0:c594c4333b76 draft default tip

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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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-1:000000000000 0:c594c4333b76
1 <tool id="pancancer_alternative_genes_pathwaymapper" name="PAPAA: PanCancer alternative genes pathwaymapper" version="@VERSION@">
2 <description>alternative genes pathwaymapper</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <version_command><![CDATA['papaa_alternative_genes_pathwaymapper.py' --version]]></version_command>
9 <command><![CDATA[
10 mkdir 'classifier' &&
11 ln -s '${classifier_decisions}' 'classifier/classifier_decisions.tsv' &&
12 papaa_alternative_genes_pathwaymapper.py
13 --classifier_decisions 'classifier'
14 #if $genes and str($genes):
15 --genes '$genes'
16 #end if
17 #if $path_genes and str($path_genes):
18 --path_genes '$path_genes'
19 #end if
20 #if $filename_mut and $filename_mut is not None:
21 --filename_mut '$filename_mut'
22 #end if
23 #if $filename_sample and $filename_sample is not None:
24 --filename_sample '$filename_sample'
25 #end if
26 @INPUTS_COPY_NUMBER_FILE_CONDITIONAL@
27 > '${log}'
28 ]]>
29 </command>
30 <inputs>
31 <param argument="--classifier_decisions" label="pancancer decisions" name="classifier_decisions" optional="false" type="data" format="tabular" help="classifier_decisions.tsv"/>
32 <param argument="--genes" label="Comma separated string of HUGO gene symbols" name="genes" optional="False" type="text" value="ERBB2,PIK3CA,KRAS,AKT1"/>
33 <param argument="--path_genes" label="string of the genes to extract or genelist file" name="path_genes" optional="true" type= "data" format="txt"/>
34 <param argument="--filename_mut" label="Filename mutations" name="filename_mut" optional="true" type="data" format="tabular" help="data/pancan_mutation_freeze.tsv"/>
35 <param argument="--filename_sample" label="Filename of sample" name="filename_sample" optional="true" type="data" format="tabular" help="data/sample_freeze.tsv"/>
36 <expand macro="inputs_copy_number_file_conditional" />
37 </inputs>
38 <outputs>
39 <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/>
40 <data format="txt" name="pathway_metrics_pathwaymapper" label="${tool.name} on ${on_string} (pathway_metrics_pathwaymapper.txt)" from_work_dir="classifier/tables/pathway_metrics_pathwaymapper.txt"/>
41 <data format="tabular" name="all_gene_metric_ranks" label="${tool.name} on ${on_string} (all_gene_metric_ranks.tsv)" from_work_dir="classifier/tables/all_gene_metric_ranks.tsv"/>
42 </outputs>
43 <tests>
44 <test>
45 <param name="classifier_decisions" value="classifier_decisions.tsv" ftype="tabular"/>
46 <param name="genes" value="ERBB2,PIK3CA,KRAS,AKT1"/>
47 <param name="path_genes" value="path_genes.txt" ftype="txt"/>
48 <param name="filename_mut" value="pancan_mutation_freeze_t1p.tsv.gz" ftype="tabular"/>
49 <param name="filename_sample" value="sample_freeze.tsv" ftype="tabular"/>
50 <param name="copy_number" value="yes"/>
51 <param name="filename_copy_loss" value="copy_number_loss_status_t10p.tsv.gz" ftype="tabular"/>
52 <param name="filename_copy_gain" value="copy_number_gain_status_t10p.tsv.gz" ftype="tabular"/>
53 <param name="filename_raw_mut" value="mc3.v0.2.8.PUBLIC_t1p.maf.gz" ftype="tabular"/>
54 <output name="log" file="alternative_genes_pathwaymapper_Log.txt"/>
55 <output name="pathway_metrics_pathwaymapper" file="pathway_metrics_pathwaymapper.txt" />
56 <output name="all_gene_metric_ranks" file="all_gene_metric_ranks.tsv" />
57 </test>
58 </tests>
59 <help><![CDATA[
60
61 **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_alternative_genes_pathwaymapper.py:**
62
63 **Inputs:**
64 --gene Comma separated string of HUGO symbols for target genes or targenes_list.csv file
65 --path_genes Comma separated string of HUGO symbols for all genes in the target pathway or path_genes.txt file
66 --classifier_decisions String of the location of classifier decisions with predictions or scores
67 --filename_mut Filename of sample/gene mutations to use in model
68 --filename_mut_burden Filename of sample mutation burden to use in model
69 --filename_sample Filename of patient/samples to use in model
70 --filename_copy_loss Filename of copy number loss
71 --filename_copy_gain Filename of copy number gain
72
73 **Outputs:**
74 Calculate and display metrics for targene classification
75
76 Calculate and display pathway metrics ("pathway_metrics_pathwaymapper.txt")
77
78 Visualize Distribution of AUROC and AUPRC for all genes and Get Metrics for All Genes ("all_gene_metric_ranks.tsv) ]]>
79 </help>
80 <expand macro="citations" />
81 </tool>