comparison macros.xml @ 11:a472e995d157 draft

"planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"

10:828dba98cdb4

<?xml version="1.0"?>
<macros>
    <macro name="barcode2_conditional" >
        <conditional name="barcode">
            <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?">
                <option value="first_read_only">Barcode on first read only</option>
                <option value="both_reads">Barcode on both reads</option>

            <when value="first_read_only"/>
            <when value="both_reads">
                <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
                       help="Use this option to specify the format of the UMI/barcode for
                             the second read pair if required." >
                </param>
            </when>
        </conditional>
    </macro>
    <xml name="input_types">

        <requirements>
            <requirement type="package" version="@VERSION@">umi_tools</requirement>
            <yield />
        </requirements>
    </xml>
    <token name="@VERSION@">0.5.3</token>
    <token name="@COMMAND_LINK@"><![CDATA[
        #set $gz = False
        #if $input_type.type == 'single':
            #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):
                ln -s '$input_type.input_single' input_single.gz &&

11:a472e995d157

<?xml version="1.0"?>
<macros>
    <macro name="barcode_sanitizer" >
        <sanitizer invalid_char="">
            <valid initial="string.letters,string.digits">
                <add value="&#40;" /><!-- left bracket -->
                <add value="&#41;" /><!-- right bracket -->
                <add value="&#42;" /><!-- asterisk -->
                <add value="&#44;" /><!-- comma -->
                <add value="&#46;" /><!-- period -->
                <add value="&#60;" /><!-- less than -->
                <add value="&#61;" /><!-- equals sign -->
                <add value="&#62;" /><!-- greater than -->
                <add value="&#63;" /><!-- question mark -->
                <add value="&#95;" /><!-- underscore -->
                <add value="&#123;"/><!-- left brace -->
                <add value="&#125;"/><!-- right brace -->
            </valid>
        </sanitizer>
    </macro>
    <macro name="barcode2_conditional" >
        <conditional name="barcode">
            <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?">
                <option value="first_read_only">Barcode on first read only</option>
                <option value="both_reads">Barcode on both reads</option>

            <when value="first_read_only"/>
            <when value="both_reads">
                <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
                       help="Use this option to specify the format of the UMI/barcode for
                             the second read pair if required." >
                    <expand macro="barcode_sanitizer" />
                </param>
            </when>
        </conditional>
    </macro>
    <xml name="input_types">

        <requirements>
            <requirement type="package" version="@VERSION@">umi_tools</requirement>
            <yield />
        </requirements>
    </xml>
    <token name="@VERSION@">0.5.5</token>
    <token name="@COMMAND_LINK@"><![CDATA[
        #set $gz = False
        #if $input_type.type == 'single':
            #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):
                ln -s '$input_type.input_single' input_single.gz &&