comparison call.xml @ 1:53d90d86fc83 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"

0:36772204dee5

<?xml version="1.0"?>
<tool id="delly_call" name="Delly call" version="@TOOL_VERSION@+galaxy0" profile="18.01">
    <description>and genotype structural variants</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
## initialize
#for $i, $current in enumerate($samples)
    ln -s '${current}' 'sample_${i}.bam' &&
    ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' &&
#end for

## run
delly call
## generic options
--svtype $generic.svtype

## discovery options
--map-qual $discovery.mapqual
--qual-tra $discovery.qualtra
--mad-cutoff $discovery.madcutoff
--minclip $discovery.minclip
--minrefsep $discovery.minrefsep
--maxreadsep $discovery.maxreadsep
## genotyping options
#if $genotyping.vcffile
    --vcffile '$genotyping.vcffile'

#for $i, $current in enumerate($samples)
    'sample_${i}.bam'
#end for

## postprocessing
#if 'log' in $oo.out
    |& tee 'log.txt'
#end if
#if 'vcf' in $oo.out
    && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
#end if
#if 'dump' in $oo.out
    && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
#end if
    ]]></command>
    <inputs>
        <expand macro="samples"/>
        <section name="generic" title="Generic options" expanded="true">
            <expand macro="svtype"/>

        <section name="discovery" title="Discovery options" expanded="true">
            <param name="mapqual" type="integer" value="1" label="Set minimum paired-end (PE) mapping quality" help="(--map-qual)"/>
            <param name="qualtra" type="integer" value="20" label="Set minimum PE quality for translocation" help="(--qual-tra)"/>
            <param name="madcutoff" type="integer" value="9" label="Set insert size cutoff" help="median+s*MAD, deletions only (--mad-cutoff)"/>
            <expand macro="minclip"/>
            <expand macro="minrefsep"/>
            <expand macro="maxreadsep"/>
        </section>
        <section name="genotyping" title="Genotyping options" expanded="true">
            <expand macro="vcffile"/>

            <section name="discovery">
                <param name="mapqual" value="2"/>
                <param name="qualtra" value="19"/>
                <param name="madcutoff" value="8"/>
                <param name="minclip" value="24"/>
                <param name="minrefsep" value="24"/>
                <param name="maxreadsep" value="39"/>
            </section>
            <section name="genotyping">
                <param name="genoqual" value="4"/>

Delly *call* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. Additionally a VCF/BCF file for genotyping can be applied.

**Output**

The output is available in BCF and VCF format. Additionally a output file for SV-reads is provided.

.. class:: infomark

**References**

1:53d90d86fc83

<?xml version="1.0"?>
<tool id="delly_call" name="Delly call" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
    <description>and genotype structural variants</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
## initialize
@BAM@

## run
delly call
## generic options
--svtype $generic.svtype

## discovery options
--map-qual $discovery.mapqual
--qual-tra $discovery.qualtra
--mad-cutoff $discovery.madcutoff
--minclip $discovery.minclip
--min-clique-size $discovery.mincliquesize
--minrefsep $discovery.minrefsep
--maxreadsep $discovery.maxreadsep
## genotyping options
#if $genotyping.vcffile
    --vcffile '$genotyping.vcffile'

#for $i, $current in enumerate($samples)
    'sample_${i}.bam'
#end for

## postprocessing
@LOG@
@VCF@
@DUMP@
    ]]></command>
    <inputs>
        <expand macro="samples"/>
        <section name="generic" title="Generic options" expanded="true">
            <expand macro="svtype"/>

        <section name="discovery" title="Discovery options" expanded="true">
            <param name="mapqual" type="integer" value="1" label="Set minimum paired-end (PE) mapping quality" help="(--map-qual)"/>
            <param name="qualtra" type="integer" value="20" label="Set minimum PE quality for translocation" help="(--qual-tra)"/>
            <param name="madcutoff" type="integer" value="9" label="Set insert size cutoff" help="median+s*MAD, deletions only (--mad-cutoff)"/>
            <expand macro="minclip"/>
            <expand macro="mincliquesize"/>
            <expand macro="minrefsep"/>
            <expand macro="maxreadsep"/>
        </section>
        <section name="genotyping" title="Genotyping options" expanded="true">
            <expand macro="vcffile"/>

            <section name="discovery">
                <param name="mapqual" value="2"/>
                <param name="qualtra" value="19"/>
                <param name="madcutoff" value="8"/>
                <param name="minclip" value="24"/>
                <param name="mincliquesize" value="1"/>
                <param name="minrefsep" value="24"/>
                <param name="maxreadsep" value="39"/>
            </section>
            <section name="genotyping">
                <param name="genoqual" value="4"/>

Delly *call* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. Additionally a VCF/BCF file for genotyping can be applied.

**Output**

The output is available in BCF and VCF format. Additionally an output file for SV-reads is provided.

.. class:: infomark

**References**