view rm_spurious_events.xml @ 0:9ad7bf370022 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
author iuc
date Tue, 14 Nov 2017 05:54:14 -0500
parents
children 84aff696aa97
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<tool id="bctools_remove_spurious_events" name="Remove spurious" version="@VERSION@">
    <description>crosslinking events</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        rm_spurious_events.py
        '$events'
        --threshold '$threshold'
        --outfile '$events_filtered'
    ]]></command>
    <inputs>
        <param name="events" type="data" format="bed" label="BED6 file containing alignments"/>
        <param name="threshold" argument="--threshold" type="float" value="0.1" optional="true" label="Threshold for spurious event removal" help="Remove all crosslinking events that combine less reads than this fraction of the maximum number of reads at this position."/>
    </inputs>
    <outputs>
        <data name="events_filtered" format="bed"/>
    </outputs>
    <tests>
        <test>
            <param name="events" value="merged_pcr_dupes_spurious.bed"/>
            <param name="threshold" value="0.5"/>
            <output name="events_filtered" file="merged_pcr_dupes_spurious_filtered_thresh05.bed"/>
        </test>
    </tests>
    <help><![CDATA[

bctools - Remove spurious events originating from errors in unique molecular identifiers (UMIs)
===============================================================================================

This tool compares all events sharing the same coordinates. Among each group
of events the maximum number of PCR duplicates is determined. By default, all events that
are supported by less than 10 percent of this maximum count are removed.

Input
-----

* BED6 containing crosslinking events with score field set to number of PCR duplicates

Output
------

* BED6 with spurious crosslinking events removed, sorted by fields chrom, start, stop, strand

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