Mercurial > repos > iuc > mothur_trim_seqs
comparison trim.seqs.xml @ 3:e695fda56931 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:33:36 -0500 |
| parents | 08692ab7170c |
| children | 4929eb3e0037 |
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| 2:92bc36f57d5b | 3:e695fda56931 |
|---|---|
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 7 <expand macro="stdio"/> | 7 <expand macro="stdio"/> |
| 8 <expand macro="version_command"/> | 8 <expand macro="version_command"/> |
| 9 <command><![CDATA[ | 9 <command><![CDATA[ |
| 10 @SHELL_OPTIONS@ | 10 @SHELL_OPTIONS@ |
| 11 | 11 |
| 12 ## create symlinks to input datasets | 12 ## create symlinks to input datasets |
| 13 ln -s "$fasta" fasta.dat && | 13 ln -s '$fasta' fasta.dat && |
| 14 ln -s "$names" names.dat && | 14 ln -s '$names' names.dat && |
| 15 ln -s "$count" count.dat && | 15 ln -s '$count' count.dat && |
| 16 #if $oligo.add == "yes": | 16 #if $oligo.add == "yes": |
| 17 ln -s "$oligo.oligos" oligo.oligos.dat && | 17 ln -s '$oligo.oligos' oligo.oligos.dat && |
| 18 #end if | 18 #end if |
| 19 #if $qual.add2 == "yes": | 19 #if $qual.add2 == "yes": |
| 20 ln -s "$qual.qfile" qual.qfile.dat && | 20 ln -s '$qual.qfile' qual.qfile.dat && |
| 21 #end if | 21 #end if |
| 22 | 22 |
| 23 echo 'trim.seqs( | 23 echo 'trim.seqs( |
| 24 fasta=fasta.dat, | 24 fasta=fasta.dat, |
| 25 minlength=$minlength, | 25 minlength=$minlength, |
| 26 maxlength=$maxlength, | 26 maxlength=$maxlength, |
| 27 maxambig=$maxambig, | 27 maxambig=$maxambig, |
| 28 maxhomop=$maxhomop, | 28 maxhomop=$maxhomop, |
| 29 keepfirst=$keepfirst, | 29 keepfirst=$keepfirst, |
| 30 removelast=$removelast, | 30 removelast=$removelast, |
| 31 #if $oligo.add == "yes": | 31 #if $oligo.add == "yes": |
| 32 oligos=oligo.oligos.dat, | 32 oligos=oligo.oligos.dat, |
| 33 bdiffs=$oligo.bdiffs, | 33 bdiffs=$oligo.bdiffs, |
| 34 pdiffs=$oligo.pdiffs, | 34 pdiffs=$oligo.pdiffs, |
| 35 tdiffs=$oligo.tdiffs, | 35 tdiffs=$oligo.tdiffs, |
| 36 ldiffs=$oligo.ldiffs, | 36 ldiffs=$oligo.ldiffs, |
| 37 sdiffs=$oligo.sdiffs, | 37 sdiffs=$oligo.sdiffs, |
| 38 keepforward=$oligo.keepforward, | 38 keepforward=$oligo.keepforward, |
| 39 allfiles=$oligo.allfiles, | 39 allfiles=$oligo.allfiles, |
| 40 #end if | 40 #end if |
| 41 #if $qual.add2 == "yes": | 41 #if $qual.add2 == "yes": |
| 42 qfile=qual.qfile.dat, | 42 qfile=qual.qfile.dat, |
| 43 qaverage=$qual.qaverage, | 43 qaverage=$qual.qaverage, |
| 44 qthreshold=$qual.qthreshold, | 44 qthreshold=$qual.qthreshold, |
| 45 qwindowaverage=$qual.qwindowaverage, | 45 qwindowaverage=$qual.qwindowaverage, |
| 46 qwindowsize=$qual.qwindowsize, | 46 qwindowsize=$qual.qwindowsize, |
| 47 rollaverage=$qual.rollaverage, | 47 rollaverage=$qual.rollaverage, |
| 48 qstepsize=$qual.qstepsize, | 48 qstepsize=$qual.qstepsize, |
| 49 qtrim=$qual.qtrim, | 49 qtrim=$qual.qtrim, |
| 50 #end if | 50 #end if |
| 51 flip=$flip, | 51 flip=$flip, |
| 52 #if $names: | 52 #if $names: |
| 53 name=names.dat, | 53 name=names.dat, |
| 54 #end if | 54 #end if |
| 55 logtransform=$logtransform, | 55 logtransform=$logtransform, |
| 56 checkorient=$checkorient, | 56 checkorient=$checkorient, |
| 57 #if $count: | 57 #if $count: |
| 58 count=count.dat, | 58 count=count.dat, |
| 59 #end if | 59 #end if |
| 60 processors='\${GALAXY_SLOTS:-8}' | 60 processors='\${GALAXY_SLOTS:-8}' |
| 61 )' | 61 )' |
| 62 | sed 's/ //g' ## mothur trips over whitespace | 62 | sed 's/ //g' ## mothur trips over whitespace |
| 63 | mothur | 63 | mothur |
| 64 | tee mothur.out.log | 64 | tee mothur.out.log |
| 65 ## prevent these two files from being gathered into collection | 65 |
| 66 && mv fasta.trim.fasta fasta.trim | 66 ## prevent these two files from being gathered into collection |
| 67 && mv fasta.scrap.fasta fasta.scrap | 67 && mv fasta.trim.fasta fasta.trim |
| 68 && mv fasta.scrap.fasta fasta.scrap | |
| 68 ]]></command> | 69 ]]></command> |
| 69 <inputs> | 70 <inputs> |
| 70 <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/> | 71 <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/> |
| 71 <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/> | 72 <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/> |
| 72 <param name="minlength" type="integer" value="0" min="0" label="minlength - Minimum Sequence Length (default 0, ignored if < 1 )"/> | 73 <param name="minlength" type="integer" value="0" min="0" label="minlength - Minimum Sequence Length (default 0, ignored if < 1 )"/> |
| 207 <output name="trim_qual" md5="3d4e2d3c7dd43b90660ab9c923d9eab1" ftype="qual454"/> | 208 <output name="trim_qual" md5="3d4e2d3c7dd43b90660ab9c923d9eab1" ftype="qual454"/> |
| 208 <output name="scrap_qual" md5="22931236d082c2b77811bbf912c1f4b1" ftype="qual454"/> | 209 <output name="scrap_qual" md5="22931236d082c2b77811bbf912c1f4b1" ftype="qual454"/> |
| 209 <expand macro="logfile-test"/> | 210 <expand macro="logfile-test"/> |
| 210 </test> | 211 </test> |
| 211 </tests> | 212 </tests> |
| 212 <help> | 213 <help><![CDATA[ |
| 213 <![CDATA[ | |
| 214 | 214 |
| 215 @MOTHUR_OVERVIEW@ | 215 @MOTHUR_OVERVIEW@ |
| 216 | 216 |
| 217 **Command Documentation** | 217 **Command Documentation** |
| 218 | 218 |
| 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. | 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. |
| 220 | 220 |
| 221 .. _trim.seqs: https://www.mothur.org/wiki/Trim.seqs | 221 .. _trim.seqs: https://www.mothur.org/wiki/Trim.seqs |
| 222 | 222 |
| 223 ]]> | 223 ]]></help> |
| 224 </help> | |
| 225 <expand macro="citations"/> | 224 <expand macro="citations"/> |
| 226 </tool> | 225 </tool> |