Mercurial > repos > iuc > mothur_align_seqs

annotate align.seqs.xml @ 2:1efe383c2c3c 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 22:00:00 -0400
parents f70e050ddb40
children 5d134e0b31fd
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f70e050ddb40 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_align_seqs" name="Align.seqs" version="@WRAPPER_VERSION@.0">
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Align sequences to a template alignment</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 ## enable mothur to find blast
1efe383c2c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s `dirname \$(which mothur)`/* . &&
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14
2
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15 ## create symlinks to input datasets
1efe383c2c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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16 ln -s '$fasta' fasta.dat &&
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17 ln -s '$alignment.reference' alignment.reference.dat &&
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18
2
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19 echo 'align.seqs(
1efe383c2c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 fasta=fasta.dat,
1efe383c2c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 reference=alignment.reference.dat,
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22 align=$align,
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23 #if $search.method == "kmer":
1efe383c2c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 ksize=$search.ksize,
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25 #else:
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26 search=$search.method,
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27 #end if
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28 #if $scoring.adjust == "yes":
1efe383c2c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 match=$scoring.match,
1efe383c2c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 mismatch=$scoring.mismatch,
1efe383c2c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 gapopen=$scoring.gapopen,
1efe383c2c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 gapextend=$scoring.gapextend,
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33 #end if
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34 #if $reverse.flip == "yes":
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35 flip=true,
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36 threshold=$reverse.threshold,
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37 #end if
1efe383c2c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 processors='\${GALAXY_SLOTS:-8}'
1efe383c2c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 )'
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40 | sed 's/ //g' ## mothur trips over whitespace
1efe383c2c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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41 | ./mothur
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42 | tee mothur.out.log
0
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43 ]]></command>
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44 <inputs>
2
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45 <param argument="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
0
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46 <conditional name="alignment">
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47 <param name="source" type="select" label="Select Reference Template from" help="">
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48 <option value="ref">Cached Reference</option>
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49 <option value="history">Your History</option>
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50 </param>
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51 <when value="ref">
2
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52 <param argument="reference" type="select" label="reference - Select an alignment database " help="">
0
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53 <options from_data_table="mothur_aligndb"/>
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54 </param>
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55 </when>
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56 <when value="history">
2
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57 <param argument="reference" type="data" format="fasta" label="reference - Reference to align with" help=""/>
0
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58 </when>
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59 </conditional>
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60 <conditional name="search">
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61 <param name="method" type="select" label="Select a search method" help="">
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62 <option value="kmer" selected="true">kmer (default)</option>
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63 <option value="suffix">suffix tree</option>
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64 <option value="blast">blast</option>
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65 </param>
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66 <when value="kmer">
2
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67 <param argument="ksize" type="integer" value="8" min="5" max="12" label="ksize - kmer length between 5 and 12"/>
0
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68 </when>
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69 <when value="suffix"/>
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70 <when value="blast"/>
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71 </conditional>
2
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72 <param argument="align" type="select" label="align - Select a pairwise alignment method">
0
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73 <option value="needleman" selected="true">needleman (default)</option>
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74 <option value="gotoh">gotoh</option>
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75 <option value="blast">blast</option>
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76 </param>
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77 <conditional name="scoring">
2
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78 <param name="adjust" type="select" label="Alignment scoring values">
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79 <option value="no">use defaults</option>
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80 <option value="yes">adjust values</option>
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81 </param>
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82 <when value="yes">
2
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83 <param argument="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
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84 <param argument="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
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85 <param argument="gapopen" type="integer" value="-5" label="gapopen - Pairwise alignment penalty for opening a gap"/>
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86 <param argument="gapextend" type="integer" value="-2" label="gapextend - Pairwise alignment penalty for extending a gap"/>
0
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87 </when>
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88 <when value="no"/>
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89 </conditional>
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90 <conditional name="reverse">
2
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91 <param argument="flip" type="select" label="flip - Try to align against the reverse complement" help="">
0
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92 <option value="no">No</option>
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93 <option value="yes">Yes values</option>
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94 </param>
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95 <when value="yes">
2
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96 <param argument="threshold" type="float" value="0.5" min="0.0" max="1.0"
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97 label="threshold - Cutoff (0. - 1.) at which an alignment is deemed 'bad' and the reverse complement may be tried."
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98 help="The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed"/>
0
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99 </when>
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100 <when value="no"/>
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101 </conditional>
2
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102 <expand macro="param-savelog"/>
0
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103 </inputs>
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104 <outputs>
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105 <expand macro="logfile-output"/>
2
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106 <data name="out_align" format="mothur.align" from_work_dir="fasta.align" label="${tool.name} on ${on_string}: align"/>
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107 <data name="report" format="mothur.align.report" from_work_dir="fasta.align.report" label="${tool.name} on ${on_string}: align.report"/>
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108 <data name="flip_accnos" format="mothur.accnos" from_work_dir="fasta.flip.accnos" label="${tool.name} on ${on_string}: flip.accnos">
0
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109 <filter>reverse['flip'] == 'yes'</filter>
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110 </data>
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111 </outputs>
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112 <tests>
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113 <test>
2
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114 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
0
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115 <param name="source" value="history"/>
2
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116 <param name="reference" value="HMP_MOCK.v35.align"/>
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117 <output name="out_align" md5="c500a4ae34a16884171f5f9c91f1636b" ftype="mothur.align">
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118 <assert_contents>
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119 <expand macro="test-align-format"/>
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120 </assert_contents>
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121 </output>
0
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122 <output name="report" file="Mock_S280_L001_R1_001_small.trim.contigs.good.align.report" ftype="mothur.align.report"/>
2
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123 <param name="savelog" value="true"/>
0
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124 <expand macro="logfile-test"/>
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125 </test>
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126 <test>
2
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127 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
0
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128 <param name="source" value="history"/>
2
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129 <param name="reference" value="HMP_MOCK.v35.align"/>
0
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130 <param name="method" value="kmer"/>
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131 <param name="adjust" value="yes"/>
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132 <param name="match" value="2"/>
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133 <param name="mismatch" value="-15"/>
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134 <param name="gapopen" value="-6"/>
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135 <param name="gapextend" value="-3"/>
2
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136 <output name="out_align" ftype="mothur.align">
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137 <assert_contents>
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138 <expand macro="test-align-format"/>
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139 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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140 </assert_contents>
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141 </output>
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142 <output name="report" ftype="mothur.align.report">
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143 <assert_contents>
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144 <expand macro="test-alignreport-format"/>
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145 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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146 </assert_contents>
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147 </output>
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148 <param name="savelog" value="true"/>
0
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149 <expand macro="logfile-test"/>
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150 </test>
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151 <test>
2
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152 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
0
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153 <param name="source" value="history"/>
2
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154 <param name="reference" value="HMP_MOCK.v35.align"/>
0
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155 <param name="method" value="suffix"/>
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156 <param name="align" value="gotoh"/>
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157 <param name="adjust" value="yes"/>
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158 <param name="match" value="2"/>
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159 <param name="mismatch" value="-15"/>
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160 <param name="gapopen" value="-6"/>
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161 <param name="gapextend" value="-3"/>
2
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162 <output name="out_align" ftype="mothur.align">
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163 <assert_contents>
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164 <expand macro="test-align-format"/>
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165 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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166 </assert_contents>
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167 </output>
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168 <output name="report" ftype="mothur.align.report">
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169 <assert_contents>
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170 <expand macro="test-alignreport-format"/>
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171 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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172 </assert_contents>
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173 </output>
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174 <param name="savelog" value="true"/>
0
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175 <expand macro="logfile-test"/>
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176 </test>
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177 <test><!-- test blast -->
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178 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
0
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179 <param name="source" value="history"/>
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180 <param name="reference" value="HMP_MOCK.v35.align"/>
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181 <param name="method" value="blast"/>
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182 <param name="align" value="blast"/>
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183 <param name="flip" value="yes"/>
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184 <param name="threshold" value="0.5"/>
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185 <output name="out_align" ftype="mothur.align">
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186 <assert_contents>
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187 <expand macro="test-align-format"/>
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188 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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189 </assert_contents>
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190 </output>
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191 <output name="report" ftype="mothur.align.report">
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192 <assert_contents>
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193 <expand macro="test-alignreport-format"/>
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194 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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195 </assert_contents>
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196 </output>
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197 <param name="savelog" value="true"/>
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198 <expand macro="logfile-test"/>
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199 </test>
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200 <test><!-- test accno file recovery with flip set to true -->
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201 <param name="fasta" value="amazon.fasta"/>
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202 <param name="source" value="history"/>
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203 <param name="reference" value="HMP_MOCK.v35.align"/>
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204 <param name="flip" value="yes"/>
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205 <param name="threshold" value="0.5"/>
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206 <output name="out_align" ftype="mothur.align">
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207 <assert_contents>
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208 <expand macro="test-align-format"/>
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209 <has_text text="U68621"/>
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210 </assert_contents>
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211 </output>
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212 <output name="report" ftype="mothur.align.report">
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213 <assert_contents>
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214 <expand macro="test-alignreport-format"/>
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215 <has_text text="U68621"/>
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216 </assert_contents>
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217 </output>
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218 <output name="flip_accnos" md5="afd8e7629be76baa74451b91423aaa2f" ftype="mothur.accnos">
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219 <assert_contents>
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220 <has_text text="U68621"/>
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221 <has_text text="reverse complement"/>
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222 </assert_contents>
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223 </output>
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224 <param name="savelog" value="true"/>
0
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225 <expand macro="logfile-test"/>
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226 </test>
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227 </tests>
2
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228 <help><![CDATA[
0
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229
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230 @MOTHUR_OVERVIEW@
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231
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232 **Command Documentation**
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233
2
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234 The align.seqs_ command aligns a user-supplied fasta-formatted fasta sequence file to a user-supplied fasta-formatted template_alignment_.
0
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235
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236 The general approach is to
2
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237 i) find the closest template for each fasta using kmer searching, blastn, or suffix tree searching;
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238 ii) to make a pairwise alignment between the fasta and de-gapped template sequences using the Needleman-Wunsch, Gotoh,or blastn algorithms; and
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239 iii) to re-insert gaps to the fasta and template pairwise alignments using the NAST algorithm so that the fasta sequence alignment is compatible with the original template alignment.
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240
2
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241 In general the alignment is very fast - we are able to align over 186,000 full-length sequences to the SILVA alignment
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242 in less than 3 hrs with a quality as good as the SINA aligner. Furthermore, this rate can be accelerated using multiple
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243 processors. While the aligner doesn't explicitly take into account the secondary structure of the 16S rRNA gene, if the
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244 template database is based on the secondary structure, then the resulting alignment will at least be implicitly based
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245 on the secondary structure.
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246
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247 .. _template_alignment: https://www.mothur.org/wiki/Alignment_database
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248 .. _align.seqs: https://www.mothur.org/wiki/Align.seqs
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249
2
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250 ]]></help>
0
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251 <expand macro="citations"/>
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252 </tool>