annotate macro.xml @ 2:876d26806584 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmsesq2 commit 611b90f1628037f05d85905c88629a422d0a2053

<macros>
    <token name="@TOOL_VERSION@">17-b804f</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">22.05</token>
    <xml name="version_command">
        <version_command><![CDATA[mmseqs version]]></version_command>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">mmseqs2</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">MMseqs2</xref>
        </xrefs>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/nbt.3988</citation>
            <citation type="doi">10.1101/079681</citation>
            <citation type="doi">10.1038/s41467-018-04964-5</citation>
            <citation type="doi">10.1093/bioinformatics/bty1057</citation>
            <citation type="doi">10.1101/2020.11.27.401018</citation>
            <citation type="doi">10.1093/bioinformatics/btab184</citation>
        </citations>
    </xml>
    <xml name="prefilter_common_parameters">
            <param argument="--add-self-matches" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Artificially add entries of queries with themselves (for clustering)" help=""/>
            <param argument="-k" name="kmer_length" type="integer" min="0" value="0" label="k-mer length" help="(0: automatically set to optimum)"/>
            <param argument="--mask" type="select" label="Mask sequences in k-mer stage" help="">
                <option value="0">Without low complexity masking</option>
                <option value="1" selected="true">With low complexity masking</option>
            </param>
            <param argument="--mask-prob" type="float" min="0" value="0.9" label="Mask sequences if probablity is above threshold" help=""/>
            <param argument="--mask-lower-case" type="select" label="Mask lower case letters" help="">
                <option value="0" selected="true">Include region</option>
                <option value="1">Exclude region</option>
            </param>
            <param argument="--mask-n-repeat" type="integer" min="0" value="0" label="Repeat letters that occur > threshold in a row" help=""/>
    </xml>
    <xml name="search_type_aa">
                    <param argument="--search-type" type="select" label="Search type" help="" >
                        <option value="0" selected="true">Auto</option>
                        <option value="1">Amino acid</option>
                        <option value="2">Translated</option>
                        <option value="3">Nucleotide</option>
                        <option value="4">Translated nucleotide alignment</option>
                    </param>
    </xml>
    <xml name="search_type_nt">
                    <param argument="--search-type" type="select" label="Search type" help="" >
                        <option value="2">Translated</option>
                        <option value="3" selected="true">Nucleotide</option>
                        <option value="4">Translated nucleotide alignment</option>
                    </param>
    </xml>
    <xml name="align_common_parameters">
            <param argument="-a" name="convertalis" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Add backtrace string" help="Convert to alignments with mmseqs convertalis module"/>
            <param argument="--alignment-output-mode" type="select" label="Alignment mode : How to compute the alignment" help="" >
                <option value="0" selected="true">Automatic</option>
                <option value="1">Only score and end_pos</option>
                <option value="2">Also start_pos and cov</option>
                <option value="3">Also seq.id</option>
                <option value="4">Only ungapped alignment</option>
                <option value="5">score only (output) cluster format</option>
            </param>
            <param argument="--wrapped-scoring" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Double the (nucleotide) query sequence during the scoring process" help="Allow wrapped diagonal scoring around end and start"/>
            <param argument="--min-aln-len" type="integer" min="0" value="0" label="Minimum alignment length" help=""/>
            <param argument="--seq-id-mode" type="select" label="Sequence identity mode" help="" >
                <option value="0" selected="true">Alignment length</option>
                <option value="1">Shorter</option>
                <option value="2">Longer sequence</option>
            </param>
            <param argument="--alt-ali" type="integer" min="0" value="0" label="Number of alternative alignments to show" help=""/>
            <param argument="--score-bias" type="float" value="0" label="Score bias when computing Smith-Waterman alignment" help=""/>
            <param argument="--realign" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Compute more conservative, shorter alignments" help="Scores and E-values not changed"/>
            <param argument="--realign-score-bias" type="float" value="-0.200" label="Additional bias when computing realignment" help=""/>
            <param argument="--realign-max-seqs" type="integer" min="0" value="2147483647" label="Maximum number of results to return in realignment" help=""/>
            <param argument="--corr-score-weight" type="float" value="0" label="Weight of backtrace correlation score that is added to the alignment score" help=""/>
    </xml>
    <xml name="common_section">
        <section name="common" title="Common">
            <param argument="--max-seq-len" type="integer" min="0" value="65535" optional="true" label="Maximum sequence length" help=""/>
        </section>
    </xml>
    <xml name="expert_common_parameters">
            <param argument="--filter-hits" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Filter hits by seq.id. and coverage" help=""/>
            <param argument="--sort-results" type="select" label="Sort results" help="">
                <option value="0" selected="true">No sorting</option>
                <option value="1">Sort by E-value (Alignment) or seq.id. (Hamming)</option>
            </param>
    </xml>
</macros>