annotate targene_summary_figures.xml @ 0:d533f991e22e draft default tip

"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"

<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>