annotate compare_within_models.xml @ 0:84ac2a86bde1 draft default tip

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

<tool id="pancancer_compare_within_models" name="PAPAA: PanCancer compare within models" version="@VERSION@">
    <description>compare within models</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <version_command><![CDATA['papaa_compare_within_models.R' --version 2>&1 | grep PAPAA]]></version_command>
    <command><![CDATA[
        mkdir 'classifier' &&
        mkdir -p 'classifier/figures' &&
        ln -s '${pancan_classifier_summary}' 'classifier/classifier_summary.txt' &&
        ln -s '${pancan_classifier_coefficients}' 'classifier/classifier_coefficients.tsv' &&
        #for $within_summary in $pancan_within_classifier_summary:
            mkdir -p 'classifier/within_disease/${within_summary.element_identifier}' &&
            ln -s '${within_summary}' 'classifier/within_disease/${within_summary.element_identifier}/classifier_summary.txt' &&
        #end for
        #for $within_coefficient in $pancan_within_classifier_coefficients:
            mkdir -p 'classifier/within_disease/${within_coefficient.element_identifier}' &&
            ln -s '${within_coefficient}' 'classifier/within_disease/${within_coefficient.element_identifier}/classifier_coefficients.tsv' &&
        #end for
        #if $include_alt.include_alt_select == 'true':
        mkdir 'alt_classifier' &&
        ln -s '${include_alt.alt_pancan_classifier_summary}' 'alt_classifier/classifier_summary.txt' &&
        ln -s '${include_alt.alt_pancan_classifier_coefficients}' 'alt_classifier/classifier_coefficients.tsv' &&
        #for $within_summary in $include_alt.alt_pancan_within_classifier_summary:
            mkdir -p 'alt_classifier/within_disease/${within_summary.element_identifier}' &&
            ln -s '${within_summary}' 'alt_classifier/within_disease/${within_summary.element_identifier}/classifier_summary.txt' &&
        #end for
        #for $within_coefficient in $include_alt.alt_pancan_within_classifier_coefficients:
            mkdir -p 'alt_classifier/within_disease/${within_coefficient.element_identifier}' &&
            ln -s '${within_coefficient}' 'alt_classifier/within_disease/${within_coefficient.element_identifier}/classifier_coefficients.tsv' &&
        #end for
        #end if
        ls -lahR &&
        papaa_compare_within_models.R
        --pancan_model 'classifier'
        #if $include_alt.include_alt_select == 'true':
        --alt_model 'alt_classifier'
        #end if
        > '${log}'
        ]]>
    </command>
    <inputs>
        <param argument="--pancan_model" label="pancancer classifier summary" name="pancan_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 label="pan_within classifier summary" name="pancan_within_classifier_summary" optional="false" type="data" format="txt" multiple="true" help="multiple classifer_summary.txt"/>
        <param label="pan_within classifier coefficients" name="pancan_within_classifier_coefficients" optional="false" type="data" format="tabular" multiple="true" help="multiple classifier_coefficients.tsv"/>
        <conditional name="include_alt">
          <param name="include_alt_select" type="select" label="Would you want to compare given model with alt gene model?" help="output of pancancer classifier and pancancer within disease for alt gene">
            <option value="false" selected="true">do not do alt gene</option>
            <option value="true">do alt gene</option>
          </param>
          <when value="true">
                <param argument="--alt_model" label="pancancer classifier summary" name="alt_pancan_classifier_summary" optional="false" type="data" format="txt" help="alt classifer_summary.txt"/>
                <param label="pancancer classifier coefficients" name="alt_pancan_classifier_coefficients" optional="false" type="data" format="tabular" help="alt classifier_coefficients.tsv"/>
                <param argument="pan_within classifier summary" label="alt_pancan_within_classifier_summary" name="alt_pancan_within_classifier_summary" optional="true" type="data" format="txt" multiple="true" help="multiple alt classifer_summary.txt"/>
                <param label="alt_pancan_within classifier coefficients" name="alt_pancan_within_classifier_coefficients" optional="true" type="data" format="tabular" multiple="true" help="multiple alt classifier_coefficients.tsv"/>
            </when>
            <when value="false">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)" />
        <data format="pdf" name="aupr_comparison" label="${tool.name} on ${on_string} (aupr_comparison.pdf)" from_work_dir="classifier/figures/aupr_comparison.pdf"/>
        <data format="pdf" name="auroc_comparison" label="${tool.name} on ${on_string} (auroc_comparison.pdf)" from_work_dir="classifier/figures/auroc_comparison.pdf"/>
        <data format="pdf" name="alt_gene_aupr_comparison" label="${tool.name} on ${on_string} (alt_gene_aupr_comparison.pdf)" from_work_dir="classifier/figures/alt_gene_aupr_comparison.pdf" >
          <filter>include_alt['include_alt_select'] == 'true' </filter> 
        </data>
        <data format="pdf" name="alt_gene_auroc_comparison" label="${tool.name} on ${on_string} (alt_gene_auroc_comparison.pdf)" from_work_dir="classifier/figures/alt_gene_auroc_comparison.pdf" >
          <filter>include_alt['include_alt_select'] == 'true' </filter> 
        </data>
    </outputs>
    <tests>
        <test>
            <param name="pancan_classifier_summary" value="classifier_summary.txt" ftype="txt"/>
            <param name="pancan_classifier_coefficients" value="classifier_coefficients.tsv" ftype="tabular"/>
            <param name="pancan_within_classifier_summary" value="classifier_summary/GBM" > <!--
                <collection type="list">
                    <element name="GBM" value="GBM_100.txt" ftype="txt"/>
                </collection> -->
            </param>
            <param name="pancan_within_classifier_coefficients" value="classifier_coefficients/GBM"> <!--
                <collection type="list">
                    <element name="GBM" value="GBM_99.tabular" ftype="tabular"/>
                </collection> -->
            </param>
            <param name="include_alt_select" value="false"/>
            <!--
            <conditional name="include_alt">
              <param name="include_alt_select" value="false"/>
                <param name="alt_pancan_summary" value="alt_pancan_summary.txt" ftype="txt"/>
                <param name="alt_pancan_classifier_coefficients" value="alt_pancan_classifier_coefficients.tsv" ftype="tabular"/>
                <param name="alt_pan_within_classifier_summary" value="alt_pan_within_classifier_summary.txt" ftype="txt"/>
                <param name="alt_pan_within_classifier_coefficients" value="alt_pan_within_classifier_coefficients.tsv" ftype="tabular"/> 
            </conditional>
            -->
            <output name="log" file="compare_within_models_Log.txt"/>
            <output name="aupr_comparison" file="aupr_comparison.pdf" compare="sim_size" delta="50"/>
            <output name="auroc_comparison" file="auroc_comparison.pdf" compare="sim_size" delta="50"/>

        </test>
    </tests>
    <help><![CDATA[

        **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_compare_within_models.R:**
            
            **Inputs:**
                --pancan_model      String of the Directory: location of Pan classifier summary file
                --alt_model         String of the Directory: location of Alt gene classifier summary file
            
            **Outputs:**
                Comparison plots for Pan and Pan_within models ("auroc_comparison.pdf" and "aupr_comparison.pdf")  

                Comparison plots for altgene, alt_within, Pan_alt models ("alt_gene_auroc_comparison.pdf" and "alt_gene_aupr_comparison.pdf")  ]]>
            
    </help>
    <expand macro="citations" />
</tool>