comparison samtools_ampliconclip.xml @ 2:6a8febad1f6c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit cd62639660bef041ba14ecff337fb98e84e75d8a

1:5f3ea90dc6ae

<tool id="samtools_ampliconclip" name="Samtools ampliconclip" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>clip primer bases from bam files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    ]]></command>
    <inputs>
        <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" />
        <param name="input_bam" type="data" format="bam" label="BAM file" />
        <param name="hard_clip_mode" argument="--hard-clip" type="boolean" checked="false" truevalue="--hard-clip" falsevalue="--soft-clip" label="hard clip" help="hard clip (remove bases), unchekced = default soft-clipping" />
        <param name="strand" argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" />
        <param name="both_ends" argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" />
        <param name="no_excluded" argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" />
        <param name="min_length" argument="--fail-len" type="integer" min="0" optional="true" label="Min Read length" help="mark reads QCFAIL at this length or shorter after clipping" />
        <param name="tolerance" argument="--tolerance" type="integer" value="5" min="0"  label="Tolerance" help="match region within this number of bases, default 5." />
    
    </inputs>
    <outputs>
        <data name="output_bam" format="bam" />
    </outputs>

2:6a8febad1f6c

<tool id="samtools_ampliconclip" name="Samtools ampliconclip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>clip primer bases from bam files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    ]]></command>
    <inputs>
        <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" />
        <param name="input_bam" type="data" format="bam" label="BAM file" />
        <param name="hard_clip_mode" argument="--hard-clip" type="boolean" checked="false" truevalue="--hard-clip" falsevalue="--soft-clip" label="hard clip" help="hard clip (remove bases), unchekced = default soft-clipping" />
        <param argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" />
        <param argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" />
        <param argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" />
        <param name="min_length" argument="--fail-len" type="integer" min="0" optional="true" label="Min Read length" help="mark reads QCFAIL at this length or shorter after clipping" />
        <param argument="--tolerance" type="integer" value="5" min="0"  label="Tolerance" help="match region within this number of bases, default 5." />
    
    </inputs>
    <outputs>
        <data name="output_bam" format="bam" />
    </outputs>