Mercurial > repos > iuc > mothur_get_lineage

annotate get.lineage.xml @ 4:d1abc038d4bd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
author iuc
date Mon, 23 Apr 2018 10:03:49 -0400
parents c5034189eb03
children 6fbd83d3a29f
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f217eb7fad54 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_lineage" name="Get.lineage" version="@WRAPPER_VERSION@.0">
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Picks by taxon</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@
0
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11
2
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12 #import re
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13 ## create symlinks to input datasets
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14 ln -s '$file.taxonomy' file.taxonomy.dat &&
c5034189eb03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 #if $file.filetype == "useconstaxonomy":
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16 ln -s '$file.shared' file.shared.dat &&
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17 ln -s '$file.list' file.list.dat &&
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18 #end if
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19 ln -s '$fasta_in' fasta_in.dat &&
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20 ln -s '$group_in' group_in.dat &&
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21 ln -s '$alignreport_in' alignreport_in.dat &&
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22 ln -s '$list_in' list_in.dat &&
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23 ln -s '$name_in' name_in.dat &&
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24 ln -s '$count' count.dat &&
0
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25
2
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26 echo 'get.lineage(
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27 #if $file.filetype == "usetaxonomy":
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28 taxonomy=file.taxonomy.dat
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29 #else
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30 constaxonomy=file.taxonomy.dat
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31 #if $file.shared:
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32 ,shared=file.shared.dat
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33 #end if
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34 #if $file.list:
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35 ,list=file.list.dat
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36 #end if
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37 #end if
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38 #if $file.taxons:
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39 #set taxonstring=str($file.taxons).replace(",","-")
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40 ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxonstring ))'"'
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41 #elif $taxon:
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42 ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxon.value )).replace(",","-")'"'
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43 #end if
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44 #if $fasta_in:
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45 ,fasta=fasta_in.dat
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46 #end if
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47 #if $group_in:
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48 ,group=group_in.dat
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49 #end if
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50 #if $alignreport_in:
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51 ,alignreport=alignreport_in.dat
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52 #end if
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53 #if $list_in:
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54 ,list=list_in.dat
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55 #end if
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56 #if $name_in:
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57 ,name=name_in.dat
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58 ,dups=$dups
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59 #end if
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60 #if $count:
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61 ,count=count.dat
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62 #end if
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63 )'
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64 | sed 's/ //g' ## mothur trips over whitespace
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65 | mothur
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66 | tee mothur.out.log
0
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67 ]]></command>
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68 <inputs>
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69 <conditional name="file">
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70 <param name="filetype" type="select" label="choose which file is used">
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71 <option value="usetaxonomy" selected="true">taxonomy</option>
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72 <option value="useconstaxonomy">constaxonomy</option>
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73 </param>
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74 <when value="usetaxonomy">
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75 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy" help="please make sure your file has no quotation marks in it"/>
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76 <param name="taxons" type="select" size="120" optional="true" multiple="true" label="Browse Taxons from Taxonomy">
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77 <options from_dataset="taxonomy">
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78 <column name="name" index="1"/>
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79 <column name="value" index="1"/>
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80 <filter type="unique_value" name="unique_taxon" column="1"/>
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81 <filter type="sort_by" name="sorted_taxon" column="1"/>
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82 </options>
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83 <sanitizer>
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84 <valid initial="default">
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85 <add preset="string.printable"/>
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86 <add value=";"/>
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87 <remove value="&quot;"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
88 <remove value="&apos;"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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89 </valid>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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90 </sanitizer>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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91 </param>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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92 </when>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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93 <when value="useconstaxonomy">
2
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94 <param name="taxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Constaxonomy file. Provide either a constaxonomy file or a taxonomy file"
c5034189eb03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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95 help="please make sure your file has no quotation marks in it"/>
0
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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96 <param name="taxons" type="select" size="120" optional="true" multiple="true" label="Browse Taxons from Taxonomy">
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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97 <options from_dataset="taxonomy">
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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98 <column name="name" index="2"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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99 <column name="value" index="2"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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100 <filter type="unique_value" name="unique_taxon" column="2"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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101 <filter type="sort_by" name="sorted_taxon" column="2"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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102 </options>
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103 <sanitizer>
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104 <valid initial="default">
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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105 <add preset="string.printable"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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106 <add value=";"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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diff changeset
107 <remove value="&quot;"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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108 <remove value="&apos;"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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109 </valid>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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110 </sanitizer>
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111 </param>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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112 <param name="shared" type="data" format="mothur.shared" optional="true" label="shared - shared file"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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113 <param name="list" type="data" format="mothur.list" optional="true" label="list - list file"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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114 </when>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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115 </conditional>
2
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116 <param name="taxon" type="text" area="True" size="5x120" label="taxon - Manually select Taxons for filtering"
c5034189eb03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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117 help="If no taxons selected from file, Enter 1 or more taxons separated by dashes here, e.g. Bacteria;Firmicutes;-Bacteria;Actinobacteria; "/>
0
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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118 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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119 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Groups"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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120 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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121 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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122 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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123 <param name="dups" type="boolean" truevalue="true" falsevalue="false" checked="true" label="dups - Apply to duplicate names"/>
2
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parents: 0
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124 <param name="count" type="data" format="mothur.count_table" optional="true" label="Count Table"
c5034189eb03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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125 help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information"/>
c5034189eb03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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126 <expand macro="param-savelog"/>
0
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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127 </inputs>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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128 <outputs>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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129 <expand macro="logfile-output"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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130 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="file.taxonomy*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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131 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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132 <filter>fasta_in</filter>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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133 </data>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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134 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.group">
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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135 <filter>group_in</filter>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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136 </data>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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137 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: pick.list">
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
138 <filter>list_in</filter>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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139 <discover_datasets pattern="list_in*?\.(?P&lt;designation&gt;.*)\.pick.*" format="mothur.list"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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140 </collection>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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141 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pick.*" label="${tool.name} on ${on_string}: pick.name">
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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142 <filter>name_in</filter>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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143 </data>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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144 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.pick.*" label="${tool.name} on ${on_string}: pick.align.report">
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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145 <filter>alignreport_in</filter>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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146 </data>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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147 </outputs>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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148 <tests>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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149 <test><!-- test with defaults and single taxon -->
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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150 <param name="filetype" value="usetaxonomy"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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151 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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152 <param name="taxon" value="Bacteria;Firmicutes;"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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153 <output name="taxonomy_out" md5="aca21af84b6bbb6ab6cd7ab8643943d2"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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154 </test>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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155 <test><!-- test with multiple taxons and all additional files -->
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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156 <param name="filetype" value="usetaxonomy"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
157 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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158 <param name="taxon" value="Bacteria;Firmicutes;,Bacteria;Actinobacteria;"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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159 <param name="group_in" value="abrecovery.groups" ftype="mothur.groups"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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160 <param name="fasta_in" value="abrecovery.fasta" ftype="fasta"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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161 <param name="name_in" value="abrecovery.names" ftype="mothur.names"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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162 <param name="alignreport_in" value="Mock_S280_L001_R1_001_small.contigs.report" ftype="mothur.align.report"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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163 <param name="list_in" value="amazon.an.list" ftype="mothur.list"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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164 <output name="taxonomy_out" md5="682af62c68e02244c1eb1c39fa295c63"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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165 <output name="group_out" md5="71eff499c4f32ff53937288c7ffe0f70" ftype="mothur.groups"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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166 <output name="fasta_out" md5="c7e5182680e48595999fbc3561c76cef" ftype="fasta"/>
f217eb7fad54 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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167 <output name="name_out" md5="424256fee5f9074465eed432c1a8fb10" ftype="mothur.names"/>
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168 <output name="alignreport_out" md5="2a579d34a3794f8ce1934147e9ea78ef" ftype="mothur.align.report"/>
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169 <output_collection name="list_out" count="36">
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170 <element name="0.05" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.list"/>
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171 </output_collection>
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172 </test>
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173 <test><!-- test with taxons from file -->
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174 <param name="filetype" value="usetaxonomy"/>
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175 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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176 <param name="taxons" value="Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Dorea(99);,Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(47);"/>
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177 <output name="taxonomy_out" md5="f4067366d8ebdf56b75b1ac7a638bcb6"/>
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178 </test>
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179 <test><!-- test with constaxonomy file -->
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180 <param name="filetype" value="useconstaxonomy"/>
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181 <param name="taxonomy" value="example.constaxonomy" ftype="mothur.cons.taxonomy"/>
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182 <param name="taxon" value="Bacteria;Bacteroidetes;"/>
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183 <output name="taxonomy_out" md5="3a70d3cc47df38f9493a8c9cf02b75b7"/>
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184 </test>
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185 <test><!-- test with constaxonomy file and taxons from file -->
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186 <param name="filetype" value="useconstaxonomy"/>
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187 <param name="taxonomy" value="example.constaxonomy" ftype="mothur.cons.taxonomy"/>
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188 <param name="taxons" value="Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;,Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;"/>
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189 <output name="taxonomy_out" md5="0ea2511f40073a95c0812268da0cf727"/>
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190 </test>
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191 </tests>
2
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192 <help><![CDATA[
0
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193
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194 @MOTHUR_OVERVIEW@
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195
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196 **Command Documentation**
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197
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198 The get.lineage_ command reads a taxonomy_ file and a taxon and generates a new file that contains only the sequences in the that are from that taxon. You may also include either a fasta, name_, group_, list_, or align.report_ file to this command and mothur will generate new files for each of those containing only the selected sequences.
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199
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200 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
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201 .. _name: https://www.mothur.org/wiki/Name_file
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202 .. _group: https://www.mothur.org/wiki/Group_file
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203 .. _list: https://www.mothur.org/wiki/List_file
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204 .. _align.report: https://www.mothur.org/wiki/Align.seqs
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205 .. _get.lineage: https://www.mothur.org/wiki/Get.lineage
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206
2
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207 ]]></help>
0
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208 <expand macro="citations"/>
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209 </tool>