Mercurial > repos > iuc > chewbbaca_downloadschema

annotate macros.xml @ 2:a707d4098f09 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 501c1cb91f4b91ec93e6df6e555323bbe8e2b703
author iuc
date Fri, 07 Jun 2024 14:27:08 +0000
parents 4683f2baa5f0
children f502e55c34a3
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18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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1 <macros>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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2 <token name="@CHEW_VERSION@">3.3.3</token>
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a707d4098f09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 501c1cb91f4b91ec93e6df6e555323bbe8e2b703
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3 <token name="@VERSION_SUFFIX@">2</token>
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18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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4 <token name="@PROFILE@">22.05</token>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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5 <xml name="requirements">
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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6 <requirements>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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7 <requirement type="package" version="@CHEW_VERSION@">chewbbaca</requirement>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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8 <requirement type="package" version="2.15.0">blast</requirement>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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9 <requirement type="package" version="3.0">zip</requirement>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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10 <requirement type="package" version="2.1.11">fasttree</requirement>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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11 <yield/>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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12 </requirements>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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13 </xml>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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14 <xml name="citations">
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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15 <citations>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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16 <citation type="doi">10.1099/mgen.0.000166</citation>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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17 </citations>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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18 </xml>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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19 <xml name="species_id">
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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20 <option value="1">Streptococcus pyogenes</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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21 <option value="2">Acinetobacter baumannii</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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22 <option value="3">Arcobacter butzleri</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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23 <option value="4">Campylobacter jejuni</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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24 <option value="5">Escherichia coli</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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25 <option value="6">Listeria monocytogenes</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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26 <option value="7">Yersinia enterocolitica</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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27 <option value="8">Salmonella enterica</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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28 <option value="9">Streptococcus agalactiae</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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29 <option value="10">Brucella melitensis</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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30 <option value="11">Brucella</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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31 <option value="12">Clostridium perfringens</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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32 <option value="13">Clostridium chauvoei</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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33 <option value="14">Bacillus anthracis</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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34 <option value="15">Klebsiella oxytoca</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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35 <option value="16">Clostridium neonatale</option>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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36 </xml>
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37 <token name="@COMMON_INPUT@">
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38 --bsr $blast_score_ratio
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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39 --l $minimum_length
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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40 --t $translation_table
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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41 --st $size_threshold
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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42 </token>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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43 <xml name="common_param">
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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44 <param argument="--blast_score-ratio" type="float" min="0.0" max="1.0" value="0.6" label="BLAST Score Ratio value" />
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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45 <param argument="--translation-table" type="integer" min="0" value="11" label="Genetic code used to predict genes and to translate coding sequences"/>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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46 <param argument="--size-threshold" type="float" min="0" value="0.2" label="CDS size variation threshold"/>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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47 </xml>
18d7d8582206 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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48 </macros>