Mercurial > repos > iuc > trinity_align_and_estimate_abundance

annotate macros.xml @ 8:a43c8a18af2a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
author iuc
date Fri, 15 Dec 2017 07:53:44 -0500
parents 3727a3fecc79
children 0bace3da1ade
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f292d57ca09e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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1 <?xml version="1.0"?>
f292d57ca09e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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2 <macros>
f292d57ca09e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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3 <xml name="requirements">
f292d57ca09e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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4 <requirements>
5
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5 <requirement type="package" version="2.4.0">trinity</requirement>
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f292d57ca09e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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6 <yield/>
f292d57ca09e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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7 </requirements>
f292d57ca09e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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8 </xml>
f292d57ca09e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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9
5
3727a3fecc79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
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10 <token name="@WRAPPER_VERSION@">2.4.0</token>
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f292d57ca09e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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12 <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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13 #if $inputs.strand.is_strand_specific:
a43c8a18af2a 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
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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15 #end if
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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17 $inputs.jaccard_clip
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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18 </token>
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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20 <xml name="input_paired_strand_jaccard">
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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21 <conditional name="strand">
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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22 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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23 <when value="false" />
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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24 <when value="true">
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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25 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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26 <option value="FR">Forward-Reverse</option>
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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27 <option value="RF">Reverse-Forward</option>
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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28 </param>
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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29 </when>
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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30 </conditional>
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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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"/>
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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32 </xml>
a43c8a18af2a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
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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>
f292d57ca09e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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39 </macros>