Mercurial > repos > iuc > obi_uniq

annotate macros.xml @ 1:e0655b546470 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
author iuc
date Fri, 12 Oct 2018 06:23:42 -0400
parents 4c2b715a258a
children c0f7b58b4ce4
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4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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2 <macros>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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3 <xml name="requirements">
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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4 <requirements>
1
e0655b546470 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 0
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5 <requirement type="package" version="@TOOL_VERSION@">obitools</requirement>
0
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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6 </requirements>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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7 </xml>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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8
1
e0655b546470 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
iuc
parents: 0
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9 <token name="@TOOL_VERSION@">1.2.11</token>
0
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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10
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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11 <xml name="stdio">
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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12 <stdio>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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13 <exit_code range="1:" level="fatal" description="Error in Obitools execution" />
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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14 </stdio>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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15 </xml>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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16
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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17 <token name="@OBITOOLS_LINK@">
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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18 <![CDATA[
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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19 --------
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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21 **Project links:**
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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22
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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23 `OBITools`_
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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25 .. _OBITools: http://metabarcoding.org/obitools/
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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26 ]]>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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27 </token>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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28
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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29 <xml name="attributes">
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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30 <option value="ali_dir" selected="true">ali_dir</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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31 <option value="ali_length">ali_length</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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32 <option value="avg_quality">avg_quality</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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33 <option value="best_match">best_match</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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34 <option value="best_identity">best_identity</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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35 <option value="class">class</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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36 <option value="cluster">cluster</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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37 <option value="complemented">complemented</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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38 <option value="count">count</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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39 <option value="cut">cut</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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40 <option value="direction">direction</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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41 <option value="distance">distance</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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42 <option value="error">error</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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43 <option value="experiment">experiment</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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44 <option value="family">family</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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45 <option value="family_name">family_name</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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46 <option value="forward_error">forward_error</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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47 <option value="forward_match">forward_match</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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48 <option value="forward_primer">forward_primer</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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49 <option value="forward_score">forward_score</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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50 <option value="forward_tag">forward_tag</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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51 <option value="forward_tm">forward_tm</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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52 <option value="genus">genus</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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53 <option value="genus_name">genus_name</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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54 <option value="head_quality">head_quality</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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55 <option value="id_status">id_status</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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56 <option value="merged_star">merged_star</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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57 <option value="merged">merged</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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58 <option value="mid_quality">mid_quality</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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59 <option value="mode">mode</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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60 <option value="obiclean_cluster">obiclean_cluster</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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61 <option value="obiclean_count">obiclean_count</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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62 <option value="obiclean_head">obiclean_head</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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63 <option value="obiclean_headcount">obiclean_headcount</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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64 <option value="obiclean_internalcount">obiclean_internalcount</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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65 <option value="obiclean_samplecount">obiclean_samplecount</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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66 <option value="obiclean_singletoncount">obiclean_singletoncount</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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67 <option value="obiclean_status">obiclean_status</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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68 <option value="occurrence">occurrence</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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69 <option value="order">order</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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70 <option value="order_name">order_name</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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71 <option value="pairend_limit ">pairend_limit </option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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72 <option value="partial ">partial </option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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73 <option value="rank">rank</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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74 <option value="reverse_error">reverse_error</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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75 <option value="reverse_match">reverse_match</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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76 <option value="reverse_primer">reverse_primer</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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77 <option value="reverse_score">reverse_score</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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78 <option value="reverse_tag">reverse_tag</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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79 <option value="reverse_tm">reverse_tm</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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80 <option value="sample">sample</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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81 <option value="scientific_name">scientific_name</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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82 <option value="score">score</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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83 <option value="score_norm">score_norm</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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84 <option value="select">select</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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85 <option value="seq_ab_match">seq_ab_match</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
parents:
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86 <option value="seq_a_single">seq_a_single</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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87 <option value="seq_a_mismatch">seq_a_mismatch</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
iuc
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88 <option value="seq_a_deletion">seq_a_deletion</option>
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89 <option value="seq_a_insertion">seq_a_insertion</option>
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90 <option value="seq_b_single">seq_b_single</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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91 <option value="seq_b_mismatch">seq_b_mismatch</option>
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92 <option value="seq_b_deletion">seq_b_deletion</option>
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93 <option value="seq_b_insertion">seq_b_insertion</option>
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94 <option value="seq_length">seq_length</option>
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95 <option value="seq_length_ori">seq_length_ori</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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96 <option value="seq_rank">seq_rank</option>
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97 <option value="sminL">sminL</option>
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98 <option value="sminR">sminR</option>
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99 <option value="species">species</option>
4c2b715a258a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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100 <option value="species_list">species_list</option>
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101 <option value="species_name">species_name</option>
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102 <option value="status">status</option>
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103 <option value="strand">strand</option>
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104 <option value="tail_quality">tail_quality</option>
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105 <option value="taxid">taxid</option>
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106 </xml>
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107
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108 <xml name="inputtype">
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109 <option value="--genbank">genbank</option>
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110 <option value="--embl">embl</option>
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111 <option value="--sanger">sanger</option>
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112 <option value="--solexa">solexa</option>
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113 <option value="--ecopcr">ecopcr</option>
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114 <option value="--ecopcrdb">ecopcrdb</option>
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115 <option value="--fasta" selected="true">fasta</option>
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116 </xml>
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117
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118 <xml name="sanitizer">
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119 <sanitizer invalid_char="test">
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120 <valid initial="default">
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121 <!--add value="&quot;"/-->
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122 </valid>
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123 <mapping initial="default">
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124 <add source="&gt;" target="\&gt;"/>
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125 <add source="&quot;" target="\&quot;"/>
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126 </mapping>
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127 </sanitizer>
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128 </xml>
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129
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130 <xml name="citation">
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131 <citations>
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132 <citation type="doi">10.1111/1755-0998.12428</citation>
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133 </citations>
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134 </xml>
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135
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136 </macros>