Mercurial > repos > iuc > mothur_get_oturep

annotate get.oturep.xml @ 0:e6758f2f744b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:19:22 -0400
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children 07d536eabf6c
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0
e6758f2f744b 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_oturep" name="Get.oturep" version="@WRAPPER_VERSION@.0">
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2 <description>Generate a fasta with a representative sequence for each OTU</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="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[
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10 @SHELL_OPTIONS@
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11
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12 ## create symlinks to input datasets
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13 ln -s "$otu" otu.dat &&
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14 #if $method_condition.method_switch == "distance":
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15 ln -s "$method_condition.matrix_condition.dist" dist.dat &&
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16 ln -s "$method_condition.matrix_condition.nameOrCount" nameOrCount.dat &&
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17 ln -s "$method_condition.fasta" fasta.dat &&
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18 #if $method_condition.pick.type == "yes":
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19 ln -s "$method_condition.pick.group" group.dat &&
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20 #end if
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21 #elif $method_condition.method_switch == "abundance":
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22 ln -s "$method_condition.nameOrCount" nameOrCount.dat &&
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23 #end if
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24
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25 echo 'get.oturep(
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26 list=otu.dat,
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27 #if $sorted:
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28 sorted=$sorted,
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29 #end if
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30 #if $label:
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31 label=${ str($label).replace(",","-") },
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32 #end if
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33 #if $method_condition.method_switch == "distance":
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34 method=distance,
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35 #if $method_condition.matrix_condition.matrix_format == "column":
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36 column=dist.dat,
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37 #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"):
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38 name=nameOrCount.dat,
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39 #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"):
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40 count=nameOrCount.dat,
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41 #end if
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42 #elif $method_condition.matrix_condition.matrix_format == "phylip":
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43 phylip=dist.dat,
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44 #if $method_condition.matrix_condition.nameOrCount:
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45 #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"):
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46 name=nameOrCount.dat,
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47 #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"):
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48 count=nameOrCount.dat,
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49 #end if
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50 #end if
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51 #end if
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52 #if $method_condition.fasta:
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53 fasta=fasta.dat,
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54 #end if
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55 #if $method_condition.pick.type == "yes":
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56 #if $method_condition.pick.group:
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57 group=group.dat,
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58 #end if
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59 #if $method_condition.pick.groups:
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60 groups=${ str($method_condition.pick.groups).replace(",","-") },
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61 #end if
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62 #end if
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63 large=$method_condition.large
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64 #elif $method_condition.method_switch == "abundance":
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65 method=abundance,
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66 #if $method_condition.nameOrCount.is_of_type("mothur.names"):
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67 name=nameOrCount.dat
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68 #elif $method_condition.nameOrCount.is_of_type("mothur.count_table"):
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69 count=nameOrCount.dat
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70 #end if
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71 #end if
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72 )'
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73 | sed 's/ //g' ## mothur trips over whitespace
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74 | mothur
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75 | tee mothur.out.log
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76 ]]></command>
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77 <inputs>
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78 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
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79 <conditional name="method_condition">
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80 <param name="method_switch" type="select" label="Method to use for the selection of the representative sequences" help="The distance method finds the sequence with the smallest maximum distance to other sequences. The abundance method chooses the most abundant sequence in the OTU as the representative.">
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81 <option value="distance" selected="true">distance</option>
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82 <option value="abundance">abundance</option>
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83 </param>
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84 <when value="distance">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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85 <conditional name="matrix_condition">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
86 <param name="matrix_format" type="select" label="Select a Distance Matrix Format" help="">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
87 <option value="column">Pairwise Column Distance Matrix</option>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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88 <option value="phylip">Phylip Distance Matrix</option>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
89 </param>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
90 <when value="column">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
91 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
92 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
93 </when>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
94 <when value="phylip">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
95 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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96 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Name reference"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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97 </when>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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98 </conditional>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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99 <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Fasta"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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100 <conditional name="pick">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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101 <param name="type" type="select" label="Parse a group file into abundant and rare groups?" help="">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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102 <option value="no" selected="true">No</option>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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103 <option value="yes">Yes</option>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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104 </param>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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105 <when value="no"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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106 <when value="yes">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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107 <param name="group" type="data" format="mothur.groups" label="group - Group file for the OTU List"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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108 <param name="groups" type="select" multiple="true" label="groups - Group Selection (all used if none are selected)">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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109 <options>
e6758f2f744b 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"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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111 </options>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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112 </param>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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113 </when>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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114 </conditional>
e6758f2f744b 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="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Distance Matrix is very Large" help="Set this parameter to Yes if your distance matric might not fit in RAM"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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116 </when>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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117 <when value="abundance">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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118 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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119 </when>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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120 </conditional>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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121 <param name="label" type="select" multiple="true" label="label - OTU Labels">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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122 <expand macro="labeloptions"/>
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iuc
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123 </param>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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124 <param name="sorted" type="select" label="sorted - Sort Sequences by">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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125 <option value="">Don't sort</option>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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126 <option value="name">Sequence Name</option>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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127 <option value="number">Bin Number</option>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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128 <option value="size">Bin Size</option>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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129 <option value="group">Group</option>
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iuc
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130 </param>
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iuc
parents:
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131 </inputs>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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132 <outputs>
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iuc
parents:
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133 <expand macro="logfile-output"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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134 <collection name="names_out" type="list" label="${tool.name} on ${on_string}: rep.names">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
135 <filter>method_condition['nameOrCount'].ext == "mothur.names"</filter>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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136 <filter>method_condition['matrix_condition']['nameOrCount'].ext == "mothur.names"</filter>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
137 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rep\.names" format="mothur.names"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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138 </collection>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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139 <collection name="fasta_out" type="list" label="${tool.name} on ${on_string}: rep.fasta">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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140 <filter>method_condition['method_switch'] == "distance"</filter>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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141 <filter>method_condition['fasta']</filter>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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142 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rep\.fasta" format="fasta"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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143 </collection>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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144 <collection name="count_out" type="list" label="${tool.name} on ${on_string}: rep.count_table">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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145 <filter>method_condition['nameOrCount'].ext == "mothur.count_table"</filter>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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146 <filter>method_condition['matrix_condition']['nameOrCount'].ext == "mothur.count_table"</filter>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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147 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rep\.count_table" format="mothur.count_table"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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148 </collection>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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149 </outputs>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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150 <tests>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
151 <!-- test with distance / phylip -->
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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152 <test>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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153 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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154 <param name="method_switch" value="distance"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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155 <param name="matrix_format" value="phylip"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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156 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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157 <param name="nameOrCount" value="amazon1.names" ftype="mothur.names"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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158 <output_collection name="names_out" count="36">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
159 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
160 </output_collection>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
161 <expand macro="logfile-test"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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162 </test>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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163 <!-- test with distance / column / label select -->
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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164 <test>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
165 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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166 <param name="method_switch" value="distance"/>
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167 <param name="matrix_format" value="column"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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168 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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169 <param name="nameOrCount" value="amazon1.names" ftype="mothur.names"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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170 <param name="label" value="unique,0.05,0.27,0.45"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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171 <output_collection name="names_out" count="4">
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diff changeset
172 <element name="0.27" md5="be6dccdd3d4619c3ac465246c826209a" ftype="mothur.names"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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173 </output_collection>
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iuc
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174 <expand macro="logfile-test"/>
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175 </test>
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176 <!-- test with distance / fasta / sorting -->
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177 <test>
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178 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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179 <param name="method_switch" value="distance"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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180 <param name="matrix_format" value="phylip"/>
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181 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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182 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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183 <param name="label" value="0.05,0.27"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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184 <param name="sorted" value="name"/>
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185 <output_collection name="names_out" count="2">
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186 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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187 </output_collection>
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188 <output_collection name="fasta_out" count="2">
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189 <element name="0.27" md5="a9d9622b6f5fcbe8acdc05df5484ffc4" ftype="fasta"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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190 </output_collection>
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191 <expand macro="logfile-test"/>
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192 </test>
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193 <!-- test with distance / group file -->
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194 <test>
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195 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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196 <param name="method_switch" value="distance"/>
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197 <param name="matrix_format" value="column"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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198 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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199 <param name="nameOrCount" value="amazon1.names" ftype="mothur.names"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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200 <param name="label" value="unique,0.05,0.27,0.45"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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201 <param name="type" value="yes"/>
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202 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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203 <param name="groups" value="forest,pasture"/>
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204 <output_collection name="names_out" count="8">
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205 <element name="0.27.pasture" md5="34f87d93fd9ebbefed9754f627f502fd" ftype="mothur.names"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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206 </output_collection>
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iuc
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207 <expand macro="logfile-test"/>
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208 </test>
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209 <!-- test with distance / count table -->
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210 <test>
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diff changeset
211 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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212 <param name="method_switch" value="distance"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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213 <param name="matrix_format" value="phylip"/>
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214 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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215 <param name="label" value="unique,0.05,0.27"/>
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216 <param name="nameOrCount" value="amazon1.count_table" ftype="mothur.count_table"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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217 <output_collection name="count_out" count="3">
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218 <element name="0.27" md5="6b1afd712825af4bf8cb4ab8304df903" ftype="mothur.count_table"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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219 </output_collection>
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220 <expand macro="logfile-test"/>
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221 </test>
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222 <!-- test with abundance / count / label -->
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223 <!-- It seems that the content of the result file can vary from one execution to another with the same parameters -->
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224 <test>
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225 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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226 <param name="method_switch" value="abundance"/>
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227 <param name="nameOrCount" value="amazon1.count_table" ftype="mothur.count_table"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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228 <param name="label" value="0.27,unique"/>
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229 <param name="sorted" value="name"/>
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230 <output_collection name="count_out" count="2">
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231 <element name="0.27" ftype="mothur.count_table">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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232 <assert_contents>
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233 <has_text_matching expression="U68\w+\t36" />
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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234 </assert_contents>
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235 </element>
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236 </output_collection>
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237 <expand macro="logfile-test"/>
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238 </test>
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239 </tests>
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240 <help>
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241 <![CDATA[
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242
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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243 @MOTHUR_OVERVIEW@
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244
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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245
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246 **Command Documentation**
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247
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248 The get.oturep_ command generates a fasta-formatted sequence file containing only a representative sequence for each OTU. The opposite of the bin.seqs command.
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249
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250 .. _get.oturep: https://www.mothur.org/wiki/Get.oturep
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251
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252 v1.23.0: Updated to Mothur 1.33, added count and method parameter
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253 ]]>
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254 </help>
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255 <expand macro="citations"/>
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256 </tool>