comparison macros.xml @ 6:0a759fe3fd43 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit fd099d17eceaa319fbfe429f4725328d88b18c9f

5:b8e3c0a52f33

            cat '$input' |
        #end if
    </token>
    <token name="@FQQUAL@">
        <![CDATA[
            #if 'fastqsanger' in $input.ext:
                -Q 33
            #elif 'fastqsolexa' in $input.ext or 'fastqillumina' in $input.ext:
                -Q 64
            #end if
        ]]>
    </token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
            <yield />
        </requirements>
    </xml>
    <token name="@VERSION@">0.0.14</token>
    <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
    <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
    <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>
    <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token>
    <token name="@FASTAS@">fasta,fasta.gz</token>

                    note = "http://hannonlab.cshl.edu/fastx_toolkit/",
                    url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
            </citation>
        </citations>
    </xml>
    <xml name="fastq_input">
        <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" />
    </xml>
</macros>

6:0a759fe3fd43

            cat '$input' |
        #end if
    </token>
    <token name="@FQQUAL@">
        <![CDATA[
            #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
                -Q 33
            #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
                -Q 64
            #end if
        ]]>
    </token>
    <token name="@GZIP@">
        <![CDATA[
            #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
                | gzip -c
            #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
                | bzip2 -c
            #end if
        ]]>
    </token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
            <yield />
        </requirements>
    </xml>
    <token name="@VERSION@">0.0.14</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
    <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
    <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>
    <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token>
    <token name="@FASTAS@">fasta,fasta.gz</token>

                    note = "http://hannonlab.cshl.edu/fastx_toolkit/",
                    url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
            </citation>
        </citations>
    </xml>
    <xml name="fasta_input">
        <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" />
    </xml>
    <xml name="fastq_input">
        <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" />
    </xml>
    <xml name="fastx_input">
        <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" />
    </xml>
</macros>