Mercurial > repos > iuc > mothur_trim_seqs

annotate trim.seqs.xml @ 0:143f949a5def 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 05:37:34 -0400
parents
children baa3df51e2b7
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0
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
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
parents:
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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
iuc
parents:
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3 <macros>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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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
iuc
parents:
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5 </macros>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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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
iuc
parents:
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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
iuc
parents:
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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
iuc
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9 <command><![CDATA[
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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10 @SHELL_OPTIONS@
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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11
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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12 ## create symlinks to input datasets
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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13 ln -s "$fasta" fasta.dat &&
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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14 ln -s "$names" names.dat &&
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
15 ln -s "$count" count.dat &&
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
16 #if $oligo.add == "yes":
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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17 ln -s "$oligo.oligos" oligo.oligos.dat &&
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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18 #end if
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
19 #if $qual.add2 == "yes":
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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20 ln -s "$qual.qfile" qual.qfile.dat &&
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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21 #end if
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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22
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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23 echo 'trim.seqs(
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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24 fasta=fasta.dat,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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25 minlength=$minlength,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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26 maxlength=$maxlength,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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27 maxambig=$maxambig,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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28 maxhomop=$maxhomop,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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29 keepfirst=$keepfirst,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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30 removelast=$removelast,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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31 #if $oligo.add == "yes":
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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32 oligos=oligo.oligos.dat,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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33 bdiffs=$oligo.bdiffs,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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34 pdiffs=$oligo.pdiffs,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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35 tdiffs=$oligo.tdiffs,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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36 ldiffs=$oligo.ldiffs,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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37 sdiffs=$oligo.sdiffs,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
38 keepforward=$oligo.keepforward,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
39 allfiles=$oligo.allfiles,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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40 #end if
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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41 #if $qual.add2 == "yes":
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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42 qfile=qual.qfile.dat,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
43 qaverage=$qual.qaverage,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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44 qthreshold=$qual.qthreshold,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
45 qwindowaverage=$qual.qwindowaverage,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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46 qwindowsize=$qual.qwindowsize,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
47 rollaverage=$qual.rollaverage,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
48 qstepsize=$qual.qstepsize,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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49 qtrim=$qual.qtrim,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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50 #end if
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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51 flip=$flip,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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52 #if $names:
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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53 name=names.dat,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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54 #end if
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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55 logtransform=$logtransform,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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56 checkorient=$checkorient,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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57 #if $count:
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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58 count=count.dat,
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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59 #end if
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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60 processors='\${GALAXY_SLOTS:-8}'
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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61 )'
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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62 | sed 's/ //g' ## mothur trips over whitespace
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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63 | mothur
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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64 | tee mothur.out.log
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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65 ## prevent these two files from being gathered into collection
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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66 && mv fasta.trim.fasta fasta.trim
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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67 && mv fasta.scrap.fasta fasta.scrap
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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68 ]]></command>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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69 <inputs>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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70 <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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71 <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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72 <param name="minlength" type="integer" value="0" min="0" label="minlength - Minimum Sequence Length (default 0, ignored if &#060; 1 )"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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73 <param name="maxlength" type="integer" value="0" min="0" label="maxlength - Maximum Sequence Length (default 0, ignored if &#060; 1)"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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74 <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
iuc
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75 <param name="maxhomop" type="integer" value="0" min="0" label="maxhomop - Maximum homopolymers (default 0, ignored if &#060; 1)"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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76 <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
iuc
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77 <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
iuc
parents:
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78 <conditional name="oligo">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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79 <param name="add" type="select" label="Trim with an oligos file?" help="">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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80 <option value="no">no</option>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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81 <option value="yes">yes</option>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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82 </param>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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83 <when value="no"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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84 <when value="yes">
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iuc
parents:
diff changeset
85 <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
iuc
parents:
diff changeset
86 <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
iuc
parents:
diff changeset
87 <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
iuc
parents:
diff changeset
88 <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
iuc
parents:
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89 <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
iuc
parents:
diff changeset
90 <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
parents:
diff changeset
91 <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
iuc
parents:
diff changeset
92 <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
iuc
parents:
diff changeset
93 </when>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
94 </conditional>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
95 <conditional name="qual">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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96 <param name="add2" type="select" label="Trim based on a quality file?" help="">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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97 <option value="no">no</option>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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98 <option value="yes">yes</option>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
99 </param>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
100 <when value="no"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
101 <when value="yes">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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102 <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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103 <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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104 <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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105 <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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106 <param name="qwindowsize" type="integer" value="50" min="0" label="qwindowsize - number of bases in a window. Default=50."/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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107 <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)"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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108 <param name="qstepsize" type="integer" value="1" min="0" label="qstepsize - number of bases to move the window over. Default=1."/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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109 <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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110 </when>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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111 </conditional>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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112 <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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113 <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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114 <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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115 <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. "/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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116 </inputs>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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117 <outputs>
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118 <expand macro="logfile-output"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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119 <data name="trim_fasta" format_source="fasta" from_work_dir="fasta.trim" label="${tool.name} on ${on_string}: trim.fasta"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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120 <data name="scrap_fasta" format_source="fasta" from_work_dir="fasta.scrap" label="${tool.name} on ${on_string}: scrap.fasta"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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121 <data name="trim_names" format="mothur.names" from_work_dir="names*.trim.names" label="${tool.name} on ${on_string}: trim.names">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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diff changeset
122 <filter>names</filter>
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123 </data>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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124 <data name="scrap_names" format="mothur.names" from_work_dir="names*.scrap.names" label="${tool.name} on ${on_string}: scrap.names">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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125 <filter>names</filter>
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126 </data>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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127 <data name="trim_count" format="mothur.count_table" from_work_dir="count*.trim.count_table" label="${tool.name} on ${on_string}: trim.count">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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128 <filter>count</filter>
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129 </data>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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130 <data name="scrap_count" format="mothur.count_table" from_work_dir="count*.scrap.count_table" label="${tool.name} on ${on_string}: scrap.count">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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diff changeset
131 <filter>count</filter>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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132 </data>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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133 <data name="trim_qual" format_source="qfile" from_work_dir="fasta*.trim.qual" label="${tool.name} on ${on_string}: trim.qual">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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diff changeset
134 <filter>qual['add2'] == 'yes'</filter>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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135 </data>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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136 <data name="scrap_qual" format_source="qfile" from_work_dir="fasta*.scrap.qual" label="${tool.name} on ${on_string}: scrap.qual">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
137 <filter>qual['add2'] == 'yes'</filter>
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138 </data>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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139 <data name="groups_file" format="mothur.groups" from_work_dir="fasta.groups" label="${tool.name} on ${on_string}: groups">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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diff changeset
140 <filter>oligo['add'] == 'yes'</filter>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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141 </data>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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142 <collection name="fasta_allfiles" type="list" label="${tool.name} on ${on_string}: allfiles fasta">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
143 <filter>oligo['add'] == 'yes' and oligo['allfiles']</filter>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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144 <discover_datasets pattern="fasta.*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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145 </collection>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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146 <collection name="groups_allfiles" type="list" label="${tool.name} on ${on_string}: allfiles groups)">
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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diff changeset
147 <filter>oligo['add'] == 'yes' and oligo['allfiles']</filter>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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148 <discover_datasets pattern="fasta.*?\.(?P&lt;designation&gt;.*)\.groups" format="mothur.groups"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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149 </collection>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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150 </outputs>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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151 <tests>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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152 <test><!-- test with fasta and names -->
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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153 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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154 <param name="names" value="amazon1.names" ftype="mothur.names"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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155 <param name="maxhomop" value="4"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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156 <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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157 <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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158 <output name="trim_names" md5="1b8c6c47052bb69524ef56ebb764fb8f" ftype="mothur.names"/>
143f949a5def planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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159 <output name="scrap_names" md5="80f9252837e4b189f06ec00469b88e85" ftype="mothur.names"/>
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160 <expand macro="logfile-test"/>
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161 </test>
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162 <test><!-- test with count table -->
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163 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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164 <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/>
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165 <param name="maxhomop" value="4"/>
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166 <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/>
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167 <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
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168 <output name="trim_count" md5="836b4d72a8cda3741ef435741783b384" ftype="mothur.count_table"/>
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169 <output name="scrap_count" md5="04ae9f50c1b6f0d8d7e1ac28f845dd4c" ftype="mothur.count_table"/>
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170 <expand macro="logfile-test"/>
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171 </test>
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172 <test><!-- test with oligos -->
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173 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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174 <param name="add" value="yes"/>
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175 <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
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176 <param name="bdiffs" value="100"/>
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177 <param name="pdiffs" value="100"/>
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178 <output name="trim_fasta" md5="75a8a3ae2d1fe1ff2b860480b84e9bd6" ftype="fasta"/>
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179 <output name="scrap_fasta" md5="c4fd14e70ab7d1c21d238e87624829d7" ftype="fasta"/>
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180 <output name="groups_file" md5="198957282c234e825414e175d926046a" ftype="mothur.groups"/>
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181 <expand macro="logfile-test"/>
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182 </test>
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183 <test><!-- test with oligos and allfiles parameter -->
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184 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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185 <param name="add" value="yes"/>
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186 <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
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187 <param name="bdiffs" value="100"/>
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188 <param name="pdiffs" value="100"/>
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189 <param name="allfiles" value="true"/>
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190 <output name="trim_fasta" md5="75a8a3ae2d1fe1ff2b860480b84e9bd6" ftype="fasta"/>
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191 <output name="scrap_fasta" md5="c4fd14e70ab7d1c21d238e87624829d7" ftype="fasta"/>
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192 <output_collection name="groups_allfiles" count="9">
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193 <element name="F003D144" md5="445124b06d0c9146ae353631794c8093" ftype="mothur.groups"/>
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194 </output_collection>
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195 <output_collection name="fasta_allfiles" count="9">
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196 <element name="F003D144" md5="025ff271ac24ecb898863d7fcbfabf10" ftype="fasta"/>
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197 </output_collection>
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198 <expand macro="logfile-test"/>
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199 </test>
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200 <test><!-- test with qfile-->
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201 <param name="fasta" value="Fasting_Example1.fasta" ftype="fasta"/>
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202 <param name="add2" value="yes"/>
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203 <param name="qfile" value="Fasting_Example1.qual" ftype="qual454"/>
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204 <param name="maxhomop" value="4"/>
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205 <output name="trim_fasta" md5="d02f74acd6d9fb52b04a93869bb79302" ftype="fasta"/>
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206 <output name="scrap_fasta" md5="a4d3ef3d91b4c0146ec84bb7aad3987c" ftype="fasta"/>
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207 <output name="trim_qual" md5="3d4e2d3c7dd43b90660ab9c923d9eab1" ftype="qual454"/>
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208 <output name="scrap_qual" md5="22931236d082c2b77811bbf912c1f4b1" ftype="qual454"/>
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209 <expand macro="logfile-test"/>
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210 </test>
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211 </tests>
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212 <help>
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213 <![CDATA[
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214
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215 @MOTHUR_OVERVIEW@
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216
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217 **Command Documentation**
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218
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219 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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220
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221 .. _trim.seqs: https://www.mothur.org/wiki/Trim.seqs
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222
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223 ]]>
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224 </help>
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225 <expand macro="citations"/>
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226 </tool>