comparison macros.xml @ 6:2626e58c493e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 82e7263f3e57a29362d981e36b82b82063f12ac3

5:852044374da1

    </xml>

    <!-- log file handling -->
    <token name="@TEE_APPEND_LOG@"><![CDATA[
        #if $output_log
            2>> $output_log &&
        #end if
    ]]></token>
    <token name="@CAT_LOG_TO_STDERR@"><![CDATA[
        #if $output_log
            cat $output_log 2>&1
        #end if
    ]]></token>
    <xml name="in_log">
        <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset" />
    </xml>

        <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) -->
    <xml name="fastq_input" token_fastq_optional="false" 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">single end or forward reads</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>

6:2626e58c493e

    </xml>

    <!-- log file handling -->
    <token name="@TEE_APPEND_LOG@"><![CDATA[
        #if $output_log
            2>> '$output_log' &&
        #end if
    ]]></token>
    <token name="@CAT_LOG_TO_STDERR@"><![CDATA[
        #if $output_log
            cat '$output_log' 2>&1
        #end if
    ]]></token>
    <xml name="in_log">
        <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset" />
    </xml>

        <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>