view bismark_deduplicate/bismark_deduplicate_wrapper.xml @ 7:fcadce4d9a06 draft

planemo upload for repository commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:18:09 -0400
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<tool id="bismark_deduplicate" name="Bismark Deduplicate" version="0.16.3">

    <description>Deduplicates reads mapped by Bismark</description>
    <!--<version_command>bismark version</version_command>-->

        <requirement type="package" version="0.1.19">samtools</requirement>
        <requirement type="package" version="2.1.0">bowtie2</requirement>

        <exit_code range="1:" />
        <exit_code range=":-1" />
        <regex match="Error:" />
        <regex match="Exception:" />

    <command interpreter="python">

        --tool_dir "$__tool_directory__"

        #if str ( $sPaired ) == "single":
        #end if

        --input "$mapping_output"

        --output_report "$output_report"
        --output_bam "$output_bam"

        ##--log_report "$log_report"

        <param name="sPaired" type="select" label="Is this library mate-paired?" format="bam">
            <option value="single">Single-end</option>
            <option value="paired">Paired-end</option>
        <param name="mapping_output" type="data" format="bam, sam" label="Submit the resulting bam/sam file from Bismark bisulfite mapper" />

        <data name="output_bam" format="bam" label="${} on ${on_string}: deduplicated mapped reads" />
        <data name="output_report" format="txt" label="${} on ${on_string}: deduplication report"/>
        <!--<data name="log_report" format="txt" label="${} on ${on_string}: log report (tool stdout)"/>-->

**What it does**

	| This tool is supposed to remove alignments to the same position in the genome from the Bismark mapping output (both single and paired-end SAM files), which can arise by e.g. excessive PCR amplification. If sequences align to the same genomic position but on different strands they will be scored individually.
	| Note that deduplication is not recommended for RRBS-type experiments!
	| For single-end alignments only use the start-coordinate of a read will be used for deduplication.
	| For paired-end alignments the start-coordinate of the first read and the end coordinate of the second read will be used for deduplication. 

      <citation type="doi">10.1093/bioinformatics/btr167</citation>