Mercurial > repos > jjohnson > mothur_toolsuite
changeset 5:e2e2071d2c62
Add missing qual params to trim.seqs
author | jj@dbw-galaxy-dev.msi.umn.edu |
---|---|
date | Thu, 09 Jun 2011 16:24:30 -0500 |
parents | 5265aa9067e0 |
children | ce6e81622c6a |
files | mothur/tools/mothur/mothur_wrapper.py mothur/tools/mothur/trim.seqs.xml |
diffstat | 2 files changed, 32 insertions(+), 12 deletions(-) [+] |
line wrap: on
line diff
--- a/mothur/tools/mothur/mothur_wrapper.py Wed Jun 08 15:02:44 2011 -0500 +++ b/mothur/tools/mothur/mothur_wrapper.py Thu Jun 09 16:24:30 2011 -0500 @@ -304,7 +304,7 @@ cmd_dict['summary.single'] = dict({'required' : [['list','sabund','rabund','shared']], 'optional' : ['calc','abund','size','label','groupmode']}) #cmd_dict['tree.shared'] = dict({'required' : [], 'optional' : ['groups','calc','cutoff','precision','label']}) cmd_dict['tree.shared'] = dict({'required' : [['shared','phylip','column']], 'optional' : ['name','groups','calc','cutoff','precision','label']}) - cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['group','oligos','qfile','qaverage','qthreshold','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast']}) + cmd_dict['trim.seqs'] = dict({'required' : ['fasta'], 'optional' : ['group','oligos','qfile','qaverage','qthreshold','qwindowaverage','qwindowsize','rollaverage','qstepsize','qtrim','flip','maxambig','maxhomop','minlength','maxlength','bdiffs','pdiffs','tdiffs','allfiles','keepfirst','removelast']}) #cmd_dict['unifrac.unweighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']}) cmd_dict['unifrac.unweighted'] = dict({'required' : ['tree'], 'optional' : ['name','group','groups','iters','distance','random','root','processors']}) #cmd_dict['unifrac.weighted'] = dict({'required' : [], 'optional' : ['groups','iters','distance','random','root','processors']}) @@ -448,6 +448,10 @@ parser.add_option( '--qfile', dest='qfile', help='Sequence read quality file (454 platform)' ) parser.add_option( '--qaverage', dest='qaverage', type="int", help='Remove sequences that have an average quality below the value' ) parser.add_option( '--qthreshold', dest='qthreshold', type="int", help='If at any point a base call in a sequence has a quality score below the value provided to the option, the sequence is terminated' ) + parser.add_option( '--qwindowaverage', dest='qwindowaverage', type="int", help='Remove sequences that have a window average quality below the value' ) + parser.add_option( '--qwindowsize', dest='qwindowsize', type="int", help='WIndow size for qwindowaverage' ) + parser.add_option( '--rollaverage', dest='rollaverage', type="int", help='Remove sequences that have a average quality below the value in a rolling window' ) + parser.add_option( '--qstepsize', dest='qstepsize', type="int", help='Distance to move a rolling window for each step' ) parser.add_option( '--qtrim', dest='qtrim', help='For sequence below qthreshold, false to scrap file, true to trimmed and in trim file' ) parser.add_option( '--flip', dest='flip', help='If true, reverse complement the sequences' ) parser.add_option( '--maxambig', dest='maxambig', type="int", help='Number of ambiguous base calls to allow' )
--- a/mothur/tools/mothur/trim.seqs.xml Wed Jun 08 15:02:44 2011 -0500 +++ b/mothur/tools/mothur/trim.seqs.xml Thu Jun 09 16:24:30 2011 -0500 @@ -5,33 +5,33 @@ --cmd='trim.seqs' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.trim\.fasta$:'$trim_fasta,'^\S+\.trim\.qual$:'$trim_qual,'^\S+\.scrap\.fasta$:'$scrap_fasta,'^\S+\.scrap\.qual$:'$scrap_qual,'^\S+\.groups$:'$groups_file --outputdir='$logfile.extra_files_path' - #if $minlength > 0: + #if int($minlength.__str__) > 0: --minlength=$minlength #end if - #if $maxlength > 0: + #if int($maxlength.__str__) > 0: --maxlength=$maxlength #end if - #if $maxambig >= 0: + #if int($maxambig.__str__) >= 0: --maxambig=$maxambig #end if - #if $maxhomop > 0: + #if int($maxhomop.__str__) > 0: --maxhomop=$maxhomop #end if - #if $keepfirst > 0: + #if int($keepfirst.__str__) > 0: --keepfirst=$keepfirst #end if - #if $removelast > 0: + #if int($removelast.__str__) > 0: --removelast=$removelast #end if #if $oligo.add == "yes": --oligos=$oligo.oligos - #if $oligo.bdiffs > 0: + #if int($oligo.bdiffs.__str__) > 0: --bdiffs=$oligo.bdiffs #end if - #if $oligo.pdiffs > 0: + #if int($oligo.pdiffs.__str__) > 0: --pdiffs=$oligo.pdiffs #end if - #if $oligo.tdiffs > 0: + #if int($oligo.tdiffs.__str__) > 0: --tdiffs=$oligo.tdiffs #end if $oligo.allfiles @@ -42,12 +42,24 @@ #end if #if $qual.add == "yes": --qfile=$qual.qfile - #if $qual.qaverage > 0: + #if int($qual.qaverage.__str__) > 0: --qaverage=$qual.qaverage #end if - #if $qual.qthreshold > 0: + #if int($qual.qthreshold.__str__) > 0: --qthreshold=$qual.qthreshold #end if + #if int($qual.qwindowaverage.__str__) > 0: + --qwindowaverage=$qual.qwindowaverage + #end if + #if int($qual.qwindowsize.__str__) > 0: + --qwindowsize=$qual.qwindowsize + #end if + #if int($qual.rollaverage.__str__) > 0: + --rollaverage=$qual.rollaverage + #end if + #if int($qual.qstepsize.__str__) > 0: + --qstepsize=$qual.qstepsize + #end if $qual.qtrim #end if $flip @@ -87,6 +99,10 @@ <param name="qfile" type="data" format="qual454" label="qfile - 454 quality file"/> <param name="qaverage" type="integer" value="0" label="qaverage - remove sequences that have an average base quality below this value (ignored if < 1)"/> <param name="qthreshold" type="integer" value="0" label="qthreshold - remove sequences that have any base quality below this value (ignored if < 1)"/> + <param name="qwindowaverage" type="integer" value="0" label="qwindowaverage - remove sequences that have an average base quality below this value over a window (ignored if < 1)"/> + <param name="qwindowsize" type="integer" value="50" label="qwindowsize - number of bases in a window. Default=50."/> + <param name="rollaverage" type="integer" value="0" label="rollaverage - remove sequences that have an average base quality below this value in a rolling window (ignored if < 1)"/> + <param name="qstepsize" type="integer" value="1" label="qstepsize - number of bases to move the window over. Default=1."/> <param name="qtrim" type="boolean" truevalue="--qtrim=true" falsevalue="" checked="false" label="qtrim - trim sequences below qthreshold and put in trim output, else put in scrap "/> </when> </conditional>