comparison hisat2_macros.xml @ 2:c37b4554f794 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit a2aaa7c9fe7b343f95450ec428250317696a9fb7

1:6d4d39720545

            <when value="paired_collection">
                <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" />
                <expand macro="paired_end_conditional" />
            </when>
            <when value="paired">
                <param format="@FTYPE@" label="Forward reads" multiple="true" name="reads_f" type="data" />
                <param format="@FTYPE@" label="Reverse reads" multiple="true" name="reads_r" type="data" />
                <expand macro="paired_end_conditional" />
            </when>
            <when value="single">
                <param format="@FTYPE@" label="Reads" multiple="true" name="reads" type="data" />
            </when>
        </conditional>
    </xml>
    <xml name="paired_end_conditional">
        <conditional name="paired_end_options">

        #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced':
            ${input_format.paired.paired_end_options.no_mixed}
            ${input_format.paired.paired_end_options.no_discordant}
        #end if
    </token>
    <token name="strandedness_parameters">
        #if str($spliced_options.spliced_options_selector) == "advanced":
            #if str($spliced_options.rna_strandness).strip() != '':
                --rna-strandness $spliced_options.rna_strandness
            #end if
        #end if

2:c37b4554f794

            <when value="paired_collection">
                <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" />
                <expand macro="paired_end_conditional" />
            </when>
            <when value="paired">
                <param format="@FTYPE@" label="Forward reads" name="reads_f" type="data" />
                <param format="@FTYPE@" label="Reverse reads" name="reads_r" type="data" />
                <expand macro="paired_end_conditional" />
            </when>
            <when value="single">
                <param format="@FTYPE@" label="Reads" name="reads" type="data" />
            </when>
        </conditional>
    </xml>
    <xml name="paired_end_conditional">
        <conditional name="paired_end_options">

        #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced':
            ${input_format.paired.paired_end_options.no_mixed}
            ${input_format.paired.paired_end_options.no_discordant}
        #end if
    </token>
    <token name="@strandedness_parameters@">
        #if str($spliced_options.spliced_options_selector) == "advanced":
            #if str($spliced_options.rna_strandness).strip() != '':
                --rna-strandness $spliced_options.rna_strandness
            #end if
        #end if