annotate targene_pharmacology.xml @ 0:aa5e0e353148 draft default tip

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

<tool id="pancancer_targene_pharmacology" name="PAPAA: PanCancer targene pharmacology" version="@VERSION@">
    <description>ccle pharmocology predictions </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <version_command><![CDATA['papaa_targene_pharmacology.R' --version 2>&1 | grep PAPAA]]></version_command>
    <command><![CDATA[
        mkdir 'classifier' &&
        mkdir -p 'classifier/figures' &&
        mkdir -p 'classifier/figures/cell_line' && 
        mkdir -p 'classifier/tables' && 
        ln -s '${gdsc1_targene_pharmacology_predictions}' 'classifier/tables/gdsc1_targene_pharmacology_predictions.tsv' &&
        ln -s '${gdsc2_targene_pharmacology_predictions}' 'classifier/tables/gdsc2_targene_pharmacology_predictions.tsv' &&
        ln -s '${gdsc1_ccle_targene_pharmacology_predictions}' 'classifier/tables/gdsc1_ccle_targene_pharmacology_predictions.tsv' &&
        ln -s '${gdsc2_ccle_targene_pharmacology_predictions}' 'classifier/tables/gdsc2_ccle_targene_pharmacology_predictions.tsv' &&
        papaa_targene_pharmacology.R
        --classifier_results 'classifier'
        #if $compound and str($compound):
        --compound '$compound'
        #end if
        > '${log}'
        ]]>
    </command>
    <inputs>
        <param label="gdsc1 targene pharmacology predictions" name="gdsc1_targene_pharmacology_predictions" optional="false" type="data" format="tabular" help="gdsc1_targene_pharmacology_predictions.tsv"/>
        <param label="gdsc2 targene pharmacology predictions" name="gdsc2_targene_pharmacology_predictions" optional="false" type="data" format="tabular" help="gdsc2_targene_pharmacology_predictions.tsv"/>
        <param label="gdsc1 ccle targene pharmacology predictions" name="gdsc1_ccle_targene_pharmacology_predictions" optional="false" type="data" format="tabular" help="gdsc1_ccle_targene_pharmacology_predictions.tsv"/>
        <param label="gdsc2 ccle targene pharmacology predictions" name="gdsc2_ccle_targene_pharmacology_predictions" optional="false" type="data" format="tabular" help="gdsc2_ccle_targene_pharmacology_predictions.tsv"/>
        <param argument="--compound" label="Filename list of compounds" name="compound" optional="false" type="data" format="txt" help="data/compounds_of_interest.txt"/>
    </inputs>
    <outputs>
        <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/>
        <data format="pdf" name="GDSC1_targene_all_drug_response" label="${tool.name} on ${on_string} (GDSC1_targene_all_drug_response.pdf)" from_work_dir="classifier/figures/cell_line/GDSC1_targene_all_drug_response.pdf"/>
        <data format="pdf" name="GDSC2_targene_all_drug_response" label="${tool.name} on ${on_string} (GDSC2_targene_all_drug_response.pdf)" from_work_dir="classifier/figures/cell_line/GDSC2_targene_all_drug_response.pdf"/>
        <data format="pdf" name="GDSC1_ccle_targene_all_drug_response" label="${tool.name} on ${on_string} (GDSC1_ccle_targene_all_drug_response.pdf)" from_work_dir="classifier/figures/cell_line/GDSC1_ccle_targene_all_drug_response.pdf"/>
        <data format="pdf" name="GDSC2_ccle_targene_all_drug_response" label="${tool.name} on ${on_string} (GDSC2_ccle_targene_all_drug_response.pdf)" from_work_dir="classifier/figures/cell_line/GDSC2_ccle_targene_all_drug_response.pdf"/>
    </outputs>
    <tests>
        <test>
          <param name="compound" value="compounds_of_interest.txt" ftype="txt"/>
          <param name="gdsc1_targene_pharmacology_predictions" value="gdsc1_targene_pharmacology_predictions.tsv" ftype="tabular"/>
          <param name="gdsc2_targene_pharmacology_predictions" value="gdsc2_targene_pharmacology_predictions.tsv" ftype="tabular"/>
          <param name="gdsc1_ccle_targene_pharmacology_predictions" value="gdsc1_ccle_targene_pharmacology_predictions.tsv" ftype="tabular"/>
          <param name="gdsc2_ccle_targene_pharmacology_predictions" value="gdsc2_ccle_targene_pharmacology_predictions.tsv" ftype="tabular"/>
          <output name="log" file="targene_pharmacology_Log.txt"/>
          <output name="GDSC1_targene_all_drug_response" file="GDSC1_targene_all_drug_response.pdf" compare="sim_size" delta="50"/>
          <output name="GDSC2_targene_all_drug_response" file="GDSC2_targene_all_drug_response.pdf" compare="sim_size" delta="50"/>
          <output name="GDSC1_ccle_targene_all_drug_response" file="GDSC1_ccle_targene_all_drug_response.pdf" compare="sim_size" delta="50"/>
          <output name="GDSC2_ccle_targene_all_drug_response" file="GDSC2_ccle_targene_all_drug_response.pdf" compare="sim_size" delta="50"/>
        </test>
    </tests>
    <help><![CDATA[
      **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/viz/papaa_targene_pharmacology.R:**

        **Inputs:**
          --classifier_results  String of the location of classifier results folder
          --compound  Filename of list of GDSC pharmacological compounds for evaluation

        **Outputs:**
          Scatter plots with visualizing drug response compared to GDSC targene classifier scores for GDSC1 pharmacological   dataset (GDSC1_targene_all_drug_response.pdf)  

          Scatter plots with visualizing drug response compared to CCLE targene classifier scores for GDSC1 pharmacological dataset (GDSC1_ccle_targene_all_drug_response.pdf)  

          Scatter plots with visualizing drug response compared to GDSC targene classifier scores for GDSC2 pharmacological dataset (GDSC2_targene_all_drug_response.pdf)  

          Scatter plots with visualizing drug response compared to CCLE targene classifier scores for GDSC2 pharmacological dataset (GDSC2_ccle_targene_all_drug_response.pdf) ]]>
    </help>
    <expand macro="citations" />
</tool>