view merge_pcr_duplicates.xml @ 2:067139d6fc88 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 758b42538f722759e7b5414f64c9a7973cc221b4"

<tool id="bctools_merge_pcr_duplicates" name="Merge PCR duplicates" version="@VERSION@+galaxy1">
    <description>according to UMIs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="8.31">coreutils</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
        merge_pcr_duplicates.py
        '$alignments_bed'
        '$barcode_library'
        --outfile '$events'
    ]]></command>
    <inputs>
        <param name="alignments_bed" type="data" format="bed" label="BED6 file containing alignments" />
        <param name="barcode_library" type="data" format="fastq" label="FASTQ barcode library" />
    </inputs>
    <outputs>
        <data name="events" format="bed"/>
    </outputs>
    <tests>
        <test>
            <param name="alignments_bed" value="pcr_dupes_sorted_2.bed"/>
            <param name="barcode_library" value="pcr_dupes_randomdict.fastq"/>
            <output name="events" file="merged_pcr_dupes.bed"/>
        </test>
    </tests>
    <help><![CDATA[

bctools - Merge PCR duplicates according to UMIs
================================================

Merge PCR duplicates according to unique molecular identifier (UMI) library. All alignments with
same outer coordinates and barcode will be merged into a single crosslinking
event.

Barcodes containing uncalled base 'N' are removed.

Input:
------

* BED6 file containing alignments with FASTQ read-id in name field
* FASTQ library of UMIs

Output:
-------

* BED6 file with a read id from a representative alignment in the name field and number of PCR duplicates as score, sorted by fields chrom, start, stop, strand, name

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