annotate targene_pathway_count_heatmaps.xml @ 0:dc1d71493ebf draft default tip

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

<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>