view macros.xml @ 1:d68b2ef52012 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1

<?xml version="1.0" ?>
<macros>
    <token name="@WRAPPER_VERSION@">1.9.1</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@WRAPPER_VERSION@">qiime</requirement>
            <yield/>
        </requirements>
    </xml>

    <xml name="citations">
        <citation type="doi">10.1038/nmeth.f.303</citation>
    </xml>

    <xml name="pick_otus_reference_source">
        <conditional name="references">
            <param name="source_selector" type="select" label="Use reference sequences from">
                <option value="cached">Local cache</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param argument="--refseqs_fp" label="Reference sequences" type="select">
                    <options from_data_table="qiime_rep_set"/>
                </param>
            </when>
            <when value="history">
                <param argument="--refseqs_fp" type="data" format="fasta" label="Reference sequences to search against"/>
            </when>
        </conditional>
    </xml>
    <xml name="assign_taxonomy_reference_source">
        <conditional name="references">
            <param name="source_selector" type="select" label="Select a reference sequence file from">
                <option value="cached">The local cache</option>
                <option value="history">The active history</option>
            </param>
            <when value="cached">
                <param argument="--reference_seqs_fp" label="Reference sequences either used to generate a blast database (Blast) or used as training sequences for the selected classifier (RDP, Mothur)" type="select">
                    <options from_data_table="qiime_rep_set"/>
                </param>
            </when>
            <when value="history">
                <param argument="--reference_seqs_fp" type="data" format="fasta" label="Reference sequences to search against"/>
            </when>
        </conditional>
    </xml>
    <xml name="pick_otus_similarity">
        <param argument="--similarity" type="float" value="0.97" label="Sequence similarity threshold"/>
    </xml>
    <xml name="pick_otus_denovo_otu_id_prefix">
        <param argument="--denovo_otu_id_prefix" type="text" value="denovo" label="OTU identifier prefix for the de novo OTU pickers"/>
    </xml>
    <xml name="pick_otus_enable_rev_strand_match">
        <param argument="--enable_rev_strand_match" type="boolean" truevalue="--enable_rev_strand_match" falsevalue="" checked="false" label="Enable reverse strand matching?" help="Will double the amount of memory used"/>
    </xml>
    <xml name="pick_otus_suppress_presort_by_abundance_uclust">
        <param argument="--suppress_presort_by_abundance_uclust" type="boolean" truevalue="--suppress_presort_by_abundance_uclust" falsevalue="" checked="false" label="Suppress presorting of sequences by abundance?"/>
    </xml>
    <xml name="pick_otus_max">
        <param argument="--max_accepts" type="integer" value="1" label="Max_accepts value"/>
        <param argument="--max_rejects" type="integer" value="8" label="Max_rejects value"/>
    </xml>
    <xml name="pick_otus_stepwords">
        <param argument="--stepwords" type="integer" value="8" label="Stepwords value"/>
    </xml>
    <xml name="pick_otus_word_length">
        <param argument="--word_length" type="integer" value="8" label="Word length value"/>
    </xml>
    <xml name="pick_otus_suppress_prefilter_exact_match">
        <param argument="--suppress_prefilter_exact_match" type="boolean" truevalue="--suppress_prefilter_exact_match" falsevalue="" checked="false" label="Don't collapse exact matches before calling?"/>
    </xml>
</macros>