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comparison mothur/tools/mothur/trim.seqs.xml @ 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 7bfe1f843858
comparison
equal deleted inserted replaced
4:5265aa9067e0 5:e2e2071d2c62
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='trim.seqs' 5 --cmd='trim.seqs'
6 --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 6 --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
7 --outputdir='$logfile.extra_files_path' 7 --outputdir='$logfile.extra_files_path'
8 #if $minlength > 0: 8 #if int($minlength.__str__) > 0:
9 --minlength=$minlength 9 --minlength=$minlength
10 #end if 10 #end if
11 #if $maxlength > 0: 11 #if int($maxlength.__str__) > 0:
12 --maxlength=$maxlength 12 --maxlength=$maxlength
13 #end if 13 #end if
14 #if $maxambig >= 0: 14 #if int($maxambig.__str__) >= 0:
15 --maxambig=$maxambig 15 --maxambig=$maxambig
16 #end if 16 #end if
17 #if $maxhomop > 0: 17 #if int($maxhomop.__str__) > 0:
18 --maxhomop=$maxhomop 18 --maxhomop=$maxhomop
19 #end if 19 #end if
20 #if $keepfirst > 0: 20 #if int($keepfirst.__str__) > 0:
21 --keepfirst=$keepfirst 21 --keepfirst=$keepfirst
22 #end if 22 #end if
23 #if $removelast > 0: 23 #if int($removelast.__str__) > 0:
24 --removelast=$removelast 24 --removelast=$removelast
25 #end if 25 #end if
26 #if $oligo.add == "yes": 26 #if $oligo.add == "yes":
27 --oligos=$oligo.oligos 27 --oligos=$oligo.oligos
28 #if $oligo.bdiffs > 0: 28 #if int($oligo.bdiffs.__str__) > 0:
29 --bdiffs=$oligo.bdiffs 29 --bdiffs=$oligo.bdiffs
30 #end if 30 #end if
31 #if $oligo.pdiffs > 0: 31 #if int($oligo.pdiffs.__str__) > 0:
32 --pdiffs=$oligo.pdiffs 32 --pdiffs=$oligo.pdiffs
33 #end if 33 #end if
34 #if $oligo.tdiffs > 0: 34 #if int($oligo.tdiffs.__str__) > 0:
35 --tdiffs=$oligo.tdiffs 35 --tdiffs=$oligo.tdiffs
36 #end if 36 #end if
37 $oligo.allfiles 37 $oligo.allfiles
38 #if $oligo.allfiles.value: 38 #if $oligo.allfiles.value:
39 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' 39 --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
40 --new_datasets='^\S+?\.(\S+\.fasta)$:${fasta.ext}','^\S+?\.(\S+\.groups)$:groups' 40 --new_datasets='^\S+?\.(\S+\.fasta)$:${fasta.ext}','^\S+?\.(\S+\.groups)$:groups'
41 #end if 41 #end if
42 #end if 42 #end if
43 #if $qual.add == "yes": 43 #if $qual.add == "yes":
44 --qfile=$qual.qfile 44 --qfile=$qual.qfile
45 #if $qual.qaverage > 0: 45 #if int($qual.qaverage.__str__) > 0:
46 --qaverage=$qual.qaverage 46 --qaverage=$qual.qaverage
47 #end if 47 #end if
48 #if $qual.qthreshold > 0: 48 #if int($qual.qthreshold.__str__) > 0:
49 --qthreshold=$qual.qthreshold 49 --qthreshold=$qual.qthreshold
50 #end if
51 #if int($qual.qwindowaverage.__str__) > 0:
52 --qwindowaverage=$qual.qwindowaverage
53 #end if
54 #if int($qual.qwindowsize.__str__) > 0:
55 --qwindowsize=$qual.qwindowsize
56 #end if
57 #if int($qual.rollaverage.__str__) > 0:
58 --rollaverage=$qual.rollaverage
59 #end if
60 #if int($qual.qstepsize.__str__) > 0:
61 --qstepsize=$qual.qstepsize
50 #end if 62 #end if
51 $qual.qtrim 63 $qual.qtrim
52 #end if 64 #end if
53 $flip 65 $flip
54 --fasta=$fasta 66 --fasta=$fasta
85 <when value="no"/> 97 <when value="no"/>
86 <when value="yes"> 98 <when value="yes">
87 <param name="qfile" type="data" format="qual454" label="qfile - 454 quality file"/> 99 <param name="qfile" type="data" format="qual454" label="qfile - 454 quality file"/>
88 <param name="qaverage" type="integer" value="0" label="qaverage - remove sequences that have an average base quality below this value (ignored if &#060; 1)"/> 100 <param name="qaverage" type="integer" value="0" label="qaverage - remove sequences that have an average base quality below this value (ignored if &#060; 1)"/>
89 <param name="qthreshold" type="integer" value="0" label="qthreshold - remove sequences that have any base quality below this value (ignored if &#060; 1)"/> 101 <param name="qthreshold" type="integer" value="0" label="qthreshold - remove sequences that have any base quality below this value (ignored if &#060; 1)"/>
102 <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)"/>
103 <param name="qwindowsize" type="integer" value="50" label="qwindowsize - number of bases in a window. Default=50."/>
104 <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)"/>
105 <param name="qstepsize" type="integer" value="1" label="qstepsize - number of bases to move the window over. Default=1."/>
90 <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 "/> 106 <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 "/>
91 </when> 107 </when>
92 </conditional> 108 </conditional>
93 <param name="flip" type="boolean" truevalue="--flip=true" falsevalue="" checked="false" label="flip - reverse complement the trimmed sequences"/> 109 <param name="flip" type="boolean" truevalue="--flip=true" falsevalue="" checked="false" label="flip - reverse complement the trimmed sequences"/>
94 </inputs> 110 </inputs>