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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
author iuc
date Tue, 08 Aug 2023 09:09:32 +0000
parents 57f477b57c35
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="@TOOL_VERSION@">trinity</requirement>
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5 <yield/>
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6 </requirements>
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7 </xml>
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8 <xml name="bio_tools">
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9 <xrefs>
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10 <xref type="bio.tools">trinity</xref>
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11 </xrefs>
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12 </xml>
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13 <token name="@TOOL_VERSION@">2.15.1</token>
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14 <token name="@VERSION_SUFFIX@">0</token>
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15
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16 <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
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17 #if $pool.inputs.strand.is_strand_specific == 'true':
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18 --SS_lib_type $pool.inputs.strand.library_type
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19 #end if
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21 $pool.inputs.jaccard_clip
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22 </token>
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23
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24 <xml name="input_paired_strand_jaccard">
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25 <conditional name="strand">
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26 <param name="is_strand_specific" type="select" label="Strand specific data">
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27 <option value="false">No</option>
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28 <option value="true">Yes</option>
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29 </param>
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30 <when value="false" />
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31 <when value="true">
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32 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
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33 <option value="FR">Forward-Reverse</option>
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34 <option value="RF">Reverse-Forward</option>
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35 </param>
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36 </when>
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37 </conditional>
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38 <param 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"/>
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39 </xml>
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40
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41 <xml name="is_strand_specific_f_r">
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42 <conditional name="strand">
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43 <param name="is_strand_specific" type="select" label="Strand specific data">
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44 <option value="false">No</option>
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45 <option value="true">Yes</option>
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46 </param>
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47 <when value="false"/>
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48 <when value="true">
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49 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
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50 <option value="F">F</option>
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51 <option value="R">R</option>
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52 </param>
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53 </when>
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54 </conditional>
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55 </xml>
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56
0
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57 <xml name="citation">
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58 <citations>
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59 <citation type="doi">10.1038/nbt.1883</citation>
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60 </citations>
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61 </xml>
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62 </macros>