<tool id="pancancer_external_sample_status_prediction" name="PAPAA: PanCancer external sample status prediction" version="@VERSION@">
    <description>external sample status</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <version_command><![CDATA['papaa_external_sample_pred_targene_classifier.py' --version]]></version_command>
    <command><![CDATA[
        mkdir 'classifier' &&
        mkdir -p 'classifier/figures' &&
        ln -s '${classifier_summary}' 'classifier/classifier_summary.txt' &&
        ln -s '${pancan_classifier_coefficients}' 'classifier/classifier_coefficients.tsv' &&
        papaa_external_sample_pred_targene_classifier.py
        --classifier_summary 'classifier'
        #if $ex_vlog and str($ex_vlog):
        --expression_file '$ex_vlog'
        #end if
        #if $sign and str($sign):
        --status_sign '$sign'
        #end if
        --figure1 '${figure1}'
        --figure2 '${figure2}'
        > '${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="--expression_file" label="external sample gene expression data" name="ex_vlog" optional="false" type="data" format="csv" help="data/vlog_trans.csv" />
        <param argument="--status_sign" label="given mutational status" name="sign" optional="false" type="data" format="txt" help="data/sign.txt" />
    </inputs>
    <outputs>
        <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)" />
        <data format="pdf" name="figure1" label="${tool.name} on ${on_string} (Figure 1)" />
        <data format="pdf" name="figure2" label="${tool.name} on ${on_string} (Figure 2)" />
    </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="ex_vlog" value="vlog_trans.csv.gz" ftype="csv"/>
          <param name="sign" value="sign.txt" ftype="txt"/>
          <output name="log" file="external_sample_status_prediction_Log.txt" />
          <output name="figure1" file="Figure_1.pdf" compare="sim_size" delta="50"/>
          <output name="figure2" file="Figure_2.pdf" compare="sim_size" delta="50"/>
        </test>
    </tests>
    <help><![CDATA[

      **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_external_sample_pred_targene_classifier.py:**
        
        **Inputs:**
          --classifier_summary  String of the location of classifier scores file

          --expression_file   File path for external sample expression data file (fpkm/rpkm/rlog/vlog/nlog values)

          --status_sign   Provide sign for tumor/mutant [1] or normal/WT [-1] along with sorted sample names
      
        **Outputs:**
          Model based classification scores distribution Plots for external normal and tumor samples   ("targene_external_sample_predictions.pdf and targene_external_sample_predictions_1.pdf")  ]]>
      
    </help>
    <expand macro="citations" />
</tool>