comparison lumpy_preprocessing.xml @ 1:80adce82354c draft default tip

"planemo upload for repository https://github.com/arq5x/lumpy-sv commit 41cb10683d89fa20e122f4c60b8f5bf0e3c390d8"

0:21f2361c32c9

<tool id="lumpy_prep" name="LUMPY preprocessing" version="@WRAPPER_VERSION@">
    <description>extracts discordant read pairs and split-read alignments from a BAM dataset</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">lumpy-sv</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
samtools collate -O --output-fmt sam '$bam_in' | samblaster $dup_handling --addMateTags | samtools view -bS - > blasted.bam &&

samtools view -b -F 1294 blasted.bam > discordants.unsorted.bam &&
samtools view -h blasted.bam | extractSplitReads_BwaMem -i stdin | samtools view -Sb - > splitters.unsorted.bam &&

    </outputs>
    <tests>
        <test>
            <param name="bam_in" ftype="bam" value="sample.bam" />
            <param name="dup_handling" value="" />
            <output name="blasted_bam" ftype="qname_sorted.bam" file="blasted.bam" />
            <output name="discordants_bam" ftype="bam" file="discordants.bam" />
            <output name="splitters_bam" ftype="bam" file="splitters.bam" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

1:80adce82354c

<tool id="lumpy_prep" name="LUMPY preprocessing" version="@WRAPPER_VERSION@" profile="20.05">
    <description>extracts discordant read pairs and split-read alignments from a BAM dataset</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">lumpy-sv</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
set -o pipefail;

samtools collate -O --output-fmt sam '$bam_in' | samblaster $dup_handling --addMateTags | samtools view -bS - > blasted.bam &&

samtools view -b -F 1294 blasted.bam > discordants.unsorted.bam &&
samtools view -h blasted.bam | extractSplitReads_BwaMem -i stdin | samtools view -Sb - > splitters.unsorted.bam &&

    </outputs>
    <tests>
        <test>
            <param name="bam_in" ftype="bam" value="sample.bam" />
            <param name="dup_handling" value="" />
            <output name="blasted_bam" ftype="qname_sorted.bam" file="blasted.bam" lines_diff="2"/>
            <output name="discordants_bam" ftype="bam" file="discordants.bam" lines_diff="2"/>
            <output name="splitters_bam" ftype="bam" file="splitters.bam" lines_diff="2"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**