Mercurial > repos > jjohnson > mothur_toolsuite

changeset 5:e2e2071d2c62

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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 &#060; 1)"/>
     <param name="qthreshold" type="integer" value="0" label="qthreshold - remove sequences that have any base quality below this value (ignored if &#060; 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 &#060; 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 &#060; 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>