Mercurial > repos > iuc > mothur_get_oturep

annotate get.oturep.xml @ 2:07d536eabf6c 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 22:11:51 -0400
parents e6758f2f744b
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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[
2
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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 &&
07d536eabf6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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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 &&
07d536eabf6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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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
0
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24
2
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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"):
07d536eabf6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 count=nameOrCount.dat,
0
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41 #end if
2
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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,
0
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49 #end if
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50 #end if
2
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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
0
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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">
2
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80 <param name="method_switch" type="select" label="Method to use for the selection of the representative sequences"
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81 help="The distance method finds the sequence with the smallest maximum distance to other sequences. The abundance
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82 method chooses the most abundant sequence in the OTU as the representative.">
0
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83 <option value="distance" selected="true">distance</option>
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84 <option value="abundance">abundance</option>
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85 </param>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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86 <when value="distance">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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87 <conditional name="matrix_condition">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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88 <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:
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89 <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
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90 <option value="phylip">Phylip Distance Matrix</option>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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91 </param>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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92 <when value="column">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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93 <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
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94 <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
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95 </when>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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96 <when value="phylip">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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97 <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
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98 <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
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99 </when>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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100 </conditional>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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101 <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
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102 <conditional name="pick">
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103 <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
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104 <option value="no" selected="true">No</option>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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105 <option value="yes">Yes</option>
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106 </param>
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iuc
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107 <when value="no"/>
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108 <when value="yes">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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109 <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
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110 <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
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111 <options>
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iuc
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112 <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
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113 </options>
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114 </param>
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115 </when>
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116 </conditional>
2
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117 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Distance Matrix is very Large"
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118 help="Set this parameter to Yes if your distance matric might not fit in RAM"/>
0
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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119 </when>
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120 <when value="abundance">
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121 <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
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122 </when>
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iuc
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123 </conditional>
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124 <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
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125 <expand macro="labeloptions"/>
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126 </param>
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127 <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
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128 <option value="">Don't sort</option>
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129 <option value="name">Sequence Name</option>
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iuc
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130 <option value="number">Bin Number</option>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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131 <option value="size">Bin Size</option>
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132 <option value="group">Group</option>
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133 </param>
2
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parents: 0
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134 <expand macro="param-savelog"/>
0
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135 </inputs>
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136 <outputs>
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iuc
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137 <expand macro="logfile-output"/>
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138 <collection name="names_out" type="list" label="${tool.name} on ${on_string}: rep.names">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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139 <filter>method_condition['nameOrCount'].ext == "mothur.names"</filter>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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140 <filter>method_condition['matrix_condition']['nameOrCount'].ext == "mothur.names"</filter>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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141 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rep\.names" format="mothur.names"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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142 </collection>
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143 <collection name="fasta_out" type="list" label="${tool.name} on ${on_string}: rep.fasta">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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144 <filter>method_condition['method_switch'] == "distance"</filter>
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145 <filter>method_condition['fasta']</filter>
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146 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rep\.fasta" format="fasta"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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147 </collection>
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148 <collection name="count_out" type="list" label="${tool.name} on ${on_string}: rep.count_table">
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149 <filter>method_condition['nameOrCount'].ext == "mothur.count_table"</filter>
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150 <filter>method_condition['matrix_condition']['nameOrCount'].ext == "mothur.count_table"</filter>
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151 <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
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152 </collection>
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153 </outputs>
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154 <tests>
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155 <!-- test with distance / phylip -->
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156 <test>
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157 <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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158 <param name="method_switch" value="distance"/>
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159 <param name="matrix_format" value="phylip"/>
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iuc
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160 <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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161 <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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162 <output_collection name="names_out" count="36">
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diff changeset
163 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/>
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164 </output_collection>
2
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parents: 0
diff changeset
165 <param name="savelog" value="true"/>
0
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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166 <expand macro="logfile-test"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
167 </test>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
168 <!-- 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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169 <test>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
170 <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:
diff changeset
171 <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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172 <param name="matrix_format" value="column"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
173 <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
iuc
parents:
diff changeset
174 <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:
diff changeset
175 <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
parents:
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176 <output_collection name="names_out" count="4">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
177 <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
iuc
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178 </output_collection>
2
07d536eabf6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
179 <param name="savelog" value="true"/>
0
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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180 <expand macro="logfile-test"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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181 </test>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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182 <!-- test with distance / fasta / sorting -->
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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183 <test>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
184 <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:
diff changeset
185 <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:
diff changeset
186 <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:
diff changeset
187 <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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188 <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
iuc
parents:
diff changeset
189 <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
iuc
parents:
diff changeset
190 <param name="sorted" value="name"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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191 <output_collection name="names_out" count="2">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
192 <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
193 </output_collection>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
194 <output_collection name="fasta_out" count="2">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
195 <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
iuc
parents:
diff changeset
196 </output_collection>
2
07d536eabf6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
197 <param name="savelog" value="true"/>
0
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
198 <expand macro="logfile-test"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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199 </test>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
200 <!-- test with distance / group file -->
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
201 <test>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
202 <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:
diff changeset
203 <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:
diff changeset
204 <param name="matrix_format" value="column"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
205 <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
iuc
parents:
diff changeset
206 <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:
diff changeset
207 <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
parents:
diff changeset
208 <param name="type" value="yes"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
209 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
210 <param name="groups" value="forest,pasture"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
211 <output_collection name="names_out" count="8">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
212 <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
iuc
parents:
diff changeset
213 </output_collection>
2
07d536eabf6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
214 <param name="savelog" value="true"/>
0
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
215 <expand macro="logfile-test"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
216 </test>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
217 <!-- test with distance / count table -->
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
218 <test>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
219 <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:
diff changeset
220 <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:
diff changeset
221 <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:
diff changeset
222 <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:
diff changeset
223 <param name="label" value="unique,0.05,0.27"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
224 <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
iuc
parents:
diff changeset
225 <output_collection name="count_out" count="3">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
226 <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
iuc
parents:
diff changeset
227 </output_collection>
2
07d536eabf6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
228 <param name="savelog" value="true"/>
0
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
229 <expand macro="logfile-test"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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230 </test>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
231 <!-- test with abundance / count / label -->
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
232 <!-- It seems that the content of the result file can vary from one execution to another with the same parameters -->
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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233 <test>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
234 <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:
diff changeset
235 <param name="method_switch" value="abundance"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
236 <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
iuc
parents:
diff changeset
237 <param name="label" value="0.27,unique"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
238 <param name="sorted" value="name"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
239 <output_collection name="count_out" count="2">
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
240 <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
iuc
parents:
diff changeset
241 <assert_contents>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
242 <has_text_matching expression="U68\w+\t36" />
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
243 </assert_contents>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
244 </element>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
245 </output_collection>
2
07d536eabf6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
246 <param name="savelog" value="true"/>
0
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
247 <expand macro="logfile-test"/>
e6758f2f744b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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248 </test>
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249 </tests>
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250 <help><![CDATA[
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251
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252 @MOTHUR_OVERVIEW@
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253
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254
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255 **Command Documentation**
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256
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257 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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258
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259 .. _get.oturep: https://www.mothur.org/wiki/Get.oturep
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260
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261 v1.23.0: Updated to Mothur 1.33, added count and method parameter
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262
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263 ]]></help>
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264 <expand macro="citations"/>
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265 </tool>