comparison artic_align_trim.xml @ 3:ba460f482c35 draft

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"

2:8bcfa2bb56cd

             2> '${start_trim_err}' |
        samtools view -bS - |
        samtools sort - -o '${trimmed_sorted_alignment}' 
    ]]></command>
    <inputs>
        <input name="input_alignment" type="data" format="bam"/>
        <param name="primer_scheme_bedfile" type="select" format="bed">
	    <options from_data_table="primer_scheme_bedfiles">
	        <validator type="no_options" message="No primer scheme .bed files are available" />
            </options>
	</param>
    </inputs>

3:ba460f482c35

             2> '${start_trim_err}' |
        samtools view -bS - |
        samtools sort - -o '${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>