comparison bamToBed.xml @ 38:fe5b4cb8356c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b822ff8f05f2396fc15bd95a71bc6878503081eb"

37:ce3c7f062223

<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
    </expand>
    <expand macro="stdio" />
    <command><![CDATA[
#if $input.extension == 'bam' and $option == "-bedpe":
    samtools sort -n -T "\${TMPDIR:-.}" '${input}' ./input &&
#else
    ln -s '${input}' ./input.bam &&
#end if

bedtools bamtobed

#end if
-i ./input.bam
> '${output}'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bam" label="Convert the following BAM file to BED"/>
        <param name="option" type="select" label="What type of BED output would you like">
            <option value="">Create a 6-column BED file</option>
            <option value="-bed12">Create a full, 12-column "blocked" BED file</option>
            <option value="-bedpe">Create a paired-end, BEDPE format</option>
        </param>

38:fe5b4cb8356c

<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy1">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
    </expand>
    <expand macro="stdio" />
    <command><![CDATA[
#if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe":
    samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' ./input &&
#else
    ln -s '${input}' ./input.bam &&
#end if

bedtools bamtobed

#end if
-i ./input.bam
> '${output}'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="unsorted.bam" label="Convert the following BAM file to BED"/>
        <param name="option" type="select" label="What type of BED output would you like">
            <option value="">Create a 6-column BED file</option>
            <option value="-bed12">Create a full, 12-column "blocked" BED file</option>
            <option value="-bedpe">Create a paired-end, BEDPE format</option>
        </param>