comparison macros.xml @ 5:f6e91108b7b1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"

4:7370bb65bad4

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>
            <requirement type="package" version="3.7">python</requirement>
            <requirement type="package" version="4.6.0">findutils</requirement>
            <yield/>
        </requirements>
    </xml>

    <token name="@STACKS_VERSION@">2.55</token>
    <token name="@WRAPPER_VERSION@">1</token>
    <token name="@PROFILE@">20.05</token>

    <xml name="citation">
        <citations>
            <citation type="doi">10.1111/mec.12354</citation>

        <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@">
            <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file"/>
        </expand>
    </xml>

    <!-- fastq input (used in denovomap, tsv2bam, ustacks)
         - fastq_optional: makes fastq input optional (true/false)
         - se_option: wording for "single end" option (for tsv2bam this is the
              reverse reads for the others its the forward reads)
         - help: help text -->
    <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help="">
        <conditional name="input_type">
            <param name="input_type_select" type="select" label="Short read data from individuals" help="@HELP@">
                <option value="single" selected="true">@SE_OPTION@</option>
                <option value="paired">(paired) dataset list</option>
            </param>
            <when value="single">
                <param name="fqinputs" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="true" optional="@FASTQ_OPTIONAL@"/>
            </when>
            <when value="paired">
                <param name="fqinputs" argument="-f" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/>
            </when>
        </conditional>
    </xml>

    <!-- helper functions for linking fastq data sets -->

5:f6e91108b7b1

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">stacks</requirement>
            <requirement type="package" version="3.7">python</requirement>
            <requirement type="package" version="4.6.0">findutils</requirement>
            <yield/>
        </requirements>
    </xml>

    <token name="@TOOL_VERSION@">2.55</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@PROFILE@">20.05</token>

    <xml name="citation">
        <citations>
            <citation type="doi">10.1111/mec.12354</citation>

        <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@">
            <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file"/>
        </expand>
    </xml>


    <xml name="barcode_selector">
        <param name="barcode_encoding" type="select" label="Barcode location">
            <option value="">Disabled</option>
            <yield/>
        </param>
        <param name="barcode" argument="-b" type="data" format="tabular,txt" optional="true" label="Barcode file" help="The barcode file is only used if barcode_input"/>
    </xml>


    <!-- fastq input (used in denovomap, tsv2bam, ustacks)
         - fastq_optional: makes fastq input optional (true/false)
         - se_option: wording for "single end" option (for tsv2bam this is the
              reverse reads for the others its the forward reads)
         - help: help text -->
    <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help="" token_multiple="false" token_listtype="paired">
        <conditional name="input_type">
            <param name="input_type_select" type="select" label="Short read data from individuals" help="@HELP@">
                <option value="single" selected="true">@SE_OPTION@</option>
                <option value="paired">(paired) dataset list</option>
            </param>
            <when value="single">
                <param name="fqinputs" argument="-f" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" type="data" label="Reads" multiple="@MULTIPLE@" optional="@FASTQ_OPTIONAL@"/>
            </when>
            <when value="paired">
                <param name="fqinputs" argument="-f" type="data_collection" collection_type="@LISTTYPE@" format="fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="List for forward reads or read pairs" optional="@FASTQ_OPTIONAL@"/>
            </when>
        </conditional>
    </xml>

    <!-- helper functions for linking fastq data sets -->