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view artic_align_trim.xml @ 8:e015f2244d4f draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
author dfornika
date Tue, 10 Mar 2020 23:21:37 +0000
parents 97b21fddeff7
children 4a7233b0a795
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<tool id="artic_align_trim" name="ARTIC align_trim" version="0.1.0+galaxy0">
    <description>Trim aligned reads based on a set of primer loci</description>
    <requirements>
        <requirement type="package" version="0.15.3">pysam</requirement>
        <requirement type="package" version="1.9">samtools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '${__tool_directory__}/align_trim.py'
            '${primer_scheme_bedfile.fields.path}'
            --start 
            --report '${start_trim_report}'
            < '${input_alignment}'
            2> '${start_trim_err}' |
        samtools view -bS - |
        samtools sort - -o '${start_trimmed_sorted_alignment}' &&
        python '${__tool_directory__}/align_trim.py'
            '${primer_scheme_bedfile.fields.path}'
            --report '${end_trim_report}'
            < '${input_alignment}'
            2> '${end_trim_err}' |
        samtools view -bS - |
        samtools sort - -o '${end_trimmed_sorted_alignment}' &&
    ]]></command>
    <inputs>
        <param name="input_alignment" type="data" format="bam" label="Input Alignment"/>
        <param name="primer_scheme_bedfile" type="select" format="bed" label="Primer Scheme">
	    <options from_data_table="primer_scheme_bedfiles">
	        <validator type="no_options" message="No primer scheme .bed files are available" />
            </options>
	</param>
    </inputs>
    <outputs>
        <data name="start_trim_report" format="tabular" label="Report (Trim to start of primers)" />
        <data name="start_trim_err" format="txt" label="Error Report (Trim to start of primers)" />
        <data name="end_trim_report" format="tabular" label="Report (Trim to end of primers)" />
        <data name="end_trim_err" format="txt" label="Error Report (Trim to end of primers)" />
        <data name="start_trimmed_sorted_alignment" format="bam" label="Trimmed Alignment (Trim to start of primers)" />
        <data name="end_trimmed_sorted_alignment" format="bam" label="Trimmed Alignment (Trim to end of primers)" />
    </outputs>
    <tests>
    </tests>
    <help><![CDATA[
    ]]></help>
    <citations>
    </citations>
</tool>