Mercurial > repos > iuc > mothur_chimera_uchime

annotate chimera.uchime.xml @ 6:f1742cf23d95 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 06:30:03 -0500
parents 4e3780d096af
children d9fe0fecb696
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6dc4f9beec9f 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_chimera_uchime" name="Chimera.uchime" version="@WRAPPER_VERSION@.0">
6dc4f9beec9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Find putative chimeras using uchime</description>
6dc4f9beec9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
6dc4f9beec9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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4 <import>macros.xml</import>
6dc4f9beec9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
6dc4f9beec9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
6dc4f9beec9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
6dc4f9beec9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
6dc4f9beec9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
0
6dc4f9beec9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
2
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12 ## create symlinks to input datasets
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$fasta' fasta.dat &&
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 #if $template.source == "self":
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$template.count' template.count.dat &&
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16 ln -s '$template.group' template.group.dat &&
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 #elif $template.source == "names":
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 ln -s '$template.name' template.name.dat &&
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 #else:
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20 ln -s '$template.reference' template.reference.dat &&
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21 #end if
0
6dc4f9beec9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22
2
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23 echo 'chimera.uchime(
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 fasta=fasta.dat,
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 #if $template.source == "self":
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26 reference=self,
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27 #if float($template.abskew) > 0:
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28 abskew=$template.abskew,
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 #end if
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30 #if $template.group:
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 group=template.group.dat,
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 #end if
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33 #if $template.count:
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34 count=template.count.dat,
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35 #end if
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36 #elif $template.source == "names":
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 name=template.name.dat,
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 #else:
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 reference=template.reference.dat,
d1e70be881e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 #end if
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41 minh=$minh,
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42 mindiv=$mindiv,
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43 xn=$xn,
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44 dn=$dn,
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45 xa=$xa,
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46 chunks=$chunks,
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47 minchunk=$minchunk,
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48 #if $idsmoothwindow:
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49 idsmoothwindow=$idsmoothwindow,
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50 #end if
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51 maxp=$maxp,
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52 minlen=$minlen,
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53 maxlen=$maxlen,
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54 skipgaps=$skipgaps,
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55 skipgaps2=$skipgaps2,
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56 #if $alignment.ucl == "local":
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57 ucl=true,
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58 #if $alignment.queryfract:
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59 queryfract=$alignment.queryfract,
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60 #end if
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61 #end if
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62 dereplicate=$dereplicate,
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63 chimealns=$chimealns,
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64 processors='\${GALAXY_SLOTS:-8}'
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65 )'
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66 | sed 's/ //g' ## mothur trips over whitespace
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67 | mothur
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68 | tee mothur.out.log
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69 2>&1 ## uchime component writes output to stderr
0
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70 ]]></command>
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71 <inputs>
2
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72 <param argument="fasta" type="data" format="mothur.align,fasta" label="fasta - Candiate Aligned Sequences"/>
0
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73 <conditional name="template">
2
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74 <param name="source" type="select" label="Select Reference Template from">
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75 <option value="hist">History</option>
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76 <option value="ref">Cached Reference</option>
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77 <option value="self">Self</option>
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78 <option value="names">Use a names file</option>
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79 </param>
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80 <when value="ref">
2
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81 <param argument="reference" type="select" label="reference - Select an alignment database">
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82 <options from_data_table="mothur_aligndb"/>
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83 </param>
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84 </when>
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85 <when value="hist">
2
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86 <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/>
0
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87 </when>
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88 <when value="self">
2
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89 <param argument="abskew" type="float" value="1.9" label="abskew - Abundance skew"
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90 help="Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query). Default 1.9"/>
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91 <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"
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92 help="use the more abundant sequences from the same sample to check the query sequence"/>
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93 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table"
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94 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."/>
0
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95 </when>
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96 <when value="names">
2
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97 <param argument="name" type="data" format="mothur.names" label="name - Sequence names"/>
0
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98 </when>
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99 </conditional>
2
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100 <param argument="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false"
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101 label="dereplicate - remove chimeric sequences from all groups?"
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102 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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103 <param argument="skipgaps" type="boolean" falsevalue="false" truevalue="true" checked="true"
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104 label="skipgaps - columns containing gaps do not count as diffs"
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105 help="controls how gapped columns affect counting of diffs"/>
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106 <param argument="skipgaps2" type="boolean" falsevalue="false" truevalue="true" checked="true"
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107 label="skipgaps2 - column is immediately adjacent to a column containing a gap, it is not counted as a diff"
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108 help="controls how gapped columns affect counting of diffs"/>
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109 <param argument="chimealns" type="boolean" falsevalue="false" truevalue="true" checked="false"
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110 label="chimealns - Produce a file containing multiple alignments of query sequences to parents in human readable format"
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111 help="Alignments show columns with differences that support or contradict a chimeric model."/>
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112 <param argument="minh" type="float" value="0.3" min="0" label="minh - mininum score to report chimera. Default 0.3"
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113 help="Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives."/>
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114 <param argument="mindiv" type="float" value="0.5" min="0" label="mindiv - minimum divergence ratio"
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115 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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116 <param argument="xn" type="float" value="8.0" min="0" label="xn - weight of a no vote. Default 8.0"
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117 help="Decreasing this weight to around 3 or 4 may give better performance on denoised data"/>
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118 <param argument="dn" type="float" value="1.4" min="0" label="dn - pseudo-count prior on number of no votes"
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119 help="Reasonable values are probably in the range from 0.2 to 2.0. Default 1.4"/>
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120 <param argument="xa" type="float" value="1.0" min="0" label="xa - eight of an abstain vote"
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121 help="Reasonable values might range from 0.1 to 2.0. Default 1.0"/>
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122 <param argument="chunks" type="integer" value="4" min="0" label="chunks - number of chunks"
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123 help="number of chunks to extract from the query sequence when searching for parents. Default 4."/>
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124 <param argument="minchunk" type="integer" value="64" min="0" label="minchunk - minimum length of a chunk" help="Default 64"/>
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125 <param argument="maxp" type="integer" value="2" min="0" label="maxp - maximum number of candidate parents to consider"
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126 help="increasing maxp gives only a very small improvement in sensivity but tends to increase the error rate quite a bit. Default 2"/>
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127 <param argument="minlen" type="integer" value="10" min="0" label="minlen - minimum unaligned sequence length"
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128 help="Applies to both query and reference sequences. Default 10"/>
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129 <param argument="maxlen" type="integer" value="10000" min="0" label="maxlen - maximum unaligned sequence length"
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130 help="Applies to both query and reference sequences. Default 10000"/>
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131 <param argument="idsmoothwindow" type="integer" value="32" min="0" optional="True" label="idsmoothwindow - the length of id smoothing window"
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132 help="Default 32"/>
0
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133 <conditional name="alignment">
2
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134 <param argument="ucl" type="select" label="ucl - Use local-X alignments" help="global-X is the default">
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135 <option value="global" selected="true">global</option>
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136 <option value="local">local</option>
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137 </param>
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138 <when value="global"/>
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139 <when value="local">
2
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140 <param argument="queryfract" type="float" value="0.5" min="0" max="1"
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141 label="queryfract - minimum fraction of the query sequence that must be covered by a local-X alignment" help="Default 0.5"/>
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142 </when>
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143 </conditional>
2
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144 <expand macro="param-savelog"/>
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145 </inputs>
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146 <outputs>
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147 <expand macro="logfile-output"/>
2
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148 <data name="uchime.chimeras" format="txt" from_work_dir="fasta.*uchime.chimeras" label="${tool.name} on ${on_string}: uchime.chimeras"/>
0
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149 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*uchime.accnos" label="${tool.name} on ${on_string}: uchime.accnos"/>
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150 <data name="out_alns" format="txt" from_work_dir="fasta.*uchime.alns" label="${tool.name} on ${on_string}: uchime.alns">
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151 <filter>chimealns</filter>
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152 </data>
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153 <data name="out_count" format="mothur.count_table" from_work_dir="template.*uchime.pick.count_table" label="${tool.name} on ${on_string}: uchime.count_table">
2
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154 <filter>template['source'] == 'self' and template['count']</filter>
0
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155 </data>
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156 </outputs>
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157 <tests>
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158 <test><!-- default params test -->
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159 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera"/>
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160 <param name="source" value="hist"/>
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161 <param name="reference" value="HMP_MOCK.v35.align"/>
2
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162 <output name="uchime.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras" ftype="txt"/>
0
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163 <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos" ftype="mothur.accnos"/>
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164 <param name="savelog" value="true"/>
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165 <expand macro="logfile-test"/>
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166 </test>
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167 <test><!-- de novo test -->
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168 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
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169 <param name="source" value="self"/>
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170 <output name="uchime.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.denovo.uchime.chimeras" ftype="txt"/>
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171 <output name="out_accnos" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.accnos"/>
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172 <param name="savelog" value="true"/>
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173 <expand macro="logfile-test"/>
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174 </test>
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175 <test><!-- with chimealns output -->
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176 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera"/>
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177 <param name="source" value="hist"/>
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178 <param name="reference" value="HMP_MOCK.v35.align"/>
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179 <param name="chimealns" value="true"/>
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180 <output name="uchime.chimeras" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras" ftype="txt"/>
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181 <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos" ftype="mothur.accnos"/>
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182 <output name="out_alns" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.alns" ftype="txt"/>
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183 <param name="savelog" value="true"/>
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184 <expand macro="logfile-test"/>
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185 </test>
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186 </tests>
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187 <help><![CDATA[
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188
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189 @MOTHUR_OVERVIEW@
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190
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191 **Command Documentation**
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192
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193 The chimera.uchime_ command reads a fasta file and reference file and outputs potentially chimeric sequences. The original uchime program was written by Robert C. Edgar and donated to the public domain, http://drive5.com/uchime
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194
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195 .. _chimera.uchime: https://www.mothur.org/wiki/Chimera.uchime
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196
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197 Version 1.23.0: Upgrades tool dependency to mothur 1.33 and adds support for count (mothur 1.28) and dereplicate (mothur 1.29) options.
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198
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199 ]]></help>
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200 <expand macro="citations">
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201 <citation type="doi">10.1093/bioinformatics/btr381</citation>
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202 </expand>
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203 </tool>