Mercurial > repos > vijay > pancancer_targene_summary_figures

diff targene_summary_figures.xml @ 0:d533f991e22e 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 23:32:26 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/targene_summary_figures.xml	Wed Dec 16 23:32:26 2020 +0000
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+<tool id="pancancer_targene_summary_figures" name="PAPAA: PanCancer targene summary figures" version="@VERSION@">
+  <description>Visualize targene summary</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <version_command><![CDATA['papaa_targene_summary_figures.R' --version 2>&1 | grep PAPAA]]></version_command>
+  <command><![CDATA[
+    mkdir 'classifier' &&
+    mkdir -p 'classifier/figures' && 
+    mkdir -p 'classifier/tables' &&
+        ln -s '${classifier_summary}' 'classifier/classifier_summary.txt' &&
+        ln -s '${pancan_classifier_coefficients}' 'classifier/classifier_coefficients.tsv' &&
+        ln -s '${summary_counts}' 'classifier/summary_counts.csv' &&
+        ln -s '${mutation_classification_scores}' 'classifier/tables/mutation_classification_scores.tsv' &&
+        ln -s '${path_events_per_sample}' 'classifier/tables/path_events_per_sample.tsv' &&
+        ln -s '${all_gene_metric_ranks}' 'classifier/tables/all_gene_metric_ranks.tsv' &&
+    papaa_targene_summary_figures.R
+    --classifier_summary 'classifier'
+    #if $seed and $seed is not None:
+    --seed '$seed'
+    #end if
+    > '${log}'
+    ]]>
+  </command>
+  <inputs>
+    <param argument="--classifier_summary" label="Classifier data" name="classifier_summary" optional="false" type="data" format="txt" help="classifer_summary.txt"/>
+    <param label="pancancer classifier coefficients" name="pancan_classifier_coefficients" optional="false" type="data" format="tabular" help="classifier_coefficients.tsv"/>
+    <param argument="--seed" label="option to set seed" name="seed" optional="true" type="integer" value="123"/>
+    <param label="summary counts" name="summary_counts" optional="false" type="data" format="csv" help="summary_counts.csv"/>
+    <param label="mutation classification scores" name="mutation_classification_scores" optional="false" type="data" format="tabular" help="mutation_classification_scores.tsv"/>
+    <param label="path events per sample" name="path_events_per_sample" optional="false" type="data" format="tabular" help="path_events_per_sample.tsv"/>
+    <param label="all gene metric ranks" name="all_gene_metric_ranks" optional="false" type="data" format="tabular" help="all_gene_metric_ranks.tsv"/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/>
+    <data format="pdf" name="targene_heatmap" label="${tool.name} on ${on_string} (targene_heatmap.pdf)" from_work_dir="classifier/figures/targene_heatmap.pdf"/>
+    <data format="pdf" name="all_targene_heatmap" label="${tool.name} on ${on_string} (all_targene_heatmap.pdf)" from_work_dir="classifier/figures/all_targene_heatmap.pdf"/>
+    <data format="pdf" name="targene_coef_plot" label="${tool.name} on ${on_string} (targene_coef_plot.pdf)" from_work_dir="classifier/figures/targene_coef_plot.pdf"/>
+    <data format="pdf" name="variant_OG_fill_map" label="${tool.name} on ${on_string} (variant_OG_fill_map.pdf)" from_work_dir="classifier/figures/variant_OG_fill_map.pdf"/>
+    <data format="pdf" name="variant_TSG_fill_map" label="${tool.name} on ${on_string} (variant_TSG_fill_map.pdf)" from_work_dir="classifier/figures/variant_TSG_fill_map.pdf"/>
+    <data format="pdf" name="aupr_distribution" label="${tool.name} on ${on_string} (aupr_distribution.pdf)" from_work_dir="classifier/figures/aupr_distribution.pdf"/>
+    <data format="pdf" name="auroc_distribution" label="${tool.name} on ${on_string} (auroc_distribution.pdf)" from_work_dir="classifier/figures/auroc_distribution.pdf"/>
+    <data format="pdf" name="targene_pathway_events_counts" label="${tool.name} on ${on_string} (targene_pathway_events_counts.pdf)" from_work_dir="classifier/figures/targene_pathway_events_counts.pdf"/>
+    <data format="txt" name="targene_pathway_variant_AUPR_ttest" label="${tool.name} on ${on_string} (targene_pathway_variant_AUPR_ttest.txt)" from_work_dir="classifier/tables/targene_pathway_variant_AUPR_ttest.txt"/>
+    <data format="tabular" name="amino_acid_mutation_scores" label="${tool.name} on ${on_string} (amino_acid_mutation_scores.tsv)" from_work_dir="classifier/tables/amino_acid_mutation_scores.tsv"/>
+    <data format="tabular" name="nucleotide_mutation_scores" label="${tool.name} on ${on_string} (nucleotide_mutation_scores.tsv)" from_work_dir="classifier/tables/nucleotide_mutation_scores.tsv"/>
+  </outputs>
+  <tests>
+        <test>
+          <param name="classifier_summary" value="classifier_summary.txt" ftype="txt"/>
+          <param name="pancan_classifier_coefficients" value="classifier_coefficients.tsv" ftype="tabular"/>
+          <param name="summary_counts" value="summary_counts.csv" ftype="csv"/>
+          <param name="all_gene_metric_ranks" value="all_gene_metric_ranks.tsv" ftype="tabular"/>
+          <param name="mutation_classification_scores" value="mutation_classification_scores.tsv" ftype="tabular"/>
+          <param name="path_events_per_sample" value="path_events_per_sample.tsv" ftype="tabular"/>
+          <param name="all_gene_metric_ranks" value="all_gene_metric_ranks.tsv" ftype="tabular"/>
+          <output name="log" file="targene_summary_figures_Log.txt"/>
+          <output name="targene_heatmap" file="targene_heatmap.pdf" compare="sim_size" delta="50"/>
+          <output name="all_targene_heatmap" file="all_targene_heatmap.pdf" compare="sim_size" delta="50"/>
+          <output name="targene_coef_plot" file="targene_coef_plot.pdf" compare="sim_size" delta="50"/>
+          <output name="variant_OG_fill_map" file="variant_OG_fill_map.pdf" compare="sim_size" delta="50"/>
+          <output name="aupr_distribution" file="aupr_distribution.pdf" compare="sim_size" delta="50"/>
+          <output name="variant_TSG_fill_map" file="variant_TSG_fill_map.pdf" compare="sim_size" delta="50"/>
+          <output name="auroc_distribution" file="auroc_distribution.pdf" compare="sim_size" delta="50"/>
+          <output name="targene_pathway_events_counts" file="targene_pathway_events_counts.pdf" compare="sim_size" delta="50"/>
+          <output name="targene_pathway_variant_AUPR_ttest" file="targene_pathway_variant_AUPR_ttest.txt" compare="sim_size" delta="50"/>
+          <output name="amino_acid_mutation_scores" file="amino_acid_mutation_scores.tsv" compare="sim_size" delta="50"/>
+          <output name="nucleotide_mutation_scores" file="nucleotide_mutation_scores.tsv" compare="sim_size" delta="50"/>
+        </test>
+    </tests>
+  <help><![CDATA[
+    **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_targene_summary_figures.R:**
+
+      **Inputs:**
+          --classifier_summary   String of the location of classifier data
+          --seed  value specifies the initial value of the random number seed default: 1234
+      
+      **Outputs:**
+          Heatmap for mutation and gain proportions for the genes used in model across all the TCGA cancer types (all_targene_heatmap.pdf)
+
+          Heatmap for total mutation and total gain proportions for the genes used in model across all the TCGA cancer types (targene_heatmap.pdf")
+
+          Gene weights/Coefficients contributing to the model (targene_coef_plot.pdf)  
+
+          Plot distributions of predictions according to variant classification for OG and TSG ("variant_OG_fill_map.pdf" and "variant_TSG_fill_map.pdf")  
+
+          Targene pathway events counts ("targene_pathway_events_counts.pdf")  
+
+          Performance Metrics Distribution across pathway members ("aupr_distribution.pdf" and "auroc_distribution.pdf")
+          T-Test for AUPR between targene pathway genes and Other genes ("targene_pathway_variant_AUPR_ttest.txt") 
+
+          Extracting sample classifier scores for nucleotide level alterations in each sample and generate "nucleotide_mutation_scores.tsv" file
+
+          Extracting sample classifier scores for amino-acid level alterations in each sample and generate "amino_acid_mutation_scores.tsv" file ]]>
+    </help>
+    <expand macro="citations" />
+</tool>