Mercurial > repos > vijay > pancancer_pathway_count_heatmaps

comparison targene_pathway_count_heatmaps.xml @ 0:dc1d71493ebf draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
author vijay
date Wed, 16 Dec 2020 23:29:47 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:dc1d71493ebf
1 <tool id="pancancer_pathway_count_heatmaps" name="PAPAA: PanCancer pathway count heatmaps" version="@VERSION@">
2 <description>pathway count heatmaps</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <version_command><![CDATA['papaa_targene_pathway_count_heatmaps.py' --version]]></version_command>
9 <command><![CDATA[
10 mkdir 'classifier' &&
11 mkdir -p 'classifier/tables' &&
12 ln -s '${classifier_decisions}' 'classifier/classifier_decisions.tsv' &&
13 ln -s '${pathway_metrics}' 'classifier/tables/pathway_metrics_pathwaymapper.txt' &&
14 ln -s '${all_gene_metric_ranks}' 'classifier/tables/all_gene_metric_ranks.tsv' &&
15 papaa_targene_pathway_count_heatmaps.py
16 --classifier_decisions 'classifier'
17 #if $genes and str($genes):
18 --genes '$genes'
19 #end if
20 #if $path_genes and str($path_genes):
21 --path_genes '$path_genes'
22 #end if
23 @INPUTS_BASIC@
24 #if $filename_copy_loss and $filename_copy_loss is not None:
25 --filename_copy_loss '$filename_copy_loss'
26 #end if
27 #if $filename_copy_gain and $filename_copy_gain is not None:
28 --filename_copy_gain '$filename_copy_gain'
29 #end if
30 #if $filename_cancer_gene_classification and $filename_cancer_gene_classification is not None:
31 --filename_cancer_gene_classification '$filename_cancer_gene_classification'
32 #end if
33 > '${log}'
34 ]]>
35 </command>
36 <inputs>
37 <param argument="--classifier_decisions" label="pancancer decisions" name="classifier_decisions" optional="false" type="data" format="tabular" help="classifier_decisions.tsv"/>
38 <param label="pancancer metrics pathwaymapper" name="pathway_metrics" optional="false" type="data" format="txt" help="pathway_metrics_pathwaymapper.txt"/>
39 <param label="all gene metric ranks" name="all_gene_metric_ranks" optional="false" type="data" format="tabular" help="all_gene_metric_ranks.tsv"/>
40 <param argument="--genes" label="Comma separated string of HUGO gene symbols" name="genes" optional="False" type="text" value="ERBB2,PIK3CA,KRAS,AKT1"/>
41 <param argument="--path_genes" label="String of the pathway genes to extract" name="path_genes" optional="true" type= "data" format="txt"/>
42 <expand macro="inputs_basic"/>
43 <param argument="--filename_mut" label="Filename mutations" name="filename_mut" optional="true" type="data" format="tabular" help="data/pancan_mutation_freeze.tsv"/>
44 <param argument="--filename_sample" label="Filename of sample" name="filename_sample" optional="true" type="data" format="tabular" help="data/sample_freeze.tsv"/>
45 <param argument="--filename_copy_loss" label="File with Copy number loss" name="filename_copy_loss" optional="false" type="data" format="tabular" help="data/copy_number_loss_status.tsv"/>
46 <param argument="--filename_copy_gain" label="File with Copy number gain" name="filename_copy_gain" optional="false" type="data" format="tabular" help="data/copy_number_gain_status.tsv"/>
47 <param argument="--filename_cancer_gene_classification" label="File with cancer gene classification table" name="filename_cancer_gene_classification" optional="false" type="data" format="tabular" help="data/cosmic_cancer_classification.tsv"/>
48 </inputs>
49 <outputs>
50 <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/>
51 <data format="pdf" name="cancer_type_mutation_heatmap" label="${tool.name} on ${on_string} (cancer_type_mutation_heatmap.pdf)" from_work_dir="classifier/cancer_type_mutation_heatmap.pdf"/>
52 <data format="pdf" name="cancer_type_copy_number_heatmap" label="${tool.name} on ${on_string} (cancer_type_copy_number_heatmap.pdf)" from_work_dir="classifier/cancer_type_copy_number_heatmap.pdf"/>
53 <data format="pdf" name="cancer_type_combined_total_heatmap" label="${tool.name} on ${on_string} (cancer_type_combined_total_heatmap.pdf)" from_work_dir="classifier/cancer_type_combined_total_heatmap.pdf"/>
54 <data format="txt" name="pathway_mapper_percentages" label="${tool.name} on ${on_string} (pathway_mapper_percentages.txt)" from_work_dir="classifier/tables/pathway_mapper_percentages.txt"/>
55 <data format="tabular" name="path_events_per_sample" label="${tool.name} on ${on_string} (path_events_per_sample.tsv)" from_work_dir="classifier/tables/path_events_per_sample.tsv"/>
56 </outputs>
57 <tests>
58 <test>
59 <param name="classifier_decisions" value="classifier_decisions.tsv" ftype="tabular"/>
60 <param name="x_matrix" value="pancan_rnaseq_freeze_t1p.tsv.gz" ftype="tabular"/>
61 <param name="genes" value="ERBB2,KRAS,PIK3CA,AKT1"/>
62 <param name="path_genes" value="path_genes.txt" ftype="txt"/>
63 <param name="pathway_metrics_pathwaymapper" value="pathway_metrics_pathwaymapper.txt" ftype="txt"/>
64 <param name="all_gene_metric_ranks" value="all_gene_metric_ranks.tsv" ftype="tabular"/>
65 <param name="filename_mut" value="pancan_mutation_freeze_t1p.tsv.gz" ftype="tabular"/>
66 <param name="filename_sample" value="sample_freeze.tsv" ftype="tabular"/>
67 <param name="copy_number" value="yes"/>
68 <param name="filename_copy_loss" value="copy_number_loss_status_t10p.tsv.gz" ftype="tabular" />
69 <param name="filename_copy_gain" value="copy_number_gain_status_t10p.tsv.gz" ftype="tabular" />
70 <param name="filename_cancer_gene_classification" value="cosmic_cancer_classification.tsv" ftype="tabular" />
71 <output name="log" file="pathway_count_heatmaps_Log.txt"/>
72 <output name="cancer_type_mutation_heatmap" file="cancer_type_mutation_heatmap.pdf" compare="sim_size" delta="50"/>
73 <output name="cancer_type_copy_number_heatmap" file="cancer_type_copy_number_heatmap.pdf" compare="sim_size" delta="50"/>
74 <output name="cancer_type_combined_total_heatmap" file="cancer_type_combined_total_heatmap.pdf" compare="sim_size" delta="50"/>
75 <output name="pathway_mapper_percentages" file="pathway_mapper_percentages.txt" />
76 <output name="path_events_per_sample" file="path_events_per_sample.tsv" />
77 </test>
78 </tests>
79 <help><![CDATA[
80
81 **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_targene_pathway_count_heatmaps.py:**
82
83 **Inputs:**
84 --genes comma separated string of HUGO symbols for target genes or targenes_list.csv file
85 --path_genes comma separated string of HUGO symbols for all genes in the target pathway or path_genes.txt file
86 --classifier_decisions String of the location of classifier scores/alt_folder
87 --x_matrix Filename of features to use in model
88 --filename_mut Filename of sample/gene mutations to use in model
89 --filename_mut_burden Filename of sample mutation burden to use in model
90 --filename_sample Filename of patient/samples to use in model
91 --filename_copy_loss Filename of copy number loss
92 --filename_copy_gain Filename of copy number gain
93 --filename_cancer_gene_classification Filename of cancer gene classification table
94
95 **Outputs:**
96 Mutational count heatmap for all genes in the target pathway with in each cancer type (cancer_type_mutation_heatmap.pdf)
97
98 Copy number count heatmap for all genes in the target pathway with in each cancer type (cancer_type_copy_number_heatmap.pdf)
99
100 Combined count heatmap for all genes in the target pathway with in each cancer type (cancer_type_combined_total_heatmap.pdf)
101
102 Calculates Mutations and copy number percentages of the genes in the pathway and generates "pathway_mapper_percentages.txt" file
103
104 Summarizes mutation, copy, and total counts per sample by targene pathway and generates "path_events_per_sample.tsv" file ]]>
105 </help>
106 <expand macro="citations" />
107 </tool>