<tool id="bamclipper" name="BAMClipper" version="@VERSION@+galaxy0">
    <description> Remove gene-specific primer sequences from BAM alignments of PCR amplicons by soft-clipping with BEDPE file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
#import re

#set bamname = re.sub('[^\s\w-]', '_', str($input1.name))
ln -sf '$input1' '$bamname' &&
ln -sf '${input1.metadata.bam_index}' '${bamname}.bai' &&

bamclipper.sh -b '$bamname' -p '$primer_pairs' -n "\${GALAXY_SLOTS:-1}"
    #if $optional.upstream:
        -u '$optional.upstream'
    #end if
    #if $optional.downstream:
        -d '$optional.downstream'
    #end if

    ]]></command>
    <inputs>
        <param name="input1" type="data" format="bam"
            label="Input Bam file"
            argument="-b"
            />
        <param name="primer_pairs" type="data" format="bedpe, interval"
            label="BEDPE file of primer pair locations"
            argument="-p"
            />
        <section name="optional" title="Optional Parameters" expanded="false" >
            <param name="upstream" type="integer" optional="true"
                label="Upstream"
                argument="-u"
                help="Number of nucleotides upstream of the 5' most nucleotide of the primer (in addition to 5' most nucleotide of primer) for assigning
                alignments to primers based on the alignment starting position. Default 1"
                />
            <param name="downstream" type="integer" optional="true"
                label="Downstream"
                argument="-d"
                help="Number of nucleotides downstream to the 5' most nucleotide of primer (in addition to 5' most nucleotide of primer) for assigning
                alignments to primers based on the alignment starting position. Default 5"
                />
        </section>
    </inputs>
    <outputs>
        <data format_source="input1" from_work_dir="*.primerclipped.bam" name="output" label="${input1.name}.primerclipped" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="SRR2075598.bam" />
            <param name="primer_pairs" value="trusight_myeloid.bedpe" />
            <output name="output" file="SRR2075598.primerclipped.bam" ftype="bam" />
        </test>
        <test>
            <param name="input1" value="SRR2075598.bam" />
            <param name="primer_pairs" value="trusight_myeloid.bedpe" />
            <section name="optional">
                <param name="upstream" value="1" />
                <param name="downstream" value="5" />
            </section>
            <output name="output" file="SRR2075598.primerclipped.bam" ftype="bam" />
        </test>
    </tests>
    <help><![CDATA[
    
Bamclipper
----------

Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format
to produce a new bam file called NAME.primerclipped.bam and its associated bam index (NAME.primerclipped.bam.bai)

Example primer pair BEDPE file lines:

::

    chr1	115256390	115256417	chr1	115256622	115256650
    chr1	115258642	115258664	chr1	115258876	115258903
    chr10	89692737	89692767	chr10	89692971	89692998
    chr10	89692943	89692970	chr10	89693177	89693206
    chr10	89717567	89717596	chr10	89717775	89717802


    ]]></help>
    <expand macro="citations" />
</tool>