Mercurial > repos > iuc > mothur_trim_seqs

annotate trim.seqs.xml @ 4:fc17c9a3c800 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
author iuc
date Mon, 23 Apr 2018 09:27:36 -0400
parents baa3df51e2b7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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1 <tool profile="16.07" id="mothur_trim_seqs" name="Trim.seqs" version="@WRAPPER_VERSION@.0">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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2 <description>Trim sequences - primers, barcodes, quality</description>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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4 <import>macros.xml</import>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
143f949a5def 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"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
2
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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10 @SHELL_OPTIONS@
0
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
2
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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12 ## create symlinks to input datasets
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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13 ln -s '$fasta' fasta.dat &&
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$names' names.dat &&
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$count' count.dat &&
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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16 #if $oligo.add == "yes":
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 ln -s '$oligo.oligos' oligo.oligos.dat &&
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 #end if
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 #if $qual.add2 == "yes":
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 ln -s '$qual.qfile' qual.qfile.dat &&
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 #end if
0
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22
2
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 echo 'trim.seqs(
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 fasta=fasta.dat,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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25 minlength=$minlength,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 maxlength=$maxlength,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 maxambig=$maxambig,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 maxhomop=$maxhomop,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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29 keepfirst=$keepfirst,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 removelast=$removelast,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 #if $oligo.add == "yes":
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 oligos=oligo.oligos.dat,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 bdiffs=$oligo.bdiffs,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 pdiffs=$oligo.pdiffs,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 tdiffs=$oligo.tdiffs,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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36 ldiffs=$oligo.ldiffs,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 sdiffs=$oligo.sdiffs,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 keepforward=$oligo.keepforward,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 allfiles=$oligo.allfiles,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 #end if
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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41 #if $qual.add2 == "yes":
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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42 qfile=qual.qfile.dat,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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43 qaverage=$qual.qaverage,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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44 qthreshold=$qual.qthreshold,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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45 qwindowaverage=$qual.qwindowaverage,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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46 qwindowsize=$qual.qwindowsize,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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47 rollaverage=$qual.rollaverage,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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48 qstepsize=$qual.qstepsize,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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49 qtrim=$qual.qtrim,
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50 #end if
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51 flip=$flip,
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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52 #if $names:
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53 name=names.dat,
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54 #end if
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55 logtransform=$logtransform,
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56 checkorient=$checkorient,
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57 #if $count:
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58 count=count.dat,
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59 #end if
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60 processors='\${GALAXY_SLOTS:-8}'
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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61 )'
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62 | sed 's/ //g' ## mothur trips over whitespace
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63 | mothur
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64 | tee mothur.out.log
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65
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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66 ## prevent these two files from being gathered into collection
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67 && mv fasta.trim.fasta fasta.trim
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68 && mv fasta.scrap.fasta fasta.scrap
0
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69 ]]></command>
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70 <inputs>
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71 <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/>
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72 <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/>
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73 <param name="minlength" type="integer" value="0" min="0" label="minlength - Minimum Sequence Length (default 0, ignored if &#060; 1 )"/>
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74 <param name="maxlength" type="integer" value="0" min="0" label="maxlength - Maximum Sequence Length (default 0, ignored if &#060; 1)"/>
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75 <param name="maxambig" type="integer" value="-1" min="-1" label="maxambig - Maximum ambiguous bases (default -1, ignored if &#060; 0)"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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76 <param name="maxhomop" type="integer" value="0" min="0" label="maxhomop - Maximum homopolymers (default 0, ignored if &#060; 1)"/>
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77 <param name="keepfirst" type="integer" value="0" min="0" label="keepfirst - ignored if &#060; 0)" help="trims the sequence to the first keepfirst number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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78 <param name="removelast" type="integer" value="0" min="0" label="removelast - ignored if &#060; 0)" help="removes the last removelast number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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79 <conditional name="oligo">
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80 <param name="add" type="select" label="Trim with an oligos file?" help="">
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81 <option value="no">no</option>
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82 <option value="yes">yes</option>
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83 </param>
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parents:
diff changeset
84 <when value="no"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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parents:
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85 <when value="yes">
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86 <param name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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88 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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89 <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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parents:
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90 <param name="ldiffs" type="integer" value="0" min="0" optional="true" label="ldiffs - total number of differences to allow in linker sequence (default 0)"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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91 <param name="sdiffs" type="integer" value="0" min="0" optional="true" label="sdiffs - total number of differences to allow in spacer sequence (default 0)"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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92 <param name="keepforward" type="boolean" truevalue="true" falsevalue="false" checked="false" label="keepforward - keep the primer"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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93 <param name="allfiles" type="boolean" truevalue="true" falsevalue="false" checked="false" label="allfiles - separate into file per barcode"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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94 </when>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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95 </conditional>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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96 <conditional name="qual">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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97 <param name="add2" type="select" label="Trim based on a quality file?" help="">
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98 <option value="no">no</option>
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99 <option value="yes">yes</option>
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100 </param>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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101 <when value="no"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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102 <when value="yes">
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103 <param name="qfile" type="data" format="qual454" label="qfile - 454 quality file"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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104 <param name="qaverage" type="integer" value="0" min="0" label="qaverage - remove sequences that have an average base quality below this value (ignored if &#060; 1)"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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105 <param name="qthreshold" type="integer" value="0" min="0" label="qthreshold - remove sequences that have any base quality below this value (ignored if &#060; 1)"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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106 <param name="qwindowaverage" type="integer" value="0" min="0" label="qwindowaverage - remove sequences that have an average base quality below this value over a window (ignored if &#060; 1)"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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107 <param name="qwindowsize" type="integer" value="50" min="0" label="qwindowsize - number of bases in a window. Default=50."/>
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108 <param name="rollaverage" type="integer" value="0" min="0" label="rollaverage - remove sequences that have an average base quality below this value in a rolling window (ignored if &#060; 1)"/>
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109 <param name="qstepsize" type="integer" value="1" min="0" label="qstepsize - number of bases to move the window over. Default=1."/>
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110 <param name="qtrim" type="boolean" truevalue="true" falsevalue="false" checked="false" label="qtrim - trim sequences below qthreshold and put in trim output, else put in scrap "/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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111 </when>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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112 </conditional>
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113 <param name="flip" type="boolean" truevalue="true" falsevalue="false" checked="false" label="flip - reverse complement the trimmed sequences"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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114 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. If you run trim.seqs with an oligos file that contains group labels, trim.seqs will create a new *.trim.count_table with the group information included. "/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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115 <param name="logtransform" type="boolean" truevalue="true" falsevalue="false" checked="false" label="logtransform" help="allows you to indicate you want the averages for the qwindowaverage, rollaverage and qaverage to be calculated using a logtransform."/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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116 <param name="checkorient" type="boolean" truevalue="true" falsevalue="false" checked="false" label="checkorient - search the reverse complement?" help="If you are running the trim.seqs command with paired barcodes or primers, you can use the checkorient parameter. When checkorient=t and mothur can't find the barcodes and primers, it will search the reverse compliment. "/>
2
baa3df51e2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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117 <expand macro="param-savelog"/>
0
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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118 </inputs>
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119 <outputs>
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120 <expand macro="logfile-output"/>
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121 <data name="trim_fasta" format_source="fasta" from_work_dir="fasta.trim" label="${tool.name} on ${on_string}: trim.fasta"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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122 <data name="scrap_fasta" format_source="fasta" from_work_dir="fasta.scrap" label="${tool.name} on ${on_string}: scrap.fasta"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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123 <data name="trim_names" format="mothur.names" from_work_dir="names*.trim.names" label="${tool.name} on ${on_string}: trim.names">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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124 <filter>names</filter>
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125 </data>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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126 <data name="scrap_names" format="mothur.names" from_work_dir="names*.scrap.names" label="${tool.name} on ${on_string}: scrap.names">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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127 <filter>names</filter>
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128 </data>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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129 <data name="trim_count" format="mothur.count_table" from_work_dir="count*.trim.count_table" label="${tool.name} on ${on_string}: trim.count">
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130 <filter>count</filter>
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131 </data>
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132 <data name="scrap_count" format="mothur.count_table" from_work_dir="count*.scrap.count_table" label="${tool.name} on ${on_string}: scrap.count">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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133 <filter>count</filter>
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134 </data>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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135 <data name="trim_qual" format_source="qfile" from_work_dir="fasta*.trim.qual" label="${tool.name} on ${on_string}: trim.qual">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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136 <filter>qual['add2'] == 'yes'</filter>
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137 </data>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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138 <data name="scrap_qual" format_source="qfile" from_work_dir="fasta*.scrap.qual" label="${tool.name} on ${on_string}: scrap.qual">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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139 <filter>qual['add2'] == 'yes'</filter>
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140 </data>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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141 <data name="groups_file" format="mothur.groups" from_work_dir="fasta.groups" label="${tool.name} on ${on_string}: groups">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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142 <filter>oligo['add'] == 'yes'</filter>
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143 </data>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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144 <collection name="fasta_allfiles" type="list" label="${tool.name} on ${on_string}: allfiles fasta">
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145 <filter>oligo['add'] == 'yes' and oligo['allfiles']</filter>
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146 <discover_datasets pattern="fasta.*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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147 </collection>
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148 <collection name="groups_allfiles" type="list" label="${tool.name} on ${on_string}: allfiles groups)">
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149 <filter>oligo['add'] == 'yes' and oligo['allfiles']</filter>
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150 <discover_datasets pattern="fasta.*?\.(?P&lt;designation&gt;.*)\.groups" format="mothur.groups"/>
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151 </collection>
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152 </outputs>
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153 <tests>
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154 <test><!-- test with fasta and names -->
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155 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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156 <param name="names" value="amazon1.names" ftype="mothur.names"/>
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157 <param name="maxhomop" value="4"/>
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158 <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/>
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159 <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
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160 <output name="trim_names" md5="1b8c6c47052bb69524ef56ebb764fb8f" ftype="mothur.names"/>
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161 <output name="scrap_names" md5="80f9252837e4b189f06ec00469b88e85" ftype="mothur.names"/>
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162 <param name="savelog" value="true"/>
0
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163 <expand macro="logfile-test"/>
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164 </test>
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165 <test><!-- test with count table -->
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166 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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167 <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/>
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168 <param name="maxhomop" value="4"/>
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169 <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/>
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170 <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
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171 <output name="trim_count" md5="836b4d72a8cda3741ef435741783b384" ftype="mothur.count_table"/>
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172 <output name="scrap_count" md5="04ae9f50c1b6f0d8d7e1ac28f845dd4c" ftype="mothur.count_table"/>
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173 <param name="savelog" value="true"/>
0
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174 <expand macro="logfile-test"/>
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175 </test>
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176 <test><!-- test with oligos -->
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177 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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178 <param name="add" value="yes"/>
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179 <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
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180 <param name="bdiffs" value="100"/>
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181 <param name="pdiffs" value="100"/>
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182 <output name="trim_fasta" md5="75a8a3ae2d1fe1ff2b860480b84e9bd6" ftype="fasta"/>
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183 <output name="scrap_fasta" md5="c4fd14e70ab7d1c21d238e87624829d7" ftype="fasta"/>
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184 <output name="groups_file" md5="198957282c234e825414e175d926046a" ftype="mothur.groups"/>
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185 <param name="savelog" value="true"/>
0
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186 <expand macro="logfile-test"/>
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187 </test>
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188 <test><!-- test with oligos and allfiles parameter -->
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189 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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190 <param name="add" value="yes"/>
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191 <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
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192 <param name="bdiffs" value="100"/>
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193 <param name="pdiffs" value="100"/>
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194 <param name="allfiles" value="true"/>
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195 <output name="trim_fasta" md5="75a8a3ae2d1fe1ff2b860480b84e9bd6" ftype="fasta"/>
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196 <output name="scrap_fasta" md5="c4fd14e70ab7d1c21d238e87624829d7" ftype="fasta"/>
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197 <output_collection name="groups_allfiles" count="9">
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198 <element name="F003D144" md5="445124b06d0c9146ae353631794c8093" ftype="mothur.groups"/>
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199 </output_collection>
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200 <output_collection name="fasta_allfiles" count="9">
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201 <element name="F003D144" md5="025ff271ac24ecb898863d7fcbfabf10" ftype="fasta"/>
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202 </output_collection>
2
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203 <param name="savelog" value="true"/>
0
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204 <expand macro="logfile-test"/>
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205 </test>
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206 <test><!-- test with qfile-->
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207 <param name="fasta" value="Fasting_Example1.fasta" ftype="fasta"/>
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208 <param name="add2" value="yes"/>
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209 <param name="qfile" value="Fasting_Example1.qual" ftype="qual454"/>
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210 <param name="maxhomop" value="4"/>
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211 <output name="trim_fasta" md5="d02f74acd6d9fb52b04a93869bb79302" ftype="fasta"/>
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212 <output name="scrap_fasta" md5="a4d3ef3d91b4c0146ec84bb7aad3987c" ftype="fasta"/>
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213 <output name="trim_qual" md5="3d4e2d3c7dd43b90660ab9c923d9eab1" ftype="qual454"/>
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214 <output name="scrap_qual" md5="22931236d082c2b77811bbf912c1f4b1" ftype="qual454"/>
2
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215 <param name="savelog" value="true"/>
0
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216 <expand macro="logfile-test"/>
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217 </test>
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218 </tests>
2
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219 <help><![CDATA[
0
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220
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221 @MOTHUR_OVERVIEW@
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222
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223 **Command Documentation**
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224
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225 The trim.seqs_ command provides the preprocessing features needed to screen and sort pyrosequences. The command will enable you to trim off primer sequences and barcodes, use the barcode information to generate a group file and split a fasta file into sub-files, screen sequences based on the qual file that comes from 454 sequencers, cull sequences based on sequence length and the presence of ambiguous bases and get the reverse complement of your sequences. While this analysis is clearly geared towards pyrosequencing collections, it can also be used with traditional Sanger sequences.
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226
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227 .. _trim.seqs: https://www.mothur.org/wiki/Trim.seqs
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228
2
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229 ]]></help>
0
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230 <expand macro="citations"/>
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231 </tool>