comparison macros.xml @ 5:b8e3c0a52f33 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 415a5c5de30530910f3039e5fc66aa15103c6f20

4:5dbca5fbdc45

            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>

                    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>

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>

                    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>