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view macros.xml @ 0:2f0dc62d0a19 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss commit 08f38b1f9b4241ba9037c64f732621efc628fd43
author iuc
date Mon, 20 Jan 2025 16:22:05 +0000
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<macros>
    <token name="@PROFILE@">23.1</token>
    <token name="@VERSION@">6.6.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">emboss</requirement>
            <requirement type="package" version="5.26">perl</requirement>
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">emboss</xref>
        </xrefs>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1016/S0168-9525(00)02024-2</citation>
            <citation type="doi">10.1101/gr.5578007</citation>
            <yield />
        </citations>
    </xml>

    <xml name="scoring_matrix">
        <param argument="-datafile" type="select" optional="true" label="Scoring matrix" help="This is the scoring matrix used when comparing sequences. By default it is EBLOSUM62 (for proteins) or EDNAFULL (for nucleic sequences)">
            <option value="EBLOSUM30">EBLOSUM30</option>
            <option value="EBLOSUM35">EBLOSUM35</option>
            <option value="EBLOSUM40">EBLOSUM40</option>
            <option value="EBLOSUM45">EBLOSUM45</option>
            <option value="EBLOSUM50">EBLOSUM50</option>
            <option value="EBLOSUM55">EBLOSUM55</option>
            <option value="EBLOSUM60">EBLOSUM60</option>
            <option value="EBLOSUM62">EBLOSUM62</option>
            <option value="EBLOSUM62-12">EBLOSUM62-12</option>
            <option value="EBLOSUM65">EBLOSUM65</option>
            <option value="EBLOSUM70">EBLOSUM70</option>
            <option value="EBLOSUM75">EBLOSUM75</option>
            <option value="EBLOSUM80">EBLOSUM80</option>
            <option value="EBLOSUM85">EBLOSUM85</option>
            <option value="EBLOSUM90">EBLOSUM90</option>
            <option value="EBLOSUMN">EBLOSUMN</option>
            <option value="EDNAFULL">EDNAFULL</option>
            <option value="EDNAMAT">EDNAMAT</option>
            <option value="EDNASIMPLE">EDNASIMPLE</option>
            <option value="ENUC.4.2">ENUC.4.2</option>
            <option value="ENUC.4.4">ENUC.4.4</option>
            <option value="EPAM10">EPAM10</option>
            <option value="EPAM100">EPAM100</option>
            <option value="EPAM110">EPAM110</option>
            <option value="EPAM120">EPAM120</option>
            <option value="EPAM130">EPAM130</option>
            <option value="EPAM140">EPAM140</option>
            <option value="EPAM150">EPAM150</option>
            <option value="EPAM160">EPAM160</option>
            <option value="EPAM170">EPAM170</option>
            <option value="EPAM180">EPAM180</option>
            <option value="EPAM190">EPAM190</option>
            <option value="EPAM20">EPAM20</option>
            <option value="EPAM200">EPAM200</option>
            <option value="EPAM210">EPAM210</option>
            <option value="EPAM220">EPAM220</option>
            <option value="EPAM230">EPAM230</option>
            <option value="EPAM240">EPAM240</option>
            <option value="EPAM250">EPAM250</option>
            <option value="EPAM260">EPAM260</option>
            <option value="EPAM270">EPAM270</option>
            <option value="EPAM280">EPAM280</option>
            <option value="EPAM290">EPAM290</option>
            <option value="EPAM30">EPAM30</option>
            <option value="EPAM300">EPAM300</option>
            <option value="EPAM310">EPAM310</option>
            <option value="EPAM320">EPAM320</option>
            <option value="EPAM330">EPAM330</option>
            <option value="EPAM340">EPAM340</option>
            <option value="EPAM350">EPAM350</option>
            <option value="EPAM360">EPAM360</option>
            <option value="EPAM370">EPAM370</option>
            <option value="EPAM380">EPAM380</option>
            <option value="EPAM390">EPAM390</option>
            <option value="EPAM40">EPAM40</option>
            <option value="EPAM400">EPAM400</option>
            <option value="EPAM410">EPAM410</option>
            <option value="EPAM420">EPAM420</option>
            <option value="EPAM430">EPAM430</option>
            <option value="EPAM440">EPAM440</option>
            <option value="EPAM450">EPAM450</option>
            <option value="EPAM460">EPAM460</option>
            <option value="EPAM470">EPAM470</option>
            <option value="EPAM480">EPAM480</option>
            <option value="EPAM490">EPAM490</option>
            <option value="EPAM50">EPAM50</option>
            <option value="EPAM500">EPAM500</option>
            <option value="EPAM60">EPAM60</option>
            <option value="EPAM70">EPAM70</option>
            <option value="EPAM80">EPAM80</option>
            <option value="EPAM90">EPAM90</option>
            <option value="SSSUB">SSSUB</option>
        </param>
    </xml>

    <xml name="param_brief">
        <param argument="-brief" type="select" label="Brief identity and similarity">
            <option value="yes">Yes</option>
            <option value="no">No</option>
        </param>
    </xml>

    <xml name="gap_penalties">
        <param argument="-gapopen" type="float" value="10.0" min="1.0" max="100.0" label="Gap open penalty" />
        <param argument="-gapextend" type="float" value="0.5" min="0.0" max="10.0"  label="Gap extension penalty" />
    </xml>

    <xml name="endgap_penalties">
        <conditional name="endgap">
            <param argument="-endweight" type="select" label="Apply end gap penalties?" help="">
                <option value="yes">yes</option>
                <option value="no" selected="true">no</option>
            </param>
            <when value="yes">
                <param argument="-endopen" type="float" value="10.0" min="0.0" max="100.0" label="Penalty for creation of and end gap." help="The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences."/>
                <param argument="-endextend" type="float" value="0.5" min="0.0" max="10.0" label="The end gap extensionpenalty" help="this penalty is added to the end gap penalty for each base or residue in the end gap."/>
            </when>
            <when value="no"/>
        </conditional>
    </xml>

    <xml name="choose_alignment_output_format">
        <param name="out_format1" type="select" label="Output alignment file format">
            <option value="srspair">SRS pair (p)</option>
            <option value="simple">Simple (m)</option>
            <option value="fasta">FASTA (m)</option>
            <option value="msf">MSF (m)</option>
            <option value="srs">SRS (m)</option>
            <option value="pair">Pair (p)</option>
            <option value="markx0">Markx0 (p)</option>
            <option value="markx1">Markx1 (p)</option>
            <option value="markx2">Markx2 (p)</option>
            <option value="markx3">Markx3 (p)</option>
            <option value="markx10">Markx10 (p)</option>
            <option value="score">Score (p)</option>
        </param>
    </xml>

    <xml name="change_alignment_output_format">
        <change_format>
            <when input="out_format1" value="fasta" format="fasta"/>
            <when input="out_format1" value="score" format="score"/>
            <when input="out_format1" value="pair" format="pair"/>
            <when input="out_format1" value="srspair" format="srspair"/>
            <when input="out_format1" value="simple" format="simple"/>
            <when input="out_format1" value="srs" format="srs"/>
            <when input="out_format1" value="msf" format="msf"/>
            <when input="out_format1" value="markx0" format="markx0"/>
            <when input="out_format1" value="markx1" format="markx1"/>
            <when input="out_format1" value="markx2" format="markx2"/>
            <when input="out_format1" value="markx3" format="markx3"/>
            <when input="out_format1" value="markx10" format="markx10"/>
        </change_format>
    </xml>
</macros>