view coords2clnt.xml @ 1:ca1320644fad draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1a8f89c930408a481143f7d6493746cd5fa30c3e
author iuc
date Wed, 18 Apr 2018 04:05:16 -0400
parents 66d1f96c5600
children 91f27e8a2535
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<tool id="bctools_extract_crosslinked_nucleotides" name="Get crosslinked nucleotides" version="@VERSION@">
    <description>from full alignments</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        coords2clnt.py
        '$alignment_coordinates'
        > '$crosslinking_coordinates'
    ]]></command>
    <inputs>
        <param name="alignment_coordinates" type="data" format="bed" label="Alignments in BED format"/>
    </inputs>
    <outputs>
        <data name="crosslinking_coordinates" format="bed"/>
    </outputs>
    <tests>
        <test>
            <param name="alignment_coordinates" value="merged_pcr_dupes.bed"/>
            <output name="crosslinking_coordinates" file="merged_pcr_dupes_clnts.bed"/>
        </test>
    </tests>
    <help><![CDATA[

bctools - Get crosslinked nucleotides from full alignments
==========================================================

Given coordinates of aligned reads in BED format, calculate positions of the
crosslinked nucleotides. Crosslinked nts are assumed to be one nt upstream of
the 5'-end of the read.

Input
-----

* six column BED file containing coordinates of aligned reads

Output
------

* six column BED file containing coordinates of crosslinking events

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