<macros>
    <macro name="requirements">
        <requirements>
            <requirement type="package" version="1.0.7">beta</requirement>
        </requirements>
    </macro>
    <token name="@VERSION@">1.0.7</token>
    <macro name="stdio">
        <stdio>
                <exit_code range=":-1"    level="fatal" description="Error: Cannot open file" />
                <exit_code range="1:"    level="fatal" description="Error" />
        </stdio>
    </macro>

    <macro name="common_params">
        <param format="bed" name="peakfile" type="data" label="BED file for Peaks">
            <validator type="unspecified_build" />
        </param>
        <param name="output_dir" type="hidden" label="Name for the output files" value="BETA_OUTPUT"/>
        <param name="name" type="hidden" label="Name for the output files" value="NA"/>
        <param name="distance" type="integer" label="the distance from gene TSS within which peaks will be selected" value="100000">
            <validator type="in_range" max="20000000" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 20000000" />
        </param>
        <param name="peaknumber" type="integer" label="Peaks considered to contribute to the genes" value="10000">
            <validator type="in_range" max="200000" min="100" message="The Relative distance is out of range, the parameter has to be between 100 to 10000" />
        </param>
    </macro>

    <macro name="boundary">
        <conditional name="boundary">
            <param name="boundaryLimit" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Use CTCF boundary to filter peaks around a gene"/>
            <when value="no"/>
            <when value="yes">
                <yield />
            </when>
        </conditional>
    </macro>

    <macro name="genome_params">
        <conditional name="refGenome">
            <param name="genomeName" type="select" label="genome reference">
                <option value="hg19">hg19 (built-in)</option>
                <option value="mm9">mm9 (built-in)</option>
                <option value="other">other</option>
            </param>
            <when value="hg19">
                <expand macro="boundary" />
            </when>
            <when value="mm9">
                <expand macro="boundary" />
            </when>
            <when value="other">
                <param name="refseq" type="data" format="tabular" label="UCSC Refseq Genes (From UCSC Table Browser)"
                 help="Columns: name,chrom,strand,txStart,txEnd,name"/>
                <expand macro="boundary">
                <param name="bl_bed" type="data" format="bed" label="BED format boundary file"/>
                </expand>
            </when>
        </conditional>
    </macro>

    <macro name="refGenomeSourceConditional">
        <conditional name="refGenomeSource">
            <param name="genomeSource" type="select" label="Use a built in reference genome or one from your history" help="Genome Reference Fasta sequence">
                <option value="cached" selected="True">Use a built-in genome</option>
                <option value="history">Use a genome from history</option>
            </param>
            <when value="cached">
                <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
                    <options from_data_table="all_fasta"/>
                </param>
            </when>
            <when value="history">
                <param name="ownFile" type="data" format="fasta" label="Select the reference genome" />
            </when>    <!-- history -->
        </conditional>    <!-- refGenomeSource -->
    </macro>

    <macro name="extended_params">
        <param format="txt" name="exprefile" type="data" label="TEXT file for differential expression data">
            <validator type="unspecified_build" />
        </param>
        <conditional name="expression">
            <param name="kind" type="select" label="Expression FIle Type" help="Preset columns for Cuffdiff, LIMMA, and BETA Specific Format">
                <option value="CUF">RNA-seq data with Cuffdiff default format</option>
                <option value="LIM">MicroArray data with LIMMA default format</option>
                <option value="BSF">BETA Specific Format</option>
                <option value="O">Other tools processed data with BETA specific format</option>
            </param>
            <when value="CUF">
                <param name="expreinfo" type="text" value="2,10,13" label="Column number of the geneid, regulate status and statistics value"/>
            </when>
            <when value="LIM">
                <param name="expreinfo" type="text" value="2,5,7" label="Column number of the geneid, regulate status and statistics value"/>
            </when>
            <when value="BSF">
                <param name="expreinfo" type="text" value="1,2,3" label="Column number of the geneid, regulate status and statistics value"/>
            </when>
            <when value="O">
                <param name="expreinfo" type="text" value="" label="Column number of the geneid, regulate status and statistics value is required">
                    <validator type="regex" message="Enter column numbers:geneid,test_stat,value">^\d+,\d+,\d+$</validator>
                </param>
            </when>
        </conditional>
        <param name="gname2" type="select" label="TRUE if gene ID in expression file identified by official gene symbol">
            <option value="Refseq">Refseq</option>
            <option value="Gene_Symbol">Gene Symbol</option>
        </param>
        <param name="diff_fdr" type="float" label="get the most significant expression differentially changed genes by this cutoff based on fdr or pvalue" value="1.0">
            <validator type="in_range" max="1.0" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 1.0" />
        </param>
        <param name="diff_amount" type="float" label="get the most significant expression differentially changed genes by amount" value="0.5">
            <validator type="in_range" max="20000" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 20000" />
        </param>
        <param name="method" type="select" label="method to do the TF/CR function prediction">
            <option value="score">regulatory potential</option>
            <option value="distance">distance to the nearest peak</option>
        </param>
    </macro>

    <template name="common_opts">
        -p "$peakfile" 
        -d $distance --pn $peaknumber -o $output_dir -n $name
    </template>

    <template name="genome_opts">
        #if $refGenome.genomeName == 'hg19':
            -g $refGenome.genomeName
            ## -r \$BETA_LIB_PATH/BETA/references/hg19.refseq
            #if $refGenome.boundary.boundaryLimit: 
                --bl
                ## --bf \$BETA_LIB_PATH/BETA/references/hg19_CTCF_bound.bed
            #end if
        #elif $refGenome.genomeName == 'mm9':
            -g $refGenome.genomeName
            ## -r \$BETA_LIB_PATH/BETA/references/mm9.refseq
            #if $refGenome.boundary.boundaryLimit: 
                --bl
                ## --bf \$BETA_LIB_PATH/BETA/references/mm9_CTCF_bound.bed
            #end if
        #else
            -r    $refGenome.refseq
            #if $refGenome.boundary.boundaryLimit: 
                --bl 
                --bf $refGenome.boundary.bl_bed
            #end if
        #end if
    </template>
    <template name="ref_genome_seq_opts">
        #if $refGenomeSource.genomeSource == 'cached':
            --gs $refGenomeSource.all_fasta_source.fields.path
        #else
            --gs $refGenomeSource.ownFile
        #end if
    </template>

    <template name="extended_opts">
        -e "$exprefile"
        -k $expression.kind --info $expression.expreinfo --method $method
        --da $diff_amount --df $diff_fdr -c 1
        #if $gname2 == "Gene_Symbol":
            --gname2"
        #end if
    </template>
    <template name="write_log">
        | tee $log | grep 'total time' > /dev/null
    </template>

    <token name="@EXTERNAL_DOCUMENTATION@">

For details about this application, please go to:
                http://cistrome.org/BETA/index.html

    </token>
    <token name="@CITATION_SECTION@">

**Citation**

For the underlying tool, please cite the following publication:
Wang, S., Sun, H., Ma, J., Zang, C., Wang, C., Wang, J., Tang Q, Meyer CA, Zhang Y, Liu, X. S. (2013). Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nature protocols, 8(12), 2502-2515. 
PMID: 24263090
    </token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/nprot.2013.150</citation>
        </citations>
    </xml>
</macros>