comparison bamToBed.xml @ 46:64e2edfe7a2c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4

45:a1a923cd89e8

<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />
    <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.bam &&

46:64e2edfe7a2c

<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>converter</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />
    <expand macro="requirements">
        <requirement type="package" version="1.18">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.bam &&