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annotate macros.xml @ 18:d3b1249af60c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
author iuc
date Tue, 19 Dec 2017 04:21:46 -0500
parents 199aa6821ca5
children 171b827eadf2
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1 <?xml version="1.0"?>
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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2 <macros>
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3 <xml name="requirements">
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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4 <requirements>
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5 <requirement type="package" version="2.4.0">trinity</requirement>
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6 <yield/>
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7 </requirements>
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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8 </xml>
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9
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10 <token name="@WRAPPER_VERSION@">2.4.0</token>
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12 <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
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13 #if $inputs.strand.is_strand_specific:
199aa6821ca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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14 --SS_lib_type $inputs.strand.library_type
199aa6821ca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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15 #end if
199aa6821ca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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17 $inputs.jaccard_clip
199aa6821ca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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18 </token>
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20 <xml name="input_paired_strand_jaccard">
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21 <conditional name="strand">
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22 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
199aa6821ca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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23 <when value="false" />
199aa6821ca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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24 <when value="true">
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25 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
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26 <option value="FR">Forward-Reverse</option>
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27 <option value="RF">Reverse-Forward</option>
199aa6821ca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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28 </param>
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29 </when>
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30 </conditional>
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31 <param name="jaccard_clip" argument="--jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="Set if you expect high gene density with UTR overlap"/>
199aa6821ca5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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32 </xml>
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33
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34 <xml name="citation">
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35 <citations>
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36 <citation type="doi">10.1038/nbt.1883</citation>
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37 </citations>
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38 </xml>
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39 </macros>