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
line wrap: on
line diff
--- /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