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planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
author artbio
date Sat, 17 Mar 2018 17:43:58 -0400
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b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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1 <?xml version="1.0"?>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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2 <macros>
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artbio
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3 <xml name="requirements">
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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4 <requirements>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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5 <requirement type="package" version="2.4.0">trinity</requirement>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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6 <yield/>
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artbio
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7 </requirements>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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8 </xml>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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9
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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10 <token name="@WRAPPER_VERSION@">2.4.0</token>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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12 <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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13 #if $pool.inputs.strand.is_strand_specific:
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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14 --SS_lib_type $pool.inputs.strand.library_type
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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15 #end if
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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16
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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17 $pool.inputs.jaccard_clip
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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18 </token>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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19
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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20 <xml name="input_paired_strand_jaccard">
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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21 <conditional name="strand">
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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22 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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23 <when value="false" />
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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24 <when value="true">
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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25 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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26 <option value="FR">Forward-Reverse</option>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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27 <option value="RF">Reverse-Forward</option>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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28 </param>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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29 </when>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
artbio
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30 </conditional>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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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"/>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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32 </xml>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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33
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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34 <xml name="citation">
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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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>
b3fe7c4ca5aa planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/trinity commit bfb22f460d6f3825ff1bd3eed924a5760c99c96d
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39 </macros>