annotate macros.xml @ 4:74f9f312c713 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">0.9.1</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">delly</requirement>
            <requirement type="package" version="1.12">bcftools</requirement>
        </requirements>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[delly -v 2>&1 | grep 'Delly version' | cut -f 3 -d ' ']]></version_command>
    </xml>
	<xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/bts378</citation>
        </citations>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">delly2</xref>
        </xrefs>
    </xml>
    <!-- command -->

    <token name="@SINGLE_BAM@"><![CDATA[
ln -s '$input' 'input.bam' &&
ln -s '$input.metadata.bam_index' 'input.bam.bai' &&
    ]]></token>
    <token name="@BAM@"><![CDATA[
#for $i, $current in enumerate($input)
    ln -s '${current}' 'input_${i}.bam' &&
    ln -s '${current.metadata.bam_index}' 'input_${i}.bam.bai' &&
#end for
    ]]></token>
    <!-- fasta needs to be linked, because .fai file is created -->
    <token name="@FASTA@"><![CDATA[
ln -s '$generic.genome' genome.fa &&
    ]]></token>
    <token name="@DUMP@"><![CDATA[
#if 'dump' in $oo.out
    && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
#end if
    ]]></token>
    <token name="@LOG@"><![CDATA[
#if 'log' in $oo.out
    |& tee '$out_log'
#end if
    ]]></token>
    <token name="@VCF@"><![CDATA[
#if 'vcf' in $oo.out
    && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
#end if
    ]]></token>

    <!-- input -->

    <xml name="cnoffset" token_default="">
        <param name="cnoffset" type="float" min="0.0" max="1.0" value="@DEFAULT@" label="Set minimum CN offset" help="(--cn-offset)"/>
    </xml>
    <xml name="coverage" token_label="">
        <param argument="--coverage" type="integer" value="10" label="@LABEL@"/>
    </xml>
    <xml name="exclude">
        <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
    </xml>
    <xml name="genome">
        <param argument="--genome" type="data" format="fasta" label="Select genome file"/>
    </xml>
    <xml name="genoqual">
        <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
    </xml>
    <xml name="input" token_format="" token_multiple="false" token_label="">
        <param name="input" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
    </xml>
    <xml name="maxreadsep" token_default="">
        <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/>
    </xml>
    <xml name="maxsize" token_default="" token_label="">
        <param argument="--maxsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
    </xml>
    <xml name="minclip">
        <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
    </xml>
    <xml name="mincliquesize">
        <param name="mincliquesize" type="integer" value="2" label="Set minimum paired-end/single-read clique size" help="(--min-clique-size)"/>
    </xml>
    <xml name="minrefsep" token_default="">
        <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/>
    </xml>
    <xml name="minsize" token_default="" token_label="">
        <param argument="--minsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
    </xml>
    <xml name="pass">
        <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>
    </xml>
    <xml name="ploidy">
        <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/>
    </xml>
    <xml name="samples">
        <param argument="--samples" type="data" format="tabular" label="Select sample file" help="Two-column sample file listing sample name and tumor or control."/>
    </xml>
    <xml name="svtype">
        <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
            <option value="ALL" selected="true">All types (ALL)</option>
            <option value="DEL">Deletion (DEL)</option>
            <option value="DUP">Duplication (DUP)</option>
            <option value="INS">Insertion (INS)</option>
            <option value="INV">Inversion (INV)</option>
            <option value="BND">Translocation (BND)</option>
        </param>
    </xml>
    <xml name="vcffile">
        <param argument="--vcffile" type="data" format="bcf,vcf" optional="true" label="Select genotyping file"/>
    </xml>

    <!-- output -->

    <xml name="bcf">
        <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
            <filter>'bcf' in oo['out']</filter>
        </data>
    </xml>
    <xml name="vcf">
        <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
            <filter>'vcf' in oo['out']</filter>
        </data>
    </xml>
    <xml name="dump">
        <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
            <filter>'dump' in oo['out']</filter>
        </data>
    </xml>
    <xml name="log">
        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
            <filter>'log' in oo['out']</filter>
        </data>
    </xml>

    <!-- help -->

    <token name="@WID@"><![CDATA[
Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.

Short-read SV calling

- *call* to discover and genotype structural variants
- *merge* structural variants across VCF/BCF files and within a single VCF/BCF file
- *filter* somatic or germline structural variants

Long-read SV calling

- *lr* for long-read SV discovery

Copy-number variant calling

- *cnv* to discover and genotype copy-number variants
- *classify* somatic or germline copy-number variants
    ]]></token>
    <token name="@REFERENCES@"><![CDATA[
More information are available on `GitHub <https://github.com/dellytools/delly>`_.
    ]]></token>
</macros>