Mercurial > repos > iuc > mothur_get_sharedseqs

annotate get.sharedseqs.xml @ 10:ea2e9c5e62b9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 12:00:29 +0000
parents d5b97213e4ba
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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>
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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="biotools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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10 <command><![CDATA[
2
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11 @SHELL_OPTIONS@
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12
2
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13 ## 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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14 ln -s '$infile.otu' infile_otu.dat &&
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15 #if $infile.intype == "in_listgroup":
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16 ln -s '$infile.group' infile.group.dat &&
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17 ln -s '$infile.fasta' infile_fasta.dat &&
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18 ln -s '$count_in' count_in.dat &&
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19 #end if
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21 echo 'get.sharedseqs(
d5b97213e4ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 #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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23 list=infile_otu.dat
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24
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25 #if $group:
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26 ,group=infile.group.dat
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27 #elif $count_in:
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28 ,count=count_in.dat
0
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29 #end if
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30
2
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31 #if $infile.fasta:
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32 ,fasta=infile_fasta.dat
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33 #end if
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34 #else
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35 shared=infile_otu.dat
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36 #end if
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37 #if $infile.label:
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38 ,label=${ str($infile.label).replace(",","-") }
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39 #end if
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40 #if $infile.seqsfrom.selection == "unique" and $infile.seqsfrom.groups:
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41 ,uniquegroups=${ str($infile.seqsfrom.groups).replace(",","-") }
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42 #end if
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43 #if $infile.seqsfrom.selection == "shared" and $infile.seqsfrom.groups:
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44 ,sharedgroups=${ str($infile.seqsfrom.groups).replace(",","-") }
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45 #end if
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46 #if $output:
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47 ,output=$output
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48 #end if
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49 )'
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50 | sed 's/ //g' ## mothur trips over whitespace
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51 | mothur
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52 | tee mothur.out.log
0
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53 ]]></command>
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54 <inputs>
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55 <conditional name="infile">
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56 <param name="intype" type="select" label="Will you be supplying a shared file or a list and group file?" help="">
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57 <option value="in_shared">Shared file</option>
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58 <option value="in_listgroup">OTU list and group file</option>
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59 </param>
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60 <when value="in_shared">
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61 <param name="otu" type="data" format="mothur.shared" label="list - OTU List or shared file"/>
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62 <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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63 <options>
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64 <filter type="data_meta" ref="otu" key="labels"/>
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65 </options>
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66 </param>
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67 <conditional name="seqsfrom">
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68 <param name="selection" type="select" label="Select Groups" help="">
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69 <option value="all" selected="true">None (use all groups)</option>
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70 <option value="unique">OTUs that contain ONLY sequences from the selected groups</option>
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71 <option value="shared">OTUs that contain sequences from the selected groups</option>
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72 </param>
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73 <when value="unique">
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74 <param name="groups" type="select" multiple="true" label="unique - Group to analyze">
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75 <options>
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76 <filter type="data_meta" ref="otu" key="groups"/>
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77 </options>
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78 </param>
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79 </when>
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80 <when value="shared">
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81 <param name="groups" type="select" multiple="true" label="shared - Groups to analyze">
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82 <options>
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83 <filter type="data_meta" ref="otu" key="groups"/>
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84 </options>
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85 </param>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
86 </when>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
87 <when value="all"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
88 </conditional>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
89 </when>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
90 <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
91 <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
92 <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
93 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
94 <options>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
95 <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
96 </options>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
97 </param>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
98 <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
99 <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
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100 <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
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101 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
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102 <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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103 <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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104 <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
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105 <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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106 <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
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107 </param>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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108 <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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109 <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
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110 <options>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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111 <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
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112 </options>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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113 </param>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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114 </when>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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115 <when value="shared">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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116 <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
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117 <options>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
118 <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:
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119 </options>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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120 </param>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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121 </when>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
122 <when value="all"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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123 </conditional>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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124 </when>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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125 </conditional>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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126 <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
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127 <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
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128 <option value="accnos">accnos (name)</option>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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129 </param>
2
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iuc
parents: 0
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130 <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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131 </inputs>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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132 <outputs>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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133 <expand macro="logfile-output"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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134 <collection name="sharedseqs" type="list" label="${tool.name} on ${on_string}: shared.seqs">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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135 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.seqs" format="tabular"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
136 <filter>output != 'accnos'</filter>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
137 </collection>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
138 <collection name="sharedaccnos" type="list" label="${tool.name} on ${on_string}: shared.accnos">
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
139 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.accnos" format="mothur.accnos"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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140 <filter>output == 'accnos'</filter>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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141 </collection>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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142 <collection name="sharedfastas" type="list" label="${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
143 <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
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144 <filter>infile['fasta']</filter>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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145 </collection>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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146 </outputs>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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147 <tests>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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148 <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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149 <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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150 <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
151 <param name="selection" value="shared"/>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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152 <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
153 <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
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154 </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
155 <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
156 <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
157 </test>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
158 <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:
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159 <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
160 <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
161 <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:
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162 <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
163 <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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164 </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
165 <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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166 <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
167 </test>
1d496917a707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
168 <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:
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169 <param name="intype" value="in_shared"/>
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170 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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171 <param name="selection" value="shared"/>
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172 <param name="groups" value="forest,pasture"/>
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173 <param name="label" value="0.03,0.33,0.41"/>
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174 <output_collection name="sharedseqs" count="3">
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175 <element name="0.41.forest_pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
0
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176 </output_collection>
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177 <param name="savelog" value="true"/>
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178 <expand macro="logfile-test"/>
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179 </test>
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180 <test><!-- test with unique seqs and subset of groups -->
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181 <param name="intype" value="in_shared"/>
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182 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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183 <param name="selection" value="unique"/>
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184 <param name="groups" value="pasture"/>
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185 <output_collection name="sharedseqs" count="34">
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186 <element name="0.41.unique.pasture" md5="f4735f56d96d13cd603ca0b11c4bc231" ftype="tabular"/>
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187 </output_collection>
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188 <param name="savelog" value="true"/>
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189 <expand macro="logfile-test"/>
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190 </test>
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191 <test><!-- test with accnos output -->
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192 <param name="intype" value="in_shared"/>
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193 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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194 <param name="output" value="accnos"/>
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195 <output_collection name="sharedaccnos" count="35">
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196 <element name="0.41.unique.forest_pasture" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.accnos"/>
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197 </output_collection>
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198 <param name="savelog" value="true"/>
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199 <expand macro="logfile-test"/>
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200 </test>
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201 <test><!-- test with fasta input and output -->
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202 <param name="intype" value="in_listgroup"/>
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203 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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204 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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205 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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206 <output_collection name="sharedseqs" count="35">
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207 <element name="0.41.unique.forest_pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
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208 </output_collection>
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209 <output_collection name="sharedfastas" count="35">
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210 <element name="0.41.unique.forest_pasture" md5="fd4265d7c139d2d3acf8e19e6337ee28" ftype="fasta"/>
0
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211 </output_collection>
2
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212 <param name="savelog" value="true"/>
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213 <expand macro="logfile-test"/>
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214 </test>
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215 </tests>
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216 <help><![CDATA[
0
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217
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218 @MOTHUR_OVERVIEW@
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219
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220 **Command Documentation**
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221
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222 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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223
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224 .. _get.sharedseqs: https://www.mothur.org/wiki/Get.sharedseqs
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225
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226 v1.21.0: Updated to Mothur 1.33, added shared file option
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227
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228 ]]></help>
0
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229 <expand macro="citations"/>
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230 </tool>