Mercurial > repos > iuc > mothur_pcr_seqs

annotate pcr.seqs.xml @ 6:0a23bfe005be draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit debdcdbb89f9bf3e2c3eed05cb078eddb27d4684"
author iuc
date Mon, 02 Dec 2019 06:20:11 -0500
parents 9a1fd25e2a1a
children 644d8a3af62d
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692381e1abfe 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_pcr_seqs" name="Pcr.seqs" version="@WRAPPER_VERSION@.0">
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2 <description>Trim sequences</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
2
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12 ## create symlinks to input datasets
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13 ln -s '$fasta' fasta.dat &&
9a1fd25e2a1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$name_in' name_in.dat &&
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15 ln -s '$group_in' group_in.dat &&
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16 ln -s '$taxonomy_in' taxonomy_in.dat &&
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17 #if $trim.method == "oligos":
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18 ln -s '$trim.oligos' trim.oligos.dat &&
9a1fd25e2a1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 #elif $trim.method == "reference":
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20 ln -s '$trim.ecoli' trim.ecoli.dat &&
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21 #end if
0
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22
2
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23 echo 'pcr.seqs(
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24 fasta=fasta.dat,
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25 #if $name_in
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26 name=name_in.dat,
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27 #end if
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28 #if $group_in:
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29 group=group_in.dat,
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30 #end if
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31 #if $taxonomy_in:
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32 taxonomy=taxonomy_in.dat,
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33 #end if
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34 #if $trim.method == "oligos":
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35 oligos=trim.oligos.dat,
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36 nomatch=$trim.nomatch,
9a1fd25e2a1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 $trim.keepprimer
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38 #elif $trim.method == "reference":
9a1fd25e2a1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 ecoli=trim.ecoli.dat,
9a1fd25e2a1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 #elif $trim.method == "position":
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41 start=$trim.start,
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42 #if $trim.end and int($trim.end) > 0:
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43 end=$trim.end,
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44 #end if
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45 #end if
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46 pdiffs=$pdiffs,
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47 rdiffs=$rdiffs,
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48 $keepdots
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49 processors='\${GALAXY_SLOTS:-8}'
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50 )'
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51 | sed 's/ //g' ## mothur trips over whitespace
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52 | mothur
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53 | tee mothur.out.log
0
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54 ]]></command>
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55 <inputs>
2
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56 <param name="fasta" type="data" format="mothur.align,fasta" label="fasta - Candiate Sequences" help="sequences must be aligned"/>
0
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57 <conditional name="trim">
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58 <param name="method" type="select" label="Trim with an oligos file?" help="">
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59 <option value="oligos">oligos</option>
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60 <option value="reference">reference sequence</option>
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61 <option value="position">start and end positions</option>
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62 </param>
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63 <when value="oligos">
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64 <param name="oligos" type="data" format="mothur.oligos" optional="true" label="oligos - barcodes and primers" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file."/>
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65 <param name="nomatch" type="select" label="nomatch - action when no primer is found">
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66 <option value="reject" selected="true">reject (default)</option>
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67 <option value="keep">keep</option>
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68 </param>
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69 <param name="keepprimer" type="boolean" falsevalue="" truevalue="keepprimer=true," checked="false" label="keepprimer - keep the primer in the output sequence"/>
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70 </when>
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71 <when value="reference">
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72 <param name="ecoli" type="data" format="mothur.align" optional="true" label="ecoli - An aligned reference sequence for trimming" help="The ecoli parameter is used to provide a fasta file containing a single reference sequence (e.g. for e. coli) this must be aligned. Mothur will trim to the start and end positions of the reference sequence."/>
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73 </when>
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74 <when value="position">
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75 <param name="start" type="integer" min="0" value="0" optional="true" label="start - a starting position to trim to"/>
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76 <param name="end" type="integer" value="" optional="true" min="0" label="end - a ending position to trim from"/>
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77 </when>
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78 </conditional>
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79 <param name="keepdots" type="boolean" falsevalue="keepdots=false," truevalue="" checked="true" label="keepdots - keep the leading and trailing alignment dots in the output sequences"/>
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80 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Sequence Taxonomy"/>
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81 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/>
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82 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Group file"/>
2
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83 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the forward primers (default 0)"/>
9a1fd25e2a1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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84 <param name="rdiffs" type="integer" value="0" min="0" label="rdiffs - number of differences to allow in the reverse primers (default 0)"/>
9a1fd25e2a1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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85 <expand macro="param-savelog"/>
0
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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86 </inputs>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 <outputs>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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88 <expand macro="logfile-output"/>
2
9a1fd25e2a1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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89 <data name="pcr_fasta" format_source="fasta" from_work_dir="fasta.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/>
9a1fd25e2a1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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90 <data name="scrap_fasta" format_source="fasta" from_work_dir="fasta.scrap.pcr.dat" label="${tool.name} on ${on_string}: pcr.scrap.fasta"/>
0
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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91 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pcr.dat" label="${tool.name} on ${on_string}: tax.summary">
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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92 <filter>taxonomy_in</filter>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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93 </data>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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94 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pcr.dat" label="${tool.name} on ${on_string}: mothur.groups">
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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95 <filter>group_in</filter>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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96 </data>
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97 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pcr.dat" label="${tool.name} on ${on_string}: mothur.names">
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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98 <filter>name_in</filter>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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99 </data>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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100 <data name="accnos_out" format="mothur.accnos" from_work_dir="fasta*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos">
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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101 <filter>trim['method'] =='oligos'</filter>
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102 </data>
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103 </outputs>
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104 <tests>
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105 <test><!-- test with position method -->
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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106 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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107 <param name="keepdots" value=""/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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108 <param name="method" value="position"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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109 <param name="start" value="0"/>
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110 <param name="end" value="0"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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111 <param name="pdiffs" value="0"/>
2
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112 <param name="savelog" value="true"/>
0
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113 <expand macro="logfile-test"/>
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114 <output name="pcr_fasta" md5="4f9c3a835bbba51c64fbf86c8a467d0e" ftype="mothur.align"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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115 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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116 </test>
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117 <test><!-- test with reference method -->
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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118 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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119 <param name="keepdots" value="keepdots=false,"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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120 <param name="method" value="reference"/>
2
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121 <param name="ecoli" value="amazon.align_head" ftype="mothur.align"/>
0
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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122 <param name="name_in" value="amazon.align_head.names"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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123 <param name="pdiffs" value="2"/>
2
9a1fd25e2a1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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124 <param name="savelog" value="true"/>
0
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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125 <expand macro="logfile-test"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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126 <output name="pcr_fasta" md5="4bef877bd45f47041f3d17dc017f21ea" ftype="mothur.align"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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diff changeset
127 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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128 <output name="name_out" md5="0c58174137c2ecabf7da9ab492ea46fc" ftype="mothur.names"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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129 </test>
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130 <test><!-- test with oligos and all outputs -->
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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131 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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132 <param name="method" value="oligos"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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133 <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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134 <param name="name_in" value="amazon.names" ftype="mothur.names"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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135 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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136 <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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137 <param name="start" value="5"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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138 <param name="end" value="50"/>
2
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139 <param name="savelog" value="true"/>
0
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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140 <expand macro="logfile-test"/>
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141 <output name="pcr_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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142 <output name="scrap_fasta" md5="0b63807f339dfd88cf958f7b069eba02" ftype="mothur.align"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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143 <output name="group_out" md5="301c358e61d38c83cc7382a8a210089a" ftype="mothur.groups"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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144 <output name="name_out" md5="62eb1162557408509c931496071add85" ftype="mothur.names"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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145 <output name="taxonomy_out" md5="4d72981cefd8b45d4f2793a28dccd9e4" ftype="mothur.seq.taxonomy"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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146 <output name="accnos_out" md5="48d019b92e4d303faf88a974e52f7a97" ftype="mothur.accnos"/>
692381e1abfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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147 </test>
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148 </tests>
2
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149 <help><![CDATA[
0
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150
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151 @MOTHUR_OVERVIEW@
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152
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153 **Command Documentation**
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154
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155 The pcr.seqs_ command assigns sequences to chosen taxonomy outline.
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156
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157 .. _pcr.seqs: https://www.mothur.org/wiki/Pcr.seqs
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158
2
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159 ]]></help>
0
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160 <expand macro="citations"/>
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161 </tool>