vsearch: search.xml annotate

annotate search.xml @ 6:9495df9dd6ef draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb"

author	iuc
date	Wed, 04 Nov 2020 07:36:19 +0000
parents	4258854759ba
children

rev	line source
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	1 <tool id="vsearch_search" name="VSearch search" version="@VERSION@.1">
0 fae6527990af Imported from capsule None iuc parents: diff changeset	2 <description></description>
fae6527990af Imported from capsule None iuc parents: diff changeset	3 <macros>
fae6527990af Imported from capsule None iuc parents: diff changeset	4 <import>vsearch_macros.xml</import>
fae6527990af Imported from capsule None iuc parents: diff changeset	5 </macros>
fae6527990af Imported from capsule None iuc parents: diff changeset	6 <expand macro="requirements" />
fae6527990af Imported from capsule None iuc parents: diff changeset	7 <expand macro="stdio" />
fae6527990af Imported from capsule None iuc parents: diff changeset	8 <expand macro="version_command" />
fae6527990af Imported from capsule None iuc parents: diff changeset	9 <command>
fae6527990af Imported from capsule None iuc parents: diff changeset	10 <![CDATA[
fae6527990af Imported from capsule None iuc parents: diff changeset	11 vsearch
fae6527990af Imported from capsule None iuc parents: diff changeset	12
fae6527990af Imported from capsule None iuc parents: diff changeset	13 @GENERAL@
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	14 --db '$dbfile'
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	15 #if $dbmask:
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	16 --dbmask "$dbmask"
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	17 #end if
0 fae6527990af Imported from capsule None iuc parents: diff changeset	18
fae6527990af Imported from capsule None iuc parents: diff changeset	19 ##--fulldp full dynamic programming alignment (always on)
fae6527990af Imported from capsule None iuc parents: diff changeset	20 ##--gapext STRING penalties for gap extension (2I/1E)
fae6527990af Imported from capsule None iuc parents: diff changeset	21 ##--gapopen STRING penalties for gap opening (20I/2E)
fae6527990af Imported from capsule None iuc parents: diff changeset	22 $hardmask
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	23 --id "$id"
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	24 --iddef "$iddef"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	25
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	26 #if str( $qmask ) != 'no':
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	27 --qmask "$qmask"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	28 #end if
fae6527990af Imported from capsule None iuc parents: diff changeset	29
fae6527990af Imported from capsule None iuc parents: diff changeset	30 ## --rowlen INT width of alignment lines in alnout output (64)
fae6527990af Imported from capsule None iuc parents: diff changeset	31
fae6527990af Imported from capsule None iuc parents: diff changeset	32 $self_param
fae6527990af Imported from capsule None iuc parents: diff changeset	33 $selfid_param
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	34 $sizeout
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	35 --strand "$strand"
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	36 --usearch_global '$queryfile'
0 fae6527990af Imported from capsule None iuc parents: diff changeset	37
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	38 #if '--alnout' in str($outputs).split( "," ):
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	39 --alnout '$alnout'
0 fae6527990af Imported from capsule None iuc parents: diff changeset	40 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	41 #if '--blast6out' in str($outputs).split( "," ):
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	42 --blast6out '$blast6out'
0 fae6527990af Imported from capsule None iuc parents: diff changeset	43 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	44 #if '--dbmatched' in str($outputs).split( "," ):
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	45 --dbmatched '$dbmatched'
0 fae6527990af Imported from capsule None iuc parents: diff changeset	46 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	47 #if '--dbnotmatched' in str($outputs).split( "," ):
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	48 --dbnotmatched '$dbnotmatched'
0 fae6527990af Imported from capsule None iuc parents: diff changeset	49 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	50 #if '--fastapairs' in str($outputs).split( "," ):
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	51 --fastapairs '$fastapairs'
0 fae6527990af Imported from capsule None iuc parents: diff changeset	52 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	53 #if '--notmatched' in str($outputs).split( "," ):
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	54 --notmatched '$notmatched'
0 fae6527990af Imported from capsule None iuc parents: diff changeset	55 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	56 #if '--matched' in str($outputs).split( "," ):
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	57 --matched '$matched'
0 fae6527990af Imported from capsule None iuc parents: diff changeset	58 #end if
fae6527990af Imported from capsule None iuc parents: diff changeset	59
fae6527990af Imported from capsule None iuc parents: diff changeset	60 #if $adv_opts.adv_opts_selector == "advanced":
fae6527990af Imported from capsule None iuc parents: diff changeset	61 $adv_opts.top_hits_only
fae6527990af Imported from capsule None iuc parents: diff changeset	62 $adv_opts.rightjust
fae6527990af Imported from capsule None iuc parents: diff changeset	63 $adv_opts.leftjust
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	64 --target_cov "$adv_opts.target_cov"
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	65 --query_cov "$adv_opts.query_cov"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	66
fae6527990af Imported from capsule None iuc parents: diff changeset	67
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	68 #if str( $adv_opts.maxid ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	69 --maxid "$adv_opts.maxid"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	70 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	71 #if str( $adv_opts.maxqt ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	72 --maxqt "$adv_opts.maxqsize"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	73 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	74 #if str( $adv_opts.maxsizeratio ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	75 --maxsizeratio "$adv_opts.maxsizeratio"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	76 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	77 #if str( $adv_opts.maxsl ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	78 --maxsl "$adv_opts.maxsl"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	79 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	80 #if str( $adv_opts.mid ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	81 --mid "$adv_opts.mid"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	82 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	83 #if str( $adv_opts.minqt ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	84 --minqt "$adv_opts.minqt"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	85 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	86 #if str( $adv_opts.minsizeratio ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	87 --minsizeratio "$adv_opts.minseqlength"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	88 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	89 #if str( $adv_opts.minsl ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	90 --minsl "$adv_opts.minsl"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	91 #end if
fae6527990af Imported from capsule None iuc parents: diff changeset	92
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	93 #if str( $adv_opts.mintsize ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	94 --mintsize "$adv_opts.mintsize"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	95 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	96 #if str( $adv_opts.mismatch ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	97 --mismatch "$adv_opts.mismatch"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	98 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	99 #if str( $adv_opts.maxqsize ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	100 --maxqsize "$adv_opts.maxqsize"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	101 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	102 #if str( $adv_opts.mincols ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	103 --mincols "$adv_opts.mincols"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	104 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	105 #if str( $adv_opts.maxsubs ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	106 --maxsubs "$adv_opts.maxsubs"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	107 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	108 #if str( $adv_opts.maxrejects ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	109 --maxrejects "$adv_opts.maxrejects"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	110 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	111 #if str( $adv_opts.maxaccepts ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	112 --maxaccepts "$adv_opts.maxaccepts"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	113 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	114 #if str( $adv_opts.maxdiffs ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	115 --maxdiffs "$adv_opts.maxdiffs"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	116 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	117 #if str( $adv_opts.maxgaps ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	118 --maxgaps "$adv_opts.maxgaps"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	119 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	120 #if str( $adv_opts.maxhits ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	121 --maxhits "$adv_opts.maxhits"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	122 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	123 #if str( $adv_opts.match ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	124 --match "$adv_opts.match"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	125 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	126 #if str( $adv_opts.idprefix ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	127 --idprefix "$adv_opts.idprefix"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	128 #end if
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	129 #if str( $adv_opts.idsuffix ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	130 --idsuffix str( $adv_opts.idsuffix )
0 fae6527990af Imported from capsule None iuc parents: diff changeset	131 #end if
fae6527990af Imported from capsule None iuc parents: diff changeset	132
fae6527990af Imported from capsule None iuc parents: diff changeset	133 #if $adv_opts.uclust_output.uclust_output_select == 'yes':
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	134 --uc '$uc'
0 fae6527990af Imported from capsule None iuc parents: diff changeset	135 $adv_opts.uclust_output.uc_allhits
fae6527990af Imported from capsule None iuc parents: diff changeset	136 #end if
fae6527990af Imported from capsule None iuc parents: diff changeset	137
fae6527990af Imported from capsule None iuc parents: diff changeset	138 #if $adv_opts.userfields_output.userfields_output_select == 'yes':
fae6527990af Imported from capsule None iuc parents: diff changeset	139 --userfields '#echo '+'.join( str($adv_opts.userfields_output.userfields).split(',') )#'
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	140 --userout '$userout'
0 fae6527990af Imported from capsule None iuc parents: diff changeset	141 #end if
fae6527990af Imported from capsule None iuc parents: diff changeset	142
fae6527990af Imported from capsule None iuc parents: diff changeset	143 ##--weak_id REAL include aligned hits with >= id; continue search
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	144 --wordlength "$adv_opts.wordlength"
0 fae6527990af Imported from capsule None iuc parents: diff changeset	145
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	146 $adv_opts.output_no_hits
0 fae6527990af Imported from capsule None iuc parents: diff changeset	147
fae6527990af Imported from capsule None iuc parents: diff changeset	148 #end if
fae6527990af Imported from capsule None iuc parents: diff changeset	149
fae6527990af Imported from capsule None iuc parents: diff changeset	150
fae6527990af Imported from capsule None iuc parents: diff changeset	151 ]]>
fae6527990af Imported from capsule None iuc parents: diff changeset	152 </command>
fae6527990af Imported from capsule None iuc parents: diff changeset	153 <inputs>
fae6527990af Imported from capsule None iuc parents: diff changeset	154 <param name="queryfile" type="data" format="fasta" label="Select your query FASTA file" help="(--usearch_global)" />
fae6527990af Imported from capsule None iuc parents: diff changeset	155 <param name="dbfile" type="data" format="fasta" label="Select your database FASTA file" help="(--db)" />
fae6527990af Imported from capsule None iuc parents: diff changeset	156
fae6527990af Imported from capsule None iuc parents: diff changeset	157 <expand macro="qmask" />
fae6527990af Imported from capsule None iuc parents: diff changeset	158 <expand macro="sizeout" />
fae6527990af Imported from capsule None iuc parents: diff changeset	159 <expand macro="strand" />
fae6527990af Imported from capsule None iuc parents: diff changeset	160 <expand macro="self_and_selfid" />
fae6527990af Imported from capsule None iuc parents: diff changeset	161 <expand macro="id_and_iddef" />
fae6527990af Imported from capsule None iuc parents: diff changeset	162 <expand macro="hardmask" />
fae6527990af Imported from capsule None iuc parents: diff changeset	163
fae6527990af Imported from capsule None iuc parents: diff changeset	164 <param name="dbmask" type="select" optional="True" label="Mask database sequences" help="(--dbmask)">
fae6527990af Imported from capsule None iuc parents: diff changeset	165 <option value="none" selected="True">No masking</option>
fae6527990af Imported from capsule None iuc parents: diff changeset	166 <option value="dust" selected="True">dust</option>
fae6527990af Imported from capsule None iuc parents: diff changeset	167 <option value="soft">soft</option>
fae6527990af Imported from capsule None iuc parents: diff changeset	168 </param>
fae6527990af Imported from capsule None iuc parents: diff changeset	169
fae6527990af Imported from capsule None iuc parents: diff changeset	170 <expand macro="general_output">
fae6527990af Imported from capsule None iuc parents: diff changeset	171 <option value="--dbmatched">FASTA file for matching database sequences</option>
fae6527990af Imported from capsule None iuc parents: diff changeset	172 <option value="--dbnotmatched">FASTA file for non-matching database sequences</option>
fae6527990af Imported from capsule None iuc parents: diff changeset	173 <option value="--notmatched">Write non-matching query sequences to separate file</option>
fae6527990af Imported from capsule None iuc parents: diff changeset	174 <option value="--matched">Write matching query sequences to separate file</option>
fae6527990af Imported from capsule None iuc parents: diff changeset	175 </expand>
fae6527990af Imported from capsule None iuc parents: diff changeset	176
fae6527990af Imported from capsule None iuc parents: diff changeset	177 <conditional name="adv_opts">
fae6527990af Imported from capsule None iuc parents: diff changeset	178 <param name="adv_opts_selector" type="select" label="Advanced Options">
fae6527990af Imported from capsule None iuc parents: diff changeset	179 <option value="basic" selected="True">Hide Advanced Options</option>
fae6527990af Imported from capsule None iuc parents: diff changeset	180 <option value="advanced">Show Advanced Options</option>
fae6527990af Imported from capsule None iuc parents: diff changeset	181 </param>
fae6527990af Imported from capsule None iuc parents: diff changeset	182 <when value="basic" />
fae6527990af Imported from capsule None iuc parents: diff changeset	183 <when value="advanced">
fae6527990af Imported from capsule None iuc parents: diff changeset	184
fae6527990af Imported from capsule None iuc parents: diff changeset	185 <param name="top_hits_only" type="boolean" truevalue="--top_hits_only" falsevalue="" checked="False"
fae6527990af Imported from capsule None iuc parents: diff changeset	186 label="Output only hits with identity equal to the best" help="(--top_hits_only)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	187 <param name="rightjust" type="boolean" truevalue="--rightjust" falsevalue="" checked="False"
fae6527990af Imported from capsule None iuc parents: diff changeset	188 label="Reject if terminal gaps at alignment right end" help="(--rightjust)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	189 <param name="leftjust" type="boolean" truevalue="--leftjust" falsevalue="" checked="False"
fae6527990af Imported from capsule None iuc parents: diff changeset	190 label="Reject if terminal gaps at alignment left end" help="(--leftjust)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	191
fae6527990af Imported from capsule None iuc parents: diff changeset	192 <param name="query_cov" type="float" value="" optional="True" label="Reject if fraction of query seq. aligned lower than this value"
fae6527990af Imported from capsule None iuc parents: diff changeset	193 help="(--query_cov)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	194 <param name="target_cov" type="float" value="" optional="True" label="Reject if fraction of target seq. aligned lower than this value"
fae6527990af Imported from capsule None iuc parents: diff changeset	195 help="(--target_cov)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	196 <param name="maxid" type="float" value="" optional="True" label="Reject if identity higher than this value"
fae6527990af Imported from capsule None iuc parents: diff changeset	197 help="(--maxid)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	198 <param name="maxqt" type="float" value="" optional="True" label="Reject if query/target length ratio higher than this value"
fae6527990af Imported from capsule None iuc parents: diff changeset	199 help="(--maxqt)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	200 <param name="maxsizeratio" type="float" value="" optional="True" label="Reject if query/target abundance ratio higher than this value"
fae6527990af Imported from capsule None iuc parents: diff changeset	201 help="(--maxsizeratio)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	202 <param name="maxsl" type="float" value="" optional="True" label="Reject if shorter/longer length ratio higher than this value"
fae6527990af Imported from capsule None iuc parents: diff changeset	203 help="(--maxsl)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	204 <param name="mid" type="float" value="" optional="True" label="Reject if percent identity lower than this value, ignoring gaps"
fae6527990af Imported from capsule None iuc parents: diff changeset	205 help="(--mid)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	206 <param name="minqt" type="float" value="" optional="True" label="Reject if query/target length ratio lower than this value"
fae6527990af Imported from capsule None iuc parents: diff changeset	207 help="(--minqt)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	208 <param name="minsl" type="float" value="" optional="True" label="Reject if shorter/longer length ratio lower than this value"
fae6527990af Imported from capsule None iuc parents: diff changeset	209 help="(--minsl)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	210 <param name="minsizeratio" type="float" value="" optional="True" label="Reject if query/target abundance ratio lower than this value"
fae6527990af Imported from capsule None iuc parents: diff changeset	211 help="(--minsizeratio)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	212
fae6527990af Imported from capsule None iuc parents: diff changeset	213 <param name="maxqsize" type="integer" value="" optional="True" label="Reject if query abundance larger than this value"
fae6527990af Imported from capsule None iuc parents: diff changeset	214 help="(--maxqsize)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	215 <param name="mincols" type="integer" value="" optional="True" label="Reject if alignment length shorter than this value"
fae6527990af Imported from capsule None iuc parents: diff changeset	216 help="(--mincols)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	217 <param name="maxsubs" type="integer" value="" optional="True" label="Reject if more substitutions than this value"
fae6527990af Imported from capsule None iuc parents: diff changeset	218 help="(--maxsubs)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	219 <expand macro="maxrejects" />
fae6527990af Imported from capsule None iuc parents: diff changeset	220 <expand macro="maxaccepts" />
fae6527990af Imported from capsule None iuc parents: diff changeset	221 <param name="maxdiffs" type="integer" value="" optional="True" label="Reject if more substitutions or indels than this value"
fae6527990af Imported from capsule None iuc parents: diff changeset	222 help="(--maxdiffs)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	223 <param name="maxgaps" type="integer" value="" optional="True" label="Reject if more indels than this value"
fae6527990af Imported from capsule None iuc parents: diff changeset	224 help="(--maxgaps)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	225 <param name="maxhits" type="integer" value="" optional="True" label="Maximum number of hits to show"
fae6527990af Imported from capsule None iuc parents: diff changeset	226 help="(--maxhits)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	227 <param name="match" type="integer" value="2" label="Score for match"
fae6527990af Imported from capsule None iuc parents: diff changeset	228 help="(--match)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	229 <param name="idprefix" type="integer" value="" optional="True" label="Reject if first n nucleotides do not match"
fae6527990af Imported from capsule None iuc parents: diff changeset	230 help="(--idprefix)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	231 <param name="idsuffix" type="integer" value="" optional="True" label="Reject if last n nucleotides do not match"
fae6527990af Imported from capsule None iuc parents: diff changeset	232 help="(--idsuffix)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	233 <param name="mintsize" type="integer" value="" optional="True" label="Reject if target abundance lower"
fae6527990af Imported from capsule None iuc parents: diff changeset	234 help="(--mintsize)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	235 <param name="mismatch" type="integer" value="-4" label="Score for mismatch"
fae6527990af Imported from capsule None iuc parents: diff changeset	236 help="(--mismatch)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	237
fae6527990af Imported from capsule None iuc parents: diff changeset	238 <conditional name="uclust_output">
fae6527990af Imported from capsule None iuc parents: diff changeset	239 <param name="uclust_output_select" type="select" label="UCLUST-like output" help="(--uc)">
fae6527990af Imported from capsule None iuc parents: diff changeset	240 <option value="yes">Yes</option>
fae6527990af Imported from capsule None iuc parents: diff changeset	241 <option value="no" selected="True">No</option>
fae6527990af Imported from capsule None iuc parents: diff changeset	242 </param>
fae6527990af Imported from capsule None iuc parents: diff changeset	243 <when value="yes">
fae6527990af Imported from capsule None iuc parents: diff changeset	244 <param name="uc_allhits" type="boolean" truevalue="--uc_allhits" falsevalue="" checked="False"
fae6527990af Imported from capsule None iuc parents: diff changeset	245 label="Show all, not just top hits" help="(--uc_allhits)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	246 </when>
fae6527990af Imported from capsule None iuc parents: diff changeset	247 <when value="no" />
fae6527990af Imported from capsule None iuc parents: diff changeset	248 </conditional>
fae6527990af Imported from capsule None iuc parents: diff changeset	249
fae6527990af Imported from capsule None iuc parents: diff changeset	250 <param name="wordlength" type="integer" value="8" min="3" max="15" label="Length of words for database index 3-15"
fae6527990af Imported from capsule None iuc parents: diff changeset	251 help="Allowed values: 3-15 (--wordlength)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	252 <param name="output_no_hits" type="boolean" truevalue="--output_no_hits" falsevalue="" checked="False"
fae6527990af Imported from capsule None iuc parents: diff changeset	253 label="Write non-matching queries to the output file" help="(--output_no_hits)"/>
fae6527990af Imported from capsule None iuc parents: diff changeset	254
fae6527990af Imported from capsule None iuc parents: diff changeset	255 <expand macro="userfields" />
fae6527990af Imported from capsule None iuc parents: diff changeset	256 </when>
fae6527990af Imported from capsule None iuc parents: diff changeset	257 </conditional>
fae6527990af Imported from capsule None iuc parents: diff changeset	258
fae6527990af Imported from capsule None iuc parents: diff changeset	259
fae6527990af Imported from capsule None iuc parents: diff changeset	260 </inputs>
fae6527990af Imported from capsule None iuc parents: diff changeset	261 <outputs>
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	262 <data name="uc" format="tabular" label="${tool.name} on ${on_string}: UCLUST like output">
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	263 <filter>adv_opts['adv_opts_selector'] == "advanced" and adv_opts['uclust_output']['uclust_output_select'] == 'yes'</filter>
0 fae6527990af Imported from capsule None iuc parents: diff changeset	264 </data>
fae6527990af Imported from capsule None iuc parents: diff changeset	265 <data name="dbnotmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched database sequences">
fae6527990af Imported from capsule None iuc parents: diff changeset	266 <filter>'--dbnotmatchedt' in outputs</filter>
fae6527990af Imported from capsule None iuc parents: diff changeset	267 </data>
fae6527990af Imported from capsule None iuc parents: diff changeset	268 <data name="dbmatched" format="fasta" label="${tool.name} on ${on_string}: Matched database sequences">
fae6527990af Imported from capsule None iuc parents: diff changeset	269 <filter>'--dbmatched' in outputs</filter>
fae6527990af Imported from capsule None iuc parents: diff changeset	270 </data>
fae6527990af Imported from capsule None iuc parents: diff changeset	271 <data name="alnout" format="fasta" label="${tool.name} on ${on_string}: Alignment">
fae6527990af Imported from capsule None iuc parents: diff changeset	272 <filter>'--alnout' in outputs</filter>
fae6527990af Imported from capsule None iuc parents: diff changeset	273 </data>
fae6527990af Imported from capsule None iuc parents: diff changeset	274 <data name="blast6out" format="tabular" label="${tool.name} on ${on_string}: BLAST like tabular">
fae6527990af Imported from capsule None iuc parents: diff changeset	275 <filter>'--blast6out' in outputs</filter>
fae6527990af Imported from capsule None iuc parents: diff changeset	276 </data>
fae6527990af Imported from capsule None iuc parents: diff changeset	277 <data name="notmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched queries">
fae6527990af Imported from capsule None iuc parents: diff changeset	278 <filter>'--notmatched' in outputs</filter>
fae6527990af Imported from capsule None iuc parents: diff changeset	279 </data>
fae6527990af Imported from capsule None iuc parents: diff changeset	280 <data name="matched" format="fasta" label="${tool.name} on ${on_string}: Matching query sequences">
fae6527990af Imported from capsule None iuc parents: diff changeset	281 <filter>'--matched' in outputs</filter>
fae6527990af Imported from capsule None iuc parents: diff changeset	282 </data>
fae6527990af Imported from capsule None iuc parents: diff changeset	283 <data name="fastapairs" format="fasta" label="${tool.name} on ${on_string}: Query/Target sequences">
fae6527990af Imported from capsule None iuc parents: diff changeset	284 <filter>'--fastapairs' in outputs</filter>
fae6527990af Imported from capsule None iuc parents: diff changeset	285 </data>
fae6527990af Imported from capsule None iuc parents: diff changeset	286 <data name="userout" format="tabular" label="${tool.name} on ${on_string}: tabular output">
2 f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2 iuc parents: 0 diff changeset	287 <filter>adv_opts['adv_opts_selector'] == "advanced" and adv_opts['userfields_output']['userfields_output_select'] == 'yes'</filter>
0 fae6527990af Imported from capsule None iuc parents: diff changeset	288 </data>
fae6527990af Imported from capsule None iuc parents: diff changeset	289 </outputs>
fae6527990af Imported from capsule None iuc parents: diff changeset	290 <tests>
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	291 <test expect_num_outputs="2">
0 fae6527990af Imported from capsule None iuc parents: diff changeset	292 <param name="dbfile" value="three_human_mRNA.fasta" ftype="fasta" />
fae6527990af Imported from capsule None iuc parents: diff changeset	293 <param name="queryfile" value="query.fasta" ftype="fasta" />
fae6527990af Imported from capsule None iuc parents: diff changeset	294 <param name="outputs" value="--blast6out,--dbmatched" />
fae6527990af Imported from capsule None iuc parents: diff changeset	295 <param name="dbmask" value="none" />
fae6527990af Imported from capsule None iuc parents: diff changeset	296 <param name="adv_opts_selector" value="advanced" />
fae6527990af Imported from capsule None iuc parents: diff changeset	297 <param name="top_hits_only" value="True" />
fae6527990af Imported from capsule None iuc parents: diff changeset	298 <output name="dbmatched" file="search_dbmatched_result1.fasta" ftype="fasta" />
fae6527990af Imported from capsule None iuc parents: diff changeset	299 <output name="blast6out" file="search_blast6out_result1.tabular" ftype="tabular" />
fae6527990af Imported from capsule None iuc parents: diff changeset	300 </test>
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	301 <test expect_num_outputs="4">
0 fae6527990af Imported from capsule None iuc parents: diff changeset	302 <param name="dbfile" value="three_human_mRNA.fasta" ftype="fasta" />
fae6527990af Imported from capsule None iuc parents: diff changeset	303 <param name="queryfile" value="query.fasta" ftype="fasta" />
fae6527990af Imported from capsule None iuc parents: diff changeset	304 <param name="outputs" value="--fastapairs,--matched" />
fae6527990af Imported from capsule None iuc parents: diff changeset	305 <param name="dbmask" value="none" />
fae6527990af Imported from capsule None iuc parents: diff changeset	306 <param name="adv_opts_selector" value="advanced" />
fae6527990af Imported from capsule None iuc parents: diff changeset	307 <param name="userfields_output_select" value="yes" />
fae6527990af Imported from capsule None iuc parents: diff changeset	308 <param name="userfields" value="query,target,evalue" />
fae6527990af Imported from capsule None iuc parents: diff changeset	309 <param name="top_hits_only" value="True" />
fae6527990af Imported from capsule None iuc parents: diff changeset	310 <param name="output_no_hits" value="True" />
6 9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	311 <param name="uclust_output_select" value="yes" />
9495df9dd6ef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb" iuc parents: 3 diff changeset	312 <output name="uc" file="search_dbmatched_uc.tsv" ftype="tabular" />
0 fae6527990af Imported from capsule None iuc parents: diff changeset	313 <output name="matched" file="search_matched_result2.fasta" ftype="fasta" />
fae6527990af Imported from capsule None iuc parents: diff changeset	314 <output name="fastapairs" file="search_fastapairs_result2.fasta" ftype="fasta" />
fae6527990af Imported from capsule None iuc parents: diff changeset	315 <output name="userout" file="search_userfields_result2.tabular" ftype="tabular" />
fae6527990af Imported from capsule None iuc parents: diff changeset	316 </test>
fae6527990af Imported from capsule None iuc parents: diff changeset	317 </tests>
fae6527990af Imported from capsule None iuc parents: diff changeset	318 <help>
fae6527990af Imported from capsule None iuc parents: diff changeset	319 <![CDATA[
fae6527990af Imported from capsule None iuc parents: diff changeset	320 What it does
fae6527990af Imported from capsule None iuc parents: diff changeset	321
fae6527990af Imported from capsule None iuc parents: diff changeset	322 Sequence search based on vsearch.
fae6527990af Imported from capsule None iuc parents: diff changeset	323
fae6527990af Imported from capsule None iuc parents: diff changeset	324 @USERFIELDS_HELP@
fae6527990af Imported from capsule None iuc parents: diff changeset	325
fae6527990af Imported from capsule None iuc parents: diff changeset	326 Searching options
fae6527990af Imported from capsule None iuc parents: diff changeset	327 --alnout FILENAME filename for human-readable alignment output
fae6527990af Imported from capsule None iuc parents: diff changeset	328 --blast6out FILENAME filename for blast-like tab-separated output
fae6527990af Imported from capsule None iuc parents: diff changeset	329 --db FILENAME filename for FASTA formatted database for search
fae6527990af Imported from capsule None iuc parents: diff changeset	330 --dbmask mask db with "dust", "soft" or "none" method (dust)
fae6527990af Imported from capsule None iuc parents: diff changeset	331 --dbmatched FILENAME FASTA file for matching database sequences
fae6527990af Imported from capsule None iuc parents: diff changeset	332 --dbnotmatched FILENAME FASTA file for non-matching database sequences
fae6527990af Imported from capsule None iuc parents: diff changeset	333 --fastapairs FILENAME FASTA file with pairs of query and target
fae6527990af Imported from capsule None iuc parents: diff changeset	334 --fulldp full dynamic programming alignment (always on)
fae6527990af Imported from capsule None iuc parents: diff changeset	335 --gapext STRING penalties for gap extension (2I/1E)
fae6527990af Imported from capsule None iuc parents: diff changeset	336 --gapopen STRING penalties for gap opening (20I/2E)
fae6527990af Imported from capsule None iuc parents: diff changeset	337 --hardmask mask by replacing with N instead of lower case
fae6527990af Imported from capsule None iuc parents: diff changeset	338 --id REAL reject if identity lower
fae6527990af Imported from capsule None iuc parents: diff changeset	339 --iddef INT id definition, 0-4=CD-HIT,all,int,MBL,BLAST (2)
fae6527990af Imported from capsule None iuc parents: diff changeset	340 --idprefix INT reject if first n nucleotides do not match
fae6527990af Imported from capsule None iuc parents: diff changeset	341 --idsuffix INT reject if last n nucleotides do not match
fae6527990af Imported from capsule None iuc parents: diff changeset	342 --leftjust reject if terminal gaps at alignment left end
fae6527990af Imported from capsule None iuc parents: diff changeset	343 --match INT score for match (2)
fae6527990af Imported from capsule None iuc parents: diff changeset	344 --matched FILENAME FASTA file for matching query sequences
fae6527990af Imported from capsule None iuc parents: diff changeset	345 --maxaccepts INT number of hits to accept and show per strand (1)
fae6527990af Imported from capsule None iuc parents: diff changeset	346 --maxdiffs INT reject if more substitutions or indels
fae6527990af Imported from capsule None iuc parents: diff changeset	347 --maxgaps INT reject if more indels
fae6527990af Imported from capsule None iuc parents: diff changeset	348 --maxhits INT maximum number of hits to show (unlimited)
fae6527990af Imported from capsule None iuc parents: diff changeset	349 --maxid REAL reject if identity higher
fae6527990af Imported from capsule None iuc parents: diff changeset	350 --maxqsize INT reject if query abundance larger
fae6527990af Imported from capsule None iuc parents: diff changeset	351 --maxqt REAL reject if query/target length ratio higher
fae6527990af Imported from capsule None iuc parents: diff changeset	352 --maxrejects INT number of non-matching hits to consider (32)
fae6527990af Imported from capsule None iuc parents: diff changeset	353 --maxsizeratio REAL reject if query/target abundance ratio higher
fae6527990af Imported from capsule None iuc parents: diff changeset	354 --maxsl REAL reject if shorter/longer length ratio higher
fae6527990af Imported from capsule None iuc parents: diff changeset	355 --maxsubs INT reject if more substitutions
fae6527990af Imported from capsule None iuc parents: diff changeset	356 --mid REAL reject if percent identity lower, ignoring gaps
fae6527990af Imported from capsule None iuc parents: diff changeset	357 --mincols INT reject if alignment length shorter
fae6527990af Imported from capsule None iuc parents: diff changeset	358 --minqt REAL reject if query/target length ratio lower
fae6527990af Imported from capsule None iuc parents: diff changeset	359 --minsizeratio REAL reject if query/target abundance ratio lower
fae6527990af Imported from capsule None iuc parents: diff changeset	360 --minsl REAL reject if shorter/longer length ratio lower
fae6527990af Imported from capsule None iuc parents: diff changeset	361 --mintsize INT reject if target abundance lower
fae6527990af Imported from capsule None iuc parents: diff changeset	362 --mismatch INT score for mismatch (-4)
fae6527990af Imported from capsule None iuc parents: diff changeset	363 --notmatched FILENAME FASTA file for non-matching query sequences
fae6527990af Imported from capsule None iuc parents: diff changeset	364 --output_no_hits output non-matching queries to output files
fae6527990af Imported from capsule None iuc parents: diff changeset	365 --qmask mask query with "dust", "soft" or "none" method (dust)
fae6527990af Imported from capsule None iuc parents: diff changeset	366 --query_cov REAL reject if fraction of query seq. aligned lower
fae6527990af Imported from capsule None iuc parents: diff changeset	367 --rightjust reject if terminal gaps at alignment right end
fae6527990af Imported from capsule None iuc parents: diff changeset	368 --rowlen INT width of alignment lines in alnout output (64)
fae6527990af Imported from capsule None iuc parents: diff changeset	369 --self reject if labels identical
fae6527990af Imported from capsule None iuc parents: diff changeset	370 --selfid reject if sequences identical
fae6527990af Imported from capsule None iuc parents: diff changeset	371 --sizeout write abundance annotation to output
fae6527990af Imported from capsule None iuc parents: diff changeset	372 --strand search "plus" or "both" strands (plus)
fae6527990af Imported from capsule None iuc parents: diff changeset	373 --target_cov REAL reject if fraction of target seq. aligned lower
fae6527990af Imported from capsule None iuc parents: diff changeset	374 --top_hits_only output only hits with identity equal to the best
fae6527990af Imported from capsule None iuc parents: diff changeset	375 --uc FILENAME filename for UCLUST-like output
fae6527990af Imported from capsule None iuc parents: diff changeset	376 --uc_allhits show all, not just top hit with uc output
fae6527990af Imported from capsule None iuc parents: diff changeset	377 --usearch_global FILENAME filename of queries for global alignment search
fae6527990af Imported from capsule None iuc parents: diff changeset	378 --userfields STRING fields to output in userout file
fae6527990af Imported from capsule None iuc parents: diff changeset	379 --userout FILENAME filename for user-defined tab-separated output
fae6527990af Imported from capsule None iuc parents: diff changeset	380 --weak_id REAL include aligned hits with >= id; continue search
fae6527990af Imported from capsule None iuc parents: diff changeset	381 --wordlength INT length of words for database index 3-15 (8)
fae6527990af Imported from capsule None iuc parents: diff changeset	382
fae6527990af Imported from capsule None iuc parents: diff changeset	383 @EXTERNAL_DOCUMENTATION@
fae6527990af Imported from capsule None iuc parents: diff changeset	384
fae6527990af Imported from capsule None iuc parents: diff changeset	385
fae6527990af Imported from capsule None iuc parents: diff changeset	386 ]]>
fae6527990af Imported from capsule None iuc parents: diff changeset	387 </help>
fae6527990af Imported from capsule None iuc parents: diff changeset	388 <expand macro="citations" />
fae6527990af Imported from capsule None iuc parents: diff changeset	389 </tool>

Mercurial > repos > iuc > vsearch

annotate search.xml @ 6:9495df9dd6ef draft default tip