comparison macros.xml @ 41:5eb7e84243f2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit fff23da3bceafb57de06af03d4c8ab4d66d4b098

40:aa784cb3810d

<macros>
    <token name="@TOOL_VERSION@">4.9</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@FASTQ_TYPES@">fastq.bz2,fastq.gz,fastq,fasta.bz2,fasta.gz,fasta</token>
    <xml name="edam_ontology">
        <edam_topics>
            <edam_topic>topic_0632</edam_topic>
        </edam_topics>

        #else:
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter}${a.single_noindels}'
        #end if
    </token>
    <xml name="adapter_sanitizer">
        <sanitizer>
            <valid initial="string.digits">
                <add value="A"/><!--standard nucleotides-->
                <add value="T"/>
                <add value="C"/>
                <add value="G"/>
                <add value="U"/><!--ambiguous nucleotides-->
                <add value="R"/>
                <add value="Y"/>
                <add value="S"/>
                <add value="W"/>
                <add value="K"/>
                <add value="M"/>
                <add value="B"/>
                <add value="D"/>
                <add value="H"/>
                <add value="V"/>
                <add value="N"/>
                <add value="X"/><!-- don't match any nucleotide-->
                <add value="{"/><!--specify repeats .. needs digits which are added as default-->
                <add value="}"/>
                <add value="^"/><!--anchoring-->
                <add value="$"/>
                <add value="."/>
                <add value="("/><!--specify what to keep-->
                <add value=")"/>
            </valid>
        </sanitizer>
    </xml>
    <xml name="adapter_conditional" tokens="adapter_type,argument">
        <conditional name="adapter_source">
            <param name="adapter_source_list" type="select" label="Source" >
                <option value="builtin" selected="true">Standard (select from the list below)</option>

41:5eb7e84243f2

<macros>
    <token name="@TOOL_VERSION@">4.9</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@FASTQ_TYPES@">fastq.bz2,fastq.gz,fastq,fasta.bz2,fasta.gz,fasta</token>
    <xml name="edam_ontology">
        <edam_topics>
            <edam_topic>topic_0632</edam_topic>
        </edam_topics>

        #else:
            $ADAPTER_ARGUMENT '${a.adapter_source.adapter}${a.single_noindels}'
        #end if
    </token>
    <xml name="adapter_sanitizer">
        <sanitizer sanitize="false" />
        <validator type="regex" message="Invalid adapter sequence. Allowed are strings consisting of digits IUPAC nucleotides (including wildcards) and any of the following '{}^$.()'. See https://cutadapt.readthedocs.io/en/stable/guide.html#specifying-adapter-sequences"><![CDATA[[0-9ATCGURYSWKMBDHVNX{}^$.()]+$]]></validator>
    </xml>
    <xml name="adapter_conditional" tokens="adapter_type,argument">
        <conditional name="adapter_source">
            <param name="adapter_source_list" type="select" label="Source" >
                <option value="builtin" selected="true">Standard (select from the list below)</option>