view macros.xml @ 10:a019807f4e67 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 75d5141110314addc160504e0a1f9cd66443de66

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">seqtk</requirement>
            <requirement type="package" version="2.3.4">pigz</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">seqtk</xref>
        </xrefs>
    </xml>
    <token name="@TOOL_VERSION@">1.4</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@AWK_VERSION@">4.2.1</token>
    <xml name="stdio">
        <stdio>
            <!-- Anything other than zero is an error -->
            <exit_code range="1:"/>
            <exit_code range=":-1"/>
            <!-- In case the return code has not been set propery check stderr too -->
            <regex match="Error:"/>
            <regex match="Exception:"/>
        </stdio>
    </xml>
    <xml name="in_fq">
        <param name="in_file" type="data" format="fastq,fastq.gz" label="Input FASTQ file"/>
    </xml>
    <xml name="in_faq">
        <param name="in_file" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file"/>
    </xml>
    <token name="@CONDITIONAL_GZIP_OUT@"><![CDATA[
    #echo "| pigz -p ${GALAXY_SLOTS:-1} --no-name --no-time" if $in_file.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
    ]]></token>
    <token name="@ATTRIBUTION@"><![CDATA[
**Attribution**

This Galaxy tool relies on the seqtk toolkit from  `lh3/seqtk
<https://github.com/lh3/seqtk/>`_, developed by Heng Li at the Broad Institute
    ]]></token>
    <xml name="citation">
        <citations>
            <citation type="bibtex">
                @misc{seqtk,
                  author = {Heng Li},
                  year = {2023},
                  title = {seqtk},
                  publisher = {GitHub},
                  journal = {GitHub repository},
                  howpublished{\url{https://github.com/lh3/seqtk}},
                }
            </citation>
        </citations>
    </xml>

</macros>