Mercurial > repos > iuc > mothur_chimera_vsearch

annotate chimera.vsearch.xml @ 0:1801019b4690 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 22:09:26 -0400
parents
children b4e60c1d77ac
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1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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1 <tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.0">
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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2 <description>find potential chimeric sequences using vsearch</description>
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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3 <macros>
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iuc
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4 <import>macros.xml</import>
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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5 </macros>
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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6 <expand macro="requirements">
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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7 <requirement type="package" version="2.6.0">vsearch</requirement>
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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8 </expand>
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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9 <expand macro="stdio"/>
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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10 <expand macro="version_command"/>
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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11 <command><![CDATA[
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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12 @SHELL_OPTIONS@
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13
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ## create symlinks to input datasets
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$fasta' fasta.dat &&
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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16 #if $template.source == "self":
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 ln -s '$template.count' template.count.dat &&
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 ln -s '$template.group' template.group.dat &&
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 #elif $template.source == "names":
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 ln -s '$template.name' template.name.dat &&
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 #else:
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 ln -s '$template.reference' template.reference.dat &&
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 #end if
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24
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 echo 'chimera.vsearch(
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 fasta=fasta.dat,
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 #if $template.source == "self":
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 reference=self,
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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29 #if float($template.abskew) > 0:
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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30 abskew=$template.abskew,
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 #end if
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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32 #if $template.group:
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 group=template.group.dat,
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 #end if
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 #if $template.count:
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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36 count=template.count.dat,
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 #end if
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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38 #elif $template.source == "names":
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 name=template.name.dat,
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 #else:
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41 reference=template.reference.dat,
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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42 #end if
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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43 minh=$minh,
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44 mindiv=$mindiv,
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45 xn=$xn,
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46 dn=$dn,
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47 dereplicate=$dereplicate,
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48 mindiffs=$mindiffs,
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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
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54 2>&1 ## uchime component writes output to stderr
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55 && cat *accnos
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56 ]]></command>
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57 <inputs>
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58 <param argument="fasta" type="data" format="mothur.align,fasta" label="fasta - Candiate Aligned Sequences"/>
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59 <conditional name="template">
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60 <param name="source" type="select" label="Select Reference Template from">
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61 <option value="hist">History</option>
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62 <option value="ref">Cached Reference</option>
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63 <option value="self">Self</option>
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64 <option value="names">Use a names file</option>
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65 </param>
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66 <when value="ref">
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67 <param argument="reference" type="select" label="reference - Select an alignment database">
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68 <options from_data_table="mothur_aligndb"/>
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69 </param>
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70 </when>
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71 <when value="hist">
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72 <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/>
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73 </when>
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74 <when value="self">
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75 <param argument="abskew" type="float" value="1.9" label="abskew - Abundance skew" help="Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query). Default 1.9"/>
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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76 <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"
1801019b4690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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77 help="use the more abundant sequences from the same sample to check the query sequence"/>
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78 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table"
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79 help="Generated by count.seqs. When you use a count file with group info and dereplicate=T, mothur will create a count table containing seqeunces after chimeras are removed."/>
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80 </when>
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81 <when value="names">
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82 <param argument="name" type="data" format="mothur.names" label="name - Sequence names"/>
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83 </when>
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84 </conditional>
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85 <param argument="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false"
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86 label="dereplicate - remove chimeric sequences from all groups?"
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87 help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric"/>
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88 <param argument="minh" type="float" value="0.3" min="0" label="minh - mininum score to report chimera. Default 0.3"
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89 help="Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives."/>
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90 <param argument="mindiv" type="float" value="0.5" min="0" label="mindiv - minimum divergence ratio"
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91 help="to ignore very close chimeras, increase mindiv to 1.0 or 2.0, to increase sensitivity decrease minh to 0.1. Default 0.5"/>
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92 <param argument="xn" type="float" value="8.0" min="0" label="xn - weight of a no vote. Default 8.0"
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93 help="Decreasing this weight to around 3 or 4 may give better performance on denoised data"/>
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94 <param argument="dn" type="float" value="1.4" min="0" label="dn - pseudo-count prior on number of no votes"
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95 help="Reasonable values are probably in the range from 0.2 to 2.0. Default 1.4"/>
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96 <param argument="mindiffs" type="integer" value="3" min="0" label="minimum number of differences in segment"/>
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97 <expand macro="param-savelog"/>
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98 </inputs>
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99 <outputs>
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100 <expand macro="logfile-output"/>
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101 <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: uchime.chimeras"/>
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102 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: uchime.accnos"/>
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103 </outputs>
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104 <tests>
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105 <test><!-- de novo test with name file -->
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106 <param name="fasta" value="stool_small.unique.fasta"/>
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107 <param name="source" value="names"/>
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108 <param name="name" value="stool_small.names"/>
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109 <output name="vsearch.chimeras" file="stool_small.vsearch.chimeras" ftype="txt"/>
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110 <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/>
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111 <param name="savelog" value="true"/>
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112 <expand macro="logfile-test"/>
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113 </test>
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114 <test><!-- de novo test with count table-->
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115 <param name="fasta" value="stool_small.unique.fasta"/>
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116 <param name="source" value="self"/>
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117 <param name="count" value="stool_small.count_table"/>
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118 <output name="vsearch.chimeras" file="stool_small.vsearch.chimeras" ftype="txt"/>
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119 <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/>
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120 <param name="savelog" value="true"/>
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121 <expand macro="logfile-test"/>
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122 </test>
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123 <test><!-- test with reference file -->
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124 <param name="fasta" value="stool_small.unique.fasta"/>
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125 <param name="source" value="hist"/>
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126 <param name="reference" value="stool_small.unique.fasta"/>
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127 <output name="vsearch.chimeras" ftype="txt">
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128 <assert_contents>
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129 <expand macro="test-chimera-format"/>
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130 <has_text text="F11Fcsw_12747"/>
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131 </assert_contents>
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132 </output>
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133 <output name="out_accnos" ftype="mothur.accnos">
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134 <assert_contents>
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135 <expand macro="test-accnos-format"/>
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136 <has_text text="F11Fcsw_23322"/>
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137 </assert_contents>
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138 </output>
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139 <param name="savelog" value="true"/>
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140 <expand macro="logfile-test"/>
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141 </test>
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142 </tests>
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143 <help><![CDATA[
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144
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145 @MOTHUR_OVERVIEW@
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146
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147 **Command Documentation**
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148
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149 The chimera.vsearch_ command reads a fasta file and reference file and outputs potentially chimeric sequences.
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150
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151 .. _chimera.vsearch: https://www.mothur.org/wiki/Chimera.vsearch
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152
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153 ]]></help>
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154 <expand macro="citations"/>
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155 </tool>