annotate macros.xml @ 0:99d944bfe9b3 draft default tip

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

<macros>
    <token name="@VERSION@">0.1.9</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">papaa</requirement>
        </requirements>
    </xml>

    <xml name="stdio">
        <stdio>
             <exit_code level="fatal" range="1:"/>
        </stdio>
    </xml>

    <xml name="inputs_basic">
        <param argument="--x_matrix" label="Filename of features to use in model" name="x_matrix" optional="true" type="data" format="tabular" help="data/pancan_rnaseq_freeze.tsv.gz"/>
        <yield/>
        <param argument="--filename_mut" label="Filename mutations" name="filename_mut" optional="true" type="data" format="tabular" help="data/pancan_mutation_freeze.tsv.gz"/>
        <param argument="--filename_mut_burden" label="Filename of mutation burden" name="filename_mut_burden" optional="true" type="data" format="tabular" help="data/mutation_burden_freeze.tsv"/>
        <param argument="--filename_sample" label="Filename of sample" name="filename_sample" optional="true" type="data" format="tabular" help="data/sample_freeze.tsv"/>
    </xml>

    <token name="@INPUTS_BASIC@"><![CDATA[
        #if $x_matrix and $x_matrix is not None:
        --x_matrix '$x_matrix'
        #end if
        #if $filename_mut and $filename_mut is not None:
        --filename_mut '$filename_mut'
        #end if
        #if $filename_mut_burden and $filename_mut_burden is not None:
        --filename_mut_burden '$filename_mut_burden'
        #end if
        #if $filename_sample and $filename_sample is not None:
        --filename_sample '$filename_sample'
        #end if
        ]]>
    </token>

    <xml name="inputs_genes_diseases">
        <param argument="--genes" label="Comma separated string of HUGO gene symbols" name="genes" optional="False" type="text" value="ERBB2,PIK3CA,KRAS,AKT1"/>
        <param argument="--diseases" label="Comma sep string of TCGA disease acronyms. If no arguments are passed, filtering will default to options given in --filter_count and --filter_prop." name="diseases" optional="true" type="text" value="BLCA,BRCA,CESC,COAD,ESCA,LUAD,LUSC,OV,PRAD,READ,STAD,UCEC,UCS"/>
    </xml>

    <token name="@INPUTS_GENES_DISEASES@"><![CDATA[
        #if $genes and $genes is not None:
        --genes '$genes'
        #end if
        #if $diseases and str($diseases) != '':
        --diseases '$diseases'
        #end if
        ]]>
    </token>


    <xml name="input_filename_raw_mut">
        <param argument="--filename_raw_mut" label="Filename of raw mut MAF" name="filename_raw_mut" optional="true" type="data" format="tabular" help="data/raw/mc3.v0.2.8.PUBLIC.maf"/>
    </xml>

    <token name="@INPUT_FILENAME_RAW_MUT@"><![CDATA[
        #if $filename_raw_mut and $filename_raw_mut is not None:
        --filename_raw_mut '$filename_raw_mut'
        #end if
        ]]>
    </token>


    <xml name="input_filename_burden">
        <param argument="--filename_burden" label="Burden file" name="filename_burden" optional="true" type="data" format="tabular" help="data/seg_based_scores.tsv"/>
    </xml>

    <token name="@INPUT_FILENAME_BURDEN@"><![CDATA[
        #if $filename_burden and $filename_burden is not None:
        --filename_burden '$filename_burden'
        #end if
        ]]>        
    </token>

    <xml name="input_filename_snaptron_samples">
        <param argument="--sample_file" label="SNAPTRON samples" name="sample_file" optional="true" type="data" format="tabular" help="scripts/snaptron/samples.tsv.gz"/>
    </xml>

    <token name="@INPUT_FILENAME_SNAPTRON_SAMPLES@"><![CDATA[
        #if $sample_file and $sample_file is not None:
        --sample_file '$sample_file'
        #end if
        ]]>       
    </token>


    <xml name="input_filename_snaptron_junctions">
        <param argument="--junction_file" label="SNAPTRON junctions" name="junction_file" optional="true" type="data" format="tabular" help="scripts/snaptron/tp53_junctions.txt.gz"/>
    </xml>

    <token name="@INPUT_FILENAME_SNAPTRON_JUNCTIONS@"><![CDATA[
        #if $junction_file and $junction_file is not None:
        --junction_file '$junction_file'
        #end if
        ]]>    
    </token>

    <xml name="inputs_copy_number_file">
        <param argument="--filename_copy_loss" label="File with Copy number loss" name="filename_copy_loss" optional="true" type="data" format="tabular" help="data/copy_number_loss_status.tsv.gz"/>
        <param argument="--filename_copy_gain" label="File with Copy number gain" name="filename_copy_gain" optional="true" type="data" format="tabular" help="data/copy_number_gain_status.tsv.gz"/>
    </xml>

    <xml name="inputs_copy_number_class_file">
        <expand macro="inputs_copy_number_file" />
        <param argument="--filename_cancer_gene_classification" label="File with cancer gene classification table" name="filename_cancer_gene_classification" optional="true" type="data" format="tabular" help="data/cosmic_cancer_classification.tsv"/>
    </xml>

    <xml name="inputs_copy_number_file_conditional">
        <conditional name="copy_number_conditional">
          <param argument="--copy_number" checked="false" label="Supplement Y matrix with copy number events" name="copy_number" type="boolean" truevalue="--copy_number" falsevalue=""/>
          <when value="--copy_number">
            <expand macro="inputs_copy_number_file" />
          </when>
          <when value=""/>
        </conditional>
    </xml>

    <xml name="inputs_copy_number_class_file_conditional">
        <conditional name="copy_number_conditional">
          <param argument="--copy_number" checked="false" label="Supplement Y matrix with copy number events" name="copy_number" type="boolean" truevalue="--copy_number" falsevalue=""/>
          <when value="--copy_number">
            <expand macro="inputs_copy_number_class_file" />
          </when>
          <when value=""/>
        </conditional>
    </xml>

    <token name="@INPUTS_COPY_NUMBER_FILE_PREFIX@"><![CDATA[
        #set $copy_number_conditional = type('',(object,),{'filename_copy_loss':$filename_copy_loss,'filename_copy_gain':$filename_copy_gain})()
                ]]>
    </token>

    <token name="@INPUTS_COPY_NUMBER_FILE@"><![CDATA[
        #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
        --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
        #end if
        #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
        --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
        #end if
        ]]>
    </token>
    
    <token name="@INPUTS_COPY_NUMBER_FILE_CONDITIONAL@"><![CDATA[
        #if $copy_number_conditional.copy_number
        $copy_number_conditional.copy_number
        #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
        --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
        #end if
        #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
        --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
        #end if
        ##@INPUTS_COPY_NUMBER_FILE@
        #end if
        ]]>
    </token>

    <token name="@INPUTS_COPY_NUMBER_CLASS_FILE_PREFIX@"><![CDATA[
        #set $copy_number_conditional = type('',(object,),{'filename_copy_loss':$filename_copy_loss,'filename_copy_gain':$filename_copy_gain,'filename_cancer_gene_classification':$filename_cancer_gene_classification})()
        ]]>
    </token>

    <token name="@INPUTS_COPY_NUMBER_CLASS_FILE@"><![CDATA[
        #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
        --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
        #end if
        #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
        --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
        #end if
        #if $copy_number_conditional.filename_cancer_gene_classification and $copy_number_conditional.filename_cancer_gene_classification is not None:
        --filename_cancer_gene_classification '$copy_number_conditional.filename_cancer_gene_classification'
        #end if
        ]]>
    </token>
    
    <token name="@INPUTS_COPY_NUMBER_CLASS_FILE_CONDITIONAL@"><![CDATA[
        #if $copy_number_conditional.copy_number
        $copy_number_conditional.copy_number
        ##
        #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
        --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
        #end if
        #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
        --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
        #end if
        #if $copy_number_conditional.filename_cancer_gene_classification and $copy_number_conditional.filename_cancer_gene_classification is not None:
        --filename_cancer_gene_classification '$copy_number_conditional.filename_cancer_gene_classification'
        #end if
        ##@INPUTS_COPY_NUMBER_CLASS_FILE@
        #end if
        ]]> 
    </token>

    <xml name="input_remove_hyper">
        <param argument="--remove_hyper" checked="false" label="Remove hypermutated samples" name="remove_hyper" type="boolean" truevalue="--remove_hyper" falsevalue=""/>
    </xml>
    <token name="@INPUT_REMOVE_HYPER@"><![CDATA[$remove_hyper]]></token>
       
    <xml name="input_alphas">
        <param argument="--alphas" label="the alphas for parameter sweep" name="alphas" optional="true" type="text" value="0.1,0.13,0.15,0.18,0.2,0.3,0.4,0.6,0.7"/>
    </xml>

    <token name="@INPUTS_ALPHAS@"><![CDATA[
        #if $alphas and $alphas is not None:
        --alphas '$alphas'
        #end if
        ]]>
    </token>

    <xml name="input_l1_ratios">
        <param argument="--l1_ratios" label="the l1 ratios for parameter sweep" name="l1_ratios" optional="true" type="text" value="0.1,0.125,0.15,0.2,0.25,0.3,0.35"/>
    </xml>

    <token name="@INPUTS_L1_RATIOS@"><![CDATA[
        #if $l1_ratios and $l1_ratios is not None:
        --l1_ratios '$l1_ratios'
        #end if
        ]]>
    </token>
    <xml name="citations">
        <citations>
            <yield />
        </citations>
    </xml>
</macros>