comparison hisat2_macros.xml @ 7:5ba8e317529a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde

6:5f4da9ec47c7

        <conditional name="paired">
            <expand macro="single_paired_selector" />
            <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">

                    help="By default, hisat looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior. (--no-discordant)" />
                <param name="skip_reverse" label="Skip reference strand of reference" type="boolean" truevalue="--norc" falsevalue="" help="(--norc) If --norc is specified, hisat will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand." />
            </when>
        </conditional>
    </xml>
    <token 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>

7:5ba8e317529a

        <conditional name="paired">
            <expand macro="single_paired_selector" />
            <when value="paired_collection">
                <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" />
                <expand macro="paired_end_conditional" />
                <expand macro="paired_end_output" />
            </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" />
                <expand macro="paired_end_output" />
            </when>
            <when value="single">
                <param format="@FTYPE@" label="Reads" name="reads" type="data" />
                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un" />
                <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al" />
            </when>
        </conditional>
    </xml>
    <xml name="paired_end_conditional">
        <conditional name="paired_end_options">

                    help="By default, hisat looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior. (--no-discordant)" />
                <param name="skip_reverse" label="Skip reference strand of reference" type="boolean" truevalue="--norc" falsevalue="" help="(--norc) If --norc is specified, hisat will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand." />
            </when>
        </conditional>
    </xml>
    <xml name="paired_end_output">
        <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un-conc" />
        <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al-conc" />
    </xml>
    <token name="@paired_end_options@">
        #if str( $input_format.paired.unaligned_file ) == "true":
            --un-conc '${output_unaligned_reads_l}'
        #end if
        #if str( $input_format.paired.aligned_file ) == "true":
            --al-conc '${output_aligned_reads_l}'
        #end if  
        #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>