Mercurial > repos > vijay > pancancer_pathway_count_heatmaps
diff targene_pathway_count_heatmaps.xml @ 0:dc1d71493ebf draft default tip
"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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/targene_pathway_count_heatmaps.xml Wed Dec 16 23:29:47 2020 +0000 @@ -0,0 +1,107 @@ +<tool id="pancancer_pathway_count_heatmaps" name="PAPAA: PanCancer pathway count heatmaps" version="@VERSION@"> + <description>pathway count heatmaps</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <version_command><![CDATA['papaa_targene_pathway_count_heatmaps.py' --version]]></version_command> + <command><![CDATA[ + mkdir 'classifier' && + mkdir -p 'classifier/tables' && + ln -s '${classifier_decisions}' 'classifier/classifier_decisions.tsv' && + ln -s '${pathway_metrics}' 'classifier/tables/pathway_metrics_pathwaymapper.txt' && + ln -s '${all_gene_metric_ranks}' 'classifier/tables/all_gene_metric_ranks.tsv' && + papaa_targene_pathway_count_heatmaps.py + --classifier_decisions 'classifier' + #if $genes and str($genes): + --genes '$genes' + #end if + #if $path_genes and str($path_genes): + --path_genes '$path_genes' + #end if + @INPUTS_BASIC@ + #if $filename_copy_loss and $filename_copy_loss is not None: + --filename_copy_loss '$filename_copy_loss' + #end if + #if $filename_copy_gain and $filename_copy_gain is not None: + --filename_copy_gain '$filename_copy_gain' + #end if + #if $filename_cancer_gene_classification and $filename_cancer_gene_classification is not None: + --filename_cancer_gene_classification '$filename_cancer_gene_classification' + #end if + > '${log}' + ]]> + </command> + <inputs> + <param argument="--classifier_decisions" label="pancancer decisions" name="classifier_decisions" optional="false" type="data" format="tabular" help="classifier_decisions.tsv"/> + <param label="pancancer metrics pathwaymapper" name="pathway_metrics" optional="false" type="data" format="txt" help="pathway_metrics_pathwaymapper.txt"/> + <param label="all gene metric ranks" name="all_gene_metric_ranks" optional="false" type="data" format="tabular" help="all_gene_metric_ranks.tsv"/> + <param argument="--genes" label="Comma separated string of HUGO gene symbols" name="genes" optional="False" type="text" value="ERBB2,PIK3CA,KRAS,AKT1"/> + <param argument="--path_genes" label="String of the pathway genes to extract" name="path_genes" optional="true" type= "data" format="txt"/> + <expand macro="inputs_basic"/> + <param argument="--filename_mut" label="Filename mutations" name="filename_mut" optional="true" type="data" format="tabular" help="data/pancan_mutation_freeze.tsv"/> + <param argument="--filename_sample" label="Filename of sample" name="filename_sample" optional="true" type="data" format="tabular" help="data/sample_freeze.tsv"/> + <param argument="--filename_copy_loss" label="File with Copy number loss" name="filename_copy_loss" optional="false" type="data" format="tabular" help="data/copy_number_loss_status.tsv"/> + <param argument="--filename_copy_gain" label="File with Copy number gain" name="filename_copy_gain" optional="false" type="data" format="tabular" help="data/copy_number_gain_status.tsv"/> + <param argument="--filename_cancer_gene_classification" label="File with cancer gene classification table" name="filename_cancer_gene_classification" optional="false" type="data" format="tabular" help="data/cosmic_cancer_classification.tsv"/> + </inputs> + <outputs> + <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/> + <data format="pdf" name="cancer_type_mutation_heatmap" label="${tool.name} on ${on_string} (cancer_type_mutation_heatmap.pdf)" from_work_dir="classifier/cancer_type_mutation_heatmap.pdf"/> + <data format="pdf" name="cancer_type_copy_number_heatmap" label="${tool.name} on ${on_string} (cancer_type_copy_number_heatmap.pdf)" from_work_dir="classifier/cancer_type_copy_number_heatmap.pdf"/> + <data format="pdf" name="cancer_type_combined_total_heatmap" label="${tool.name} on ${on_string} (cancer_type_combined_total_heatmap.pdf)" from_work_dir="classifier/cancer_type_combined_total_heatmap.pdf"/> + <data format="txt" name="pathway_mapper_percentages" label="${tool.name} on ${on_string} (pathway_mapper_percentages.txt)" from_work_dir="classifier/tables/pathway_mapper_percentages.txt"/> + <data format="tabular" name="path_events_per_sample" label="${tool.name} on ${on_string} (path_events_per_sample.tsv)" from_work_dir="classifier/tables/path_events_per_sample.tsv"/> + </outputs> + <tests> + <test> + <param name="classifier_decisions" value="classifier_decisions.tsv" ftype="tabular"/> + <param name="x_matrix" value="pancan_rnaseq_freeze_t1p.tsv.gz" ftype="tabular"/> + <param name="genes" value="ERBB2,KRAS,PIK3CA,AKT1"/> + <param name="path_genes" value="path_genes.txt" ftype="txt"/> + <param name="pathway_metrics_pathwaymapper" value="pathway_metrics_pathwaymapper.txt" ftype="txt"/> + <param name="all_gene_metric_ranks" value="all_gene_metric_ranks.tsv" ftype="tabular"/> + <param name="filename_mut" value="pancan_mutation_freeze_t1p.tsv.gz" ftype="tabular"/> + <param name="filename_sample" value="sample_freeze.tsv" ftype="tabular"/> + <param name="copy_number" value="yes"/> + <param name="filename_copy_loss" value="copy_number_loss_status_t10p.tsv.gz" ftype="tabular" /> + <param name="filename_copy_gain" value="copy_number_gain_status_t10p.tsv.gz" ftype="tabular" /> + <param name="filename_cancer_gene_classification" value="cosmic_cancer_classification.tsv" ftype="tabular" /> + <output name="log" file="pathway_count_heatmaps_Log.txt"/> + <output name="cancer_type_mutation_heatmap" file="cancer_type_mutation_heatmap.pdf" compare="sim_size" delta="50"/> + <output name="cancer_type_copy_number_heatmap" file="cancer_type_copy_number_heatmap.pdf" compare="sim_size" delta="50"/> + <output name="cancer_type_combined_total_heatmap" file="cancer_type_combined_total_heatmap.pdf" compare="sim_size" delta="50"/> + <output name="pathway_mapper_percentages" file="pathway_mapper_percentages.txt" /> + <output name="path_events_per_sample" file="path_events_per_sample.tsv" /> + </test> + </tests> + <help><![CDATA[ + + **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_targene_pathway_count_heatmaps.py:** + + **Inputs:** + --genes comma separated string of HUGO symbols for target genes or targenes_list.csv file + --path_genes comma separated string of HUGO symbols for all genes in the target pathway or path_genes.txt file + --classifier_decisions String of the location of classifier scores/alt_folder + --x_matrix Filename of features to use in model + --filename_mut Filename of sample/gene mutations to use in model + --filename_mut_burden Filename of sample mutation burden to use in model + --filename_sample Filename of patient/samples to use in model + --filename_copy_loss Filename of copy number loss + --filename_copy_gain Filename of copy number gain + --filename_cancer_gene_classification Filename of cancer gene classification table + + **Outputs:** + Mutational count heatmap for all genes in the target pathway with in each cancer type (cancer_type_mutation_heatmap.pdf) + + Copy number count heatmap for all genes in the target pathway with in each cancer type (cancer_type_copy_number_heatmap.pdf) + + Combined count heatmap for all genes in the target pathway with in each cancer type (cancer_type_combined_total_heatmap.pdf) + + Calculates Mutations and copy number percentages of the genes in the pathway and generates "pathway_mapper_percentages.txt" file + + Summarizes mutation, copy, and total counts per sample by targene pathway and generates "path_events_per_sample.tsv" file ]]> + </help> + <expand macro="citations" /> +</tool> \ No newline at end of file