view artic_align_trim.xml @ 10:1ae3d853cac8 draft default tip

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit fc533961a332436c344ecbed6e7b0a17e108ae50-dirty"

<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[
        #if str( $primer_scheme_source.primer_scheme_source_selector ) == "tool_data_table":
          #set $primer_scheme = str( $primer_scheme_source.primer_scheme_bedfile.fields.path )
        #else:
          #set $primer_scheme = str( $primer_scheme_source.primer_scheme_bedfile )
        #end if
        python '${__tool_directory__}/align_trim.py'
            '${primer_scheme}'
            --start 
            --report '${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'
            '${primer_scheme}'
            --report '${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"/>
        <conditional name="primer_scheme_source">
            <param name="primer_scheme_source_selector" type="select" label="Select a primer scheme from your history or use one from a tool data table?"
                   help="Screening files must be stored in the 'primer_scheme_bedfiles' tool data table">
                <option value="tool_data_table">From tool data table</option>
                <option value="history">From history</option>
            </param>
            <when value="tool_data_table">
                <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>
            </when>
            <when value="history">
                <param name="primer_scheme_bedfile" type="data" format="bed" label="Primer Scheme" />
            </when>
        </conditional>
    </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>