Mercurial > repos > iuc > mothur_get_sharedseqs

annotate get.sharedseqs.xml @ 2:d5b97213e4ba draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:23:51 -0400
parents 1d496917a707
children ea2e9c5e62b9
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1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_get_sharedseqs" name="Get.sharedseqs" version="@WRAPPER_VERSION@.0">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Get shared sequences at each distance from list and group</description>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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12 ## create symlinks to input datasets
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$infile.otu' infile_otu.dat &&
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 #if $infile.intype == "in_listgroup":
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$infile.group' infile.group.dat &&
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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16 ln -s '$infile.fasta' infile_fasta.dat &&
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 ln -s '$count_in' count_in.dat &&
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 #end if
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19
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20 echo 'get.sharedseqs(
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 #if $infile.intype == "in_listgroup":
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 list=infile_otu.dat
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 #if $group:
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 ,group=infile.group.dat
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 #elif $count_in:
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 ,count=count_in.dat
0
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28 #end if
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29
2
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30 #if $infile.fasta:
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 ,fasta=infile_fasta.dat
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 #end if
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33 #else
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34 shared=infile_otu.dat
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 #end if
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36 #if $infile.label:
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 ,label=${ str($infile.label).replace(",","-") }
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 #end if
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39 #if $infile.seqsfrom.selection == "unique" and $infile.seqsfrom.groups:
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 ,uniquegroups=${ str($infile.seqsfrom.groups).replace(",","-") }
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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41 #end if
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42 #if $infile.seqsfrom.selection == "shared" and $infile.seqsfrom.groups:
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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43 ,sharedgroups=${ str($infile.seqsfrom.groups).replace(",","-") }
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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44 #end if
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45 #if $output:
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46 ,output=$output
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47 #end if
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48 )'
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49 | sed 's/ //g' ## mothur trips over whitespace
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50 | mothur
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51 | tee mothur.out.log
0
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52 ]]></command>
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53 <inputs>
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54 <conditional name="infile">
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55 <param name="intype" type="select" label="Will you be supplying a shared file or a list and group file?" help="">
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56 <option value="in_shared">Shared file</option>
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57 <option value="in_listgroup">OTU list and group file</option>
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58 </param>
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59 <when value="in_shared">
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60 <param name="otu" type="data" format="mothur.shared" label="list - OTU List or shared file"/>
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61 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made.">
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62 <options>
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63 <filter type="data_meta" ref="otu" key="labels"/>
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64 </options>
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65 </param>
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66 <conditional name="seqsfrom">
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67 <param name="selection" type="select" label="Select Groups" help="">
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68 <option value="all" selected="true">None (use all groups)</option>
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69 <option value="unique">OTUs that contain ONLY sequences from the selected groups</option>
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70 <option value="shared">OTUs that contain sequences from the selected groups</option>
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71 </param>
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72 <when value="unique">
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73 <param name="groups" type="select" multiple="true" label="unique - Group to analyze">
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74 <options>
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75 <filter type="data_meta" ref="otu" key="groups"/>
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76 </options>
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77 </param>
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78 </when>
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79 <when value="shared">
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80 <param name="groups" type="select" multiple="true" label="shared - Groups to analyze">
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81 <options>
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82 <filter type="data_meta" ref="otu" key="groups"/>
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83 </options>
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84 </param>
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85 </when>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
86 <when value="all"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
87 </conditional>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
88 </when>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
89 <when value="in_listgroup">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
90 <param name="otu" type="data" format="mothur.list" label="list - OTU List or shared file"/>
2
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
91 <param name="label" type="select" optional="true" multiple="true" label="label - Select OTU Labels to include"
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
92 help="By default all are included if no selection is made">
0
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
93 <options>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
94 <filter type="data_meta" ref="otu" key="labels"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
95 </options>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
96 </param>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
97 <param name="group" type="data" format="mothur.groups" optional="true" label="group - not required if using a shared file"/>
2
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
98 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
99 <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Dataset"
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
100 help="will output a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified"/>
0
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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101 <conditional name="seqsfrom">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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102 <param name="selection" type="select" label="Select Groups" help="">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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103 <option value="all" selected="true">None (use all groups)</option>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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104 <option value="unique">OTUs that contain ONLY sequences from the selected groups</option>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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105 <option value="shared">OTUs that contain sequences from the selected groups</option>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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106 </param>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
107 <when value="unique">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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108 <param name="groups" type="select" multiple="true" label="unique - Group to analyze">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
109 <options>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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110 <filter type="data_meta" ref="group" key="groups"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
111 </options>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
112 </param>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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113 </when>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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114 <when value="shared">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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115 <param name="groups" type="select" multiple="true" label="shared - Groups to analyze">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
116 <options>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
117 <filter type="data_meta" ref="group" key="groups"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
118 </options>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
119 </param>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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120 </when>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
121 <when value="all"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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122 </conditional>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
123 </when>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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124 </conditional>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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125 <param name="output" type="select" label="output - select the output format" help="accnos can be used with get.seqs, list.seqs and remove.seqs">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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126 <option value="" selected="true">default: (name group bin_number)</option>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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127 <option value="accnos">accnos (name)</option>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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128 </param>
2
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
129 <expand macro="param-savelog"/>
0
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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130 </inputs>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
131 <outputs>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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132 <expand macro="logfile-output"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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133 <collection name="sharedseqs" type="list" label="${tool.name} on ${on_string}: shared.seqs">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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134 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.seqs" format="tabular"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
135 <filter>output != 'accnos'</filter>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
136 </collection>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
137 <collection name="sharedaccnos" type="list" label="${tool.name} on ${on_string}: shared.accnos">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
138 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.accnos" format="mothur.accnos"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
139 <filter>output == 'accnos'</filter>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
140 </collection>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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141 <collection name="sharedfastas" type="list" label="${tool.name} on ${on_string}: shared.fastas">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
142 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.fasta" format="fasta"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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143 <filter>infile['fasta']</filter>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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144 </collection>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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145 </outputs>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
146 <tests>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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147 <test><!-- test with shared file -->
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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148 <param name="intype" value="in_shared"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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149 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
150 <param name="selection" value="shared"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
151 <output_collection name="sharedseqs" count="35">
2
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
152 <element name="0.41.unique.forest_pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
0
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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153 </output_collection>
2
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
154 <param name="savelog" value="true"/>
0
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
155 <expand macro="logfile-test"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
156 </test>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
157 <test><!-- test with list and group file -->
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
158 <param name="intype" value="in_listgroup"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
159 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
160 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
161 <output_collection name="sharedseqs" count="35">
2
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
162 <element name="0.41.unique.forest_pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
0
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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163 </output_collection>
2
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
164 <param name="savelog" value="true"/>
0
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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165 <expand macro="logfile-test"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
166 </test>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
167 <test><!-- test with shared seqs and subset of labels -->
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
168 <param name="intype" value="in_shared"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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169 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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170 <param name="selection" value="shared"/>
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171 <param name="groups" value="forest,pasture"/>
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172 <param name="label" value="0.03,0.33,0.41"/>
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173 <output_collection name="sharedseqs" count="3">
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174 <element name="0.41.forest_pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
0
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175 </output_collection>
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176 <param name="savelog" value="true"/>
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177 <expand macro="logfile-test"/>
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178 </test>
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179 <test><!-- test with unique seqs and subset of groups -->
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180 <param name="intype" value="in_shared"/>
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181 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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182 <param name="selection" value="unique"/>
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183 <param name="groups" value="pasture"/>
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184 <output_collection name="sharedseqs" count="34">
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185 <element name="0.41.unique.pasture" md5="f4735f56d96d13cd603ca0b11c4bc231" ftype="tabular"/>
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186 </output_collection>
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187 <param name="savelog" value="true"/>
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188 <expand macro="logfile-test"/>
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189 </test>
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190 <test><!-- test with accnos output -->
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191 <param name="intype" value="in_shared"/>
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192 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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193 <param name="output" value="accnos"/>
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194 <output_collection name="sharedaccnos" count="35">
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195 <element name="0.41.unique.forest_pasture" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.accnos"/>
0
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196 </output_collection>
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197 <param name="savelog" value="true"/>
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198 <expand macro="logfile-test"/>
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199 </test>
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200 <test><!-- test with fasta input and output -->
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201 <param name="intype" value="in_listgroup"/>
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202 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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203 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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204 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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205 <output_collection name="sharedseqs" count="35">
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206 <element name="0.41.unique.forest_pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
0
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207 </output_collection>
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208 <output_collection name="sharedfastas" count="35">
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209 <element name="0.41.unique.forest_pasture" md5="fd4265d7c139d2d3acf8e19e6337ee28" ftype="fasta"/>
0
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210 </output_collection>
2
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211 <param name="savelog" value="true"/>
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212 <expand macro="logfile-test"/>
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213 </test>
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214 </tests>
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215 <help><![CDATA[
0
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216
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217 @MOTHUR_OVERVIEW@
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218
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219 **Command Documentation**
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220
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221 The get.sharedseqs_ command takes a list and group file and outputs a .shared.seqs file for each distance. This is useful for those cases where you might be interested in identifying sequences that are either unique or shared by specific groups, which you could then classify.
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222
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223 .. _get.sharedseqs: https://www.mothur.org/wiki/Get.sharedseqs
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224
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225 v1.21.0: Updated to Mothur 1.33, added shared file option
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226
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227 ]]></help>
0
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228 <expand macro="citations"/>
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229 </tool>