Mercurial > repos > iuc > mothur_align_seqs

annotate align.seqs.xml @ 0:f70e050ddb40 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:34:59 -0400
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children 1efe383c2c3c
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0
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[
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10 @SHELL_OPTIONS@
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11
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## enable mothur to find blast
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 loc=`which mothur` && ln -s "\${loc%/mothur}"/* . &&
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 ## create symlinks to input datasets
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 ln -s "$candidate" candidate.dat &&
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17 ln -s "$alignment.template" alignment.template.dat &&
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18
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19 echo 'align.seqs(
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 fasta=candidate.dat,
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 reference=alignment.template.dat,
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22 align=$align,
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23 #if $search.method == "kmer":
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24 ksize=$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 $scoring.adjust == "yes":
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29 match=$scoring.match,
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 mismatch=$scoring.mismatch,
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31 gapopen=$scoring.gapopen,
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 gapextend=$scoring.gapextend,
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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
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38 processors='\${GALAXY_SLOTS:-8}'
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 )'
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40 | sed 's/ //g' ## mothur trips over whitespace
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 | ./mothur
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42 | tee mothur.out.log
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43 ]]></command>
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44 <inputs>
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45 <param name="candidate" type="data" format="fasta" label="fasta - Candiate Sequences"/>
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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">
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52 <param name="template" type="select" label="reference - Select an alignment database " help="">
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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">
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57 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
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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">
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67 <param name="ksize" type="integer" value="8" min="5" max="12" label="ksize - kmer length between 5 and 12"/>
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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>
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72 <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
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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">
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78 <param name="adjust" type="select" label="Alignment scoring values" help="">
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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">
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83 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
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84 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
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85 <param name="gapopen" type="integer" value="-5" label="gapopen - Pairwise alignment penalty for opening a gap"/>
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86 <param name="gapextend" type="integer" value="-2" label="gapextend - Pairwise alignment penalty for extending a gap"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
87 </when>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
88 <when value="no"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
89 </conditional>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
90 <conditional name="reverse">
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
91 <param name="flip" type="select" label="flip - Try to align against the reverse complement" help="">
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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92 <option value="no">No</option>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
93 <option value="yes">Yes values</option>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
94 </param>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
95 <when value="yes">
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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96 <param name="threshold" type="float" value="0.5" min="0.0" max="1.0" label="threshold - Cutoff (0. - 1.) at which an alignment is deemed 'bad' and the reverse complement may be tried." 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"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
97 </when>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
98 <when value="no"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
99 </conditional>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
100 </inputs>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
101 <outputs>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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102 <expand macro="logfile-output"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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103 <data name="out_file" format="mothur.align" from_work_dir="candidate.align" label="${tool.name} on ${on_string}: align"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
104 <data name="report" format="mothur.align.report" from_work_dir="candidate.align.report" label="${tool.name} on ${on_string}: align.report"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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105 <data name="flip_accnos" format="mothur.accnos" from_work_dir="candidate.flip.accnos" label="${tool.name} on ${on_string}: flip.accnos">
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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106 <filter>reverse['flip'] == 'yes'</filter>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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107 </data>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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108 </outputs>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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109 <tests>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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110 <test>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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111 <param name="candidate" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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112 <param name="source" value="history"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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113 <param name="template" value="HMP_MOCK.v35.align"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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114 <output name="out_file" md5="c500a4ae34a16884171f5f9c91f1636b" ftype="mothur.align"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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115 <output name="report" file="Mock_S280_L001_R1_001_small.trim.contigs.good.align.report" ftype="mothur.align.report"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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116 <expand macro="logfile-test"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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117 </test>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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118 <test>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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119 <param name="candidate" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
120 <param name="source" value="history"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
121 <param name="template" value="HMP_MOCK.v35.align"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
122 <param name="method" value="kmer"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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123 <param name="adjust" value="yes"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
124 <param name="match" value="2"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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125 <param name="mismatch" value="-15"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
126 <param name="gapopen" value="-6"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
127 <param name="gapextend" value="-3"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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128 <output name="out_file" md5="3ce542a29ed1e3fb71c3c711ae9e5c3c" ftype="mothur.align"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
129 <output name="report" md5="6d7b4f0a51e81d7984a4f77758b8cfaf" ftype="mothur.align.report"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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130 <expand macro="logfile-test"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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131 </test>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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132 <test>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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133 <param name="candidate" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
134 <param name="source" value="history"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
135 <param name="template" value="HMP_MOCK.v35.align"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
136 <param name="method" value="suffix"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
137 <param name="align" value="gotoh"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
138 <param name="adjust" value="yes"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
139 <param name="match" value="2"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
140 <param name="mismatch" value="-15"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
141 <param name="gapopen" value="-6"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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142 <param name="gapextend" value="-3"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
143 <output name="out_file" md5="6aea1563e1d2e65e331968961da715d3" ftype="mothur.align"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
144 <output name="report" md5="714474e4ac446f5a112f9c44b11a6fae" ftype="mothur.align.report"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
145 <expand macro="logfile-test"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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146 </test>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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147 <test><!-- test blast -->
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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148 <param name="candidate" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
149 <param name="source" value="history"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
150 <param name="template" value="HMP_MOCK.v35.align"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
151 <param name="method" value="blast"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
152 <param name="align" value="blast"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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153 <param name="flip" value="yes"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
154 <param name="threshold" value="0.5"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
155 <output name="out_file" md5="3b89c0afbec5f46e9c0c2974a234bc6e" ftype="mothur.align"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
156 <output name="report" md5="9ec830c9a278e20d8499ba55fef6f501" ftype="mothur.align.report"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
157 <expand macro="logfile-test"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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158 </test>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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159 <test><!-- test accno file recovery with flip set to true -->
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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160 <param name="candidate" value="amazon.fasta"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
161 <param name="source" value="history"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
162 <param name="template" value="HMP_MOCK.v35.align"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
163 <param name="flip" value="yes"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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164 <param name="threshold" value="0.5"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
165 <output name="out_file" md5="73b3b1d0c1176ed9731eedbda70b5957" ftype="mothur.align"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
166 <output name="report" md5="e502a984ffb97026f1d84c9aee616003" ftype="mothur.align.report"/>
f70e050ddb40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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167 <output name="flip_accnos" md5="afd8e7629be76baa74451b91423aaa2f" ftype="mothur.accnos"/>
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168 <expand macro="logfile-test"/>
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169 </test>
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170 </tests>
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171 <help>
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172 <![CDATA[
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173
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174 @MOTHUR_OVERVIEW@
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175
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176 **Command Documentation**
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177
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178 The align.seqs_ command aligns a user-supplied fasta-formatted candidate sequence file to a user-supplied fasta-formatted template_alignment_.
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179
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180 The general approach is to
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181 i) find the closest template for each candidate using kmer searching, blastn, or suffix tree searching;
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182 ii) to make a pairwise alignment between the candidate and de-gapped template sequences using the Needleman-Wunsch, Gotoh, or blastn algorithms; and
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183 iii) to re-insert gaps to the candidate and template pairwise alignments using the NAST algorithm so that the candidate sequence alignment is compatible with the original template alignment.
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184
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185 In general the alignment is very fast - we are able to align over 186,000 full-length sequences to the SILVA alignment in less than 3 hrs with a quality as good as the SINA aligner. Furthermore, this rate can be accelerated using multiple processors. While the aligner doesn't explicitly take into account the secondary structure of the 16S rRNA gene, if the template database is based on the secondary structure, then the resulting alignment will at least be implicitly based on the secondary structure.
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186
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187 .. _template_alignment: https://www.mothur.org/wiki/Alignment_database
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188 .. _align.seqs: https://www.mothur.org/wiki/Align.seqs
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189
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190 ]]>
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191 </help>
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192 <expand macro="citations"/>
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193 </tool>