hmmer3: macros.xml annotate

annotate macros.xml @ 2:54b6b4d0613a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b

author	iuc
date	Thu, 01 Oct 2015 11:13:19 -0400
parents	b5066aa77fea
children

rev	line source
0 62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1 <?xml version="1.0"?>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	2 <macros>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	3 <xml name="requirements">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	4 <requirements>
2 54b6b4d0613a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b iuc parents: 1 diff changeset	5 <requirement type="package" version="3.1b1">hmmer</requirement>
0 62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	6 <yield/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	7 </requirements>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	8 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	9 <token name="@WRAPPER_VERSION@">0.1</token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	10 <xml name="stdio">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	11 <stdio>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	12 <!-- Anything other than zero is an error -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	13 <exit_code range="1:"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	14 <exit_code range=":-1"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	15 <!-- In case the return code has not been set propery check stderr too -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	16 <regex match="Error:"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	17 <regex match="Exception:"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	18 </stdio>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	19 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	20 <token name="@THRESHOLDS@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	21 -E $E
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	22 --domE $domE
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	23
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	24 #if $T:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	25 -T $T
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	26 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	27
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	28 #if $domT:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	29 --domT $domT
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	30 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	31
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	32 #if $incE:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	33 --incE $incE
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	34 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	35
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	36 #if $incT:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	37 --incT $incT
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	38 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	39
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	40 #if $incdomE:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	41 --incdomE $incdomE
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	42 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	43
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	44 #if $incdomT:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	45 --incdomT $incdomT
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	46 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	47 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	48 <xml name="thresholds_xml">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	49 <!-- Options controlling reporting thresholds -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	50 <param name="E" label="report sequences <= this E-Value threshold in output" help="(-E)" value="10.0" type="float" min="0"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	51 <param name="domE" label="report domains <= this E-Value threshold in output" help="(--domE)" value="10.0" type="float" min="0"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	52 <param name="T" label="report sequences >= this score threshold in output" help="(-T)" type="float" optional="True"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	53 <param name="domT" label="report domains >= this score threshold in output" help="(--domT)" type="float" optional="True"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	54 <!-- Options controlling inclusion (significance) thresholds -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	55 <param name="incE" label="consider sequences <= this E-Value threshold as significant" help="(--incE)" type="float" optional="True"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	56 <param name="incdomE" label="consider domains <= this E-Value threshold as significant" help="(--incdomE)" type="float" optional="True"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	57 <param name="incT" label="consider sequences >= this score threshold as significant" help="(--incT)" type="float" optional="True"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	58 <param name="incdomT" label="consider domains >= this score threshold as significant" help="(--incdomT)" type="float" optional="True"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	59 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	60 <token name="@THRESHOLDS_NODOM@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	61 -E $E
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	62
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	63 #if $T:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	64 -T $T
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	65 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	66
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	67 #if $incE:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	68 --incE $incE
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	69 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	70
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	71 #if $incT:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	72 --incT $incT
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	73 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	74 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	75 <xml name="thresholds_nodom">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	76 <!-- Options controlling reporting thresholds -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	77 <param name="E" label="report sequences <= this E-Value threshold in output" help="(-E)" value="10.0" type="float" min="0"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	78 <param name="T" label="report sequences >= this score threshold in output" help="(-T)" type="float" optional="True"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	79 <!-- Options controlling inclusion (significance) thresholds -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	80 <param name="incE" label="consider sequences <= this E-Value threshold as significant" help="(--incE)" type="float" optional="True"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	81 <param name="incT" label="consider sequences >= this score threshold as significant" help="(--incT)" type="float" optional="True"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	82 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	83 <token name="@ACCEL_HEUR@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	84 $max
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	85 --F1 $F1
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	86 --F2 $F2
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	87 --F3 $F3
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	88 $nobias
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	89
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	90 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	91 <xml name="accel_heur_xml">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	92 <!-- Options controlling acceleration heuristics -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	93 <param name="max" type="boolean" truevalue="--max" label="Turn all heuristic filters off (less speed, more power)" help="(--max)" falsevalue=""/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	94 <param name="F1" type="float" label="Stage 1 (MSV) threshold: promote hits w/ P <= F1" help="(--F1)" value="0.02"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	95 <param name="F2" type="float" label="Stage 2 (Vit) threshold: promote hits w/ P <= F2" help="(--F2)" value="1e-3"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	96 <param name="F3" type="float" label="Stage 3 (Fwd) threshold: promote hits w/ P <= F3" help="(--F3)" value="1e-5"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	97 <param name="nobias" type="boolean" truevalue="--nobias" label="Turn off composition bias filter" help="(--nobias)" falsevalue=""/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	98 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	99 <token name="@EVAL_CALIB@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	100 --EmL $EmL
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	101 --EmN $EmN
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	102 --EvL $EvL
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	103 --EvN $EvN
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	104 --EfL $EfL
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	105 --EfN $EfN
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	106 --Eft $Eft
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	107 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	108 <xml name="eval_calib_xml">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	109 <!-- Control of E-value calibration -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	110 <param name="EmL" type="integer" value="200" min="1" help="(--EmL)" label="Length of sequences for MSV Gumbel mu fit"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	111 <param name="EmN" type="integer" value="200" min="1" help="(--EmN)" label="Number of sequences for MSV Gumbel mu fit"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	112 <param name="EvL" type="integer" value="200" min="1" help="(--EvL)" label="Length of sequences for Viterbi Gumbel mu fit"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	113 <param name="EvN" type="integer" value="200" min="1" help="(--EvN)" label="Number of sequences for Viterbi Gumbel mu fit"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	114 <param name="EfL" type="integer" value="100" min="1" help="(--EfL)" label="Length of sequences for Forward exp tail tau fit"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	115 <param name="EfN" type="integer" value="200" min="1" help="(--EfN)" label="Number of sequences for Forward exp tail tau fit"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	116 <param name="Eft" type="float" value="0.04" min="0" max="1" help="(--Eft)" label="tail mass for Forward exponential tail tau fit"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	117 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	118 <token name="@OFORMAT_WITH_OPTS_NOPFAM@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	119 #if 'tblout' in str($oformat):
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	120 --tblout $tblout
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	121 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	122
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	123 #if 'domtblout' in str($oformat):
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	124 --domtblout $domtblout
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	125 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	126
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	127 $acc $noali $notextw
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	128 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	129 <xml name="oformat_with_opts_nopfam">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	130 <!-- Options directing output -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	131 <param name="oformat" multiple="True" display="checkboxes" label="Output Formats" type="select">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	132 <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	133 <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	134 </param>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	135 <param name="acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" help="(--acc)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	136 <param name="noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" help="(--noali)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	137 <param name="notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" help="(--notextw)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	138 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	139 <token name="@OFORMAT_WITH_OPTS@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	140 #if 'tblout' in str($oformat):
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	141 --tblout $tblout
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	142 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	143
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	144 #if 'domtblout' in str($oformat):
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	145 --domtblout $domtblout
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	146 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	147
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	148 #if 'pfamtblout' in str($oformat):
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	149 --pfamtblout $pfamtblout
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	150 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	151
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	152 $acc $noali $notextw
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	153 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	154 <xml name="oformat_with_opts">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	155 <!-- Options directing output -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	156 <param name="oformat" multiple="True" display="checkboxes" label="Output Formats" type="select">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	157 <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	158 <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	159 <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	160 </param>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	161 <param name="acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" help="(--acc)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	162 <param name="noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" help="(--noali)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	163 <param name="notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" help="(--notextw)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	164 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	165 <xml name="oformat_test">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	166 <param name="notextw" value="True" />
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	167 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	168 <!-- TODO: tblout will match 'pfamtblout,dfamtblout' -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	169 <token name="@OFORMAT_WITH_OPTS_N@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	170 #if 'tblout' in str($oformat):
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	171 --tblout $tblout
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	172 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	173
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	174 #if 'dfamtblout' in str($oformat):
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	175 --dfamtblout $dfamtblout
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	176 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	177
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	178 #if 'aliscoresout' in str($oformat):
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	179 --aliscoresout $aliscoresout
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	180 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	181
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	182 $acc $noali $notextw
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	183 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	184 <xml name="oformat_with_opts_n">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	185 <!-- Options directing output -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	186 <param name="oformat" multiple="True" display="checkboxes" label="Output Formats" type="select">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	187 <option value="tblout" selected="true">Table of hits (--tblout)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	188 <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	189 <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	190 </param>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	191 <param name="acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" help="(--acc)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	192 <param name="noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" help="(--noali)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	193 <param name="notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" help="(--notextw)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	194 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	195 <token name="@HSSI@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	196 #if $hssi.hssi_select == "singlemx":
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	197 --popen $hssi.popen
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	198 --pextend $hssi.pextend
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	199 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	200 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	201 <xml name="hssi">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	202 <!-- Handling single sequence inputs -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	203 <conditional name="hssi">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	204 <param name="hssi_select" type="select" label="Options for handling single sequence inputs">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	205 <option value="false" selected="true">Disable</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	206 <option value="singlemx">Use substitution score matrix for single-sequence inputs</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	207 </param>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	208 <when value="singlemx">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	209 <param name="popen" type="float" value="0.02" label="Gap open probability" help="(--popen)" min="0.0" max="0.5"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	210 <param name="pextend" type="float" value="0.4" label="Gap extend probability" help="(--pextend)" min="0.0" max="1.0"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	211 </when>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	212 <when value="false">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	213 </when>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	214 <!-- -mx <s> : substitution score matrix (built-in matrices, with -singlemx)-->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	215 <!-- -mxfile <f> : read substitution score matrix from file <f> (with -singlemx)-->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	216 </conditional>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	217 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	218 <token name="@CPU@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	219 --cpu \${GALAXY_SLOTS:-2}
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	220 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	221 <token name="@SEED@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	222 --seed $seed
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	223 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	224 <xml name="seed">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	225 <param name="seed" label="RNG seed, 0 generates a random seed" value="42" type="integer" help="(--seed)" min="0"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	226 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	227 <xml name="seed_test">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	228 <param name="seed" value="4" />
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	229 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	230 <token name="@ADV_OPTS@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	231 $nonull2
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	232
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	233 #if $Z:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	234 -Z $Z
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	235 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	236
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	237 #if $domZ:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	238 --domZ $domZ
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	239 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	240 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	241 <xml name="adv_opts">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	242 <!-- Other options -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	243 <param name="nonull2" type="boolean" truevalue="--nonull2" label="Turn off biased composition score corrections" help="(--nonull2)" falsevalue=""/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	244 <param name="Z" type="integer" label="# of comparisons done for E-value calculation" help="(-Z)" optional="True"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	245 <param name="domZ" type="integer" label="# of significant sequences, for domain E-value calculation" help="(--domZ)" optional="True"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	246 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	247 <token name="@FORMAT_SELECTOR@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	248 $input_format_select
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	249 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	250 <xml name="format_selector">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	251 <param name="input_format_select" type="select" label="Format of sequence and model">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	252 <option value="--amino">Protein</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	253 <option value="--dna">DNA</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	254 <option value="--rna">RNA</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	255 </param>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	256 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	257 <xml name="format_selector_noprot">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	258 <param name="input_format_select" type="select" label="Format of sequence and model">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	259 <option value="--dna">DNA</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	260 <option value="--rna">RNA</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	261 </param>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	262 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	263 <token name="@ARSWS@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	264 $arsws.arsws_select
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	265
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	266 #if $arsws.arsws_select == "--wblosum":
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	267 --wid $arsws.wid
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	268 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	269 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	270 <xml name="arsws">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	271 <!-- Alternative relative sequence weighting strategies -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	272 <conditional name="arsws">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	273 <param name="arsws_select" type="select" label="Alternative relative sequence weighting strategies">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	274 <option value="--wpb" selected="true">Henikoff position-based weights (--wpb)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	275 <option value="--wgsc">Gerstein/Sonnhammer/Chothia tree weights (--wgsc)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	276 <option value="--wblosum">Henikoff simple filter weights (--wblosum)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	277 <option value="--wnone">don't do any relative weighting; set all to 1 (--wnnoe)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	278 <option value="--wgiven">use weights as given in MSA file (--wgiven)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	279 </param>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	280 <when value="--wpb">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	281 </when>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	282 <when value="--wgsc">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	283 </when>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	284 <when value="--wblosum">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	285 <param name="wid" label="Set identity cutoff" value="0.62" type="float" help="(--wid)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	286 </when>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	287 <when value="--wnone">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	288 </when>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	289 <when value="--wgiven">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	290 </when>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	291 </conditional>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	292 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	293 <token name="@AEEWS@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	294 #if $aeews.aeews_select != "":
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	295 --$aeews.aeews_select
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	296 #if $aeews.aeews_select == "eent":
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	297 --eset $aeews.eset
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	298 --ere $aeews.ere
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	299 --esigma $aeews.esigma
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	300 #elif $aeews.aeews_select == "eclust":
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	301 --eset $aeews.eset
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	302 --eid $aeews.eid
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	303 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	304 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	305 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	306 <xml name="aeews">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	307 <!-- Alternative effective sequence weighting strategies -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	308 <conditional name="aeews">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	309 <param name="aeews_select" type="select" label="Alternative effective sequence weighting strategies">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	310 <option value="">Disabled</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	311 <option value="eent">Adjust eff seq # to achieve relative entropy target (--eent)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	312 <option value="eclust">Eff seq # is the # of single linkage clusters (--eclust)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	313 <option value="enone">No effective seq # weighting: just use nseq (--enone)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	314 </param>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	315 <when value="">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	316 </when>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	317 <when value="eent">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	318 <param name="eset" type="float" value="0" label="set eff seq # for all models" help="(--eset)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	319 <param name="ere" type="float" value="0" label="set minimum rel entropy/position" help="(--ere)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	320 <param name="esigma" type="float" value="45" label="set sigma param" help="(--esigma)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	321 </when>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	322 <when value="eclust">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	323 <param name="eset" type="float" value="0" label="set eff seq # for all models" help="(--eset)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	324 <param name="eid" type="float" value="0.62" label="set fractional identity cutoff" min="0" max="1" help="(--eid)"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	325 </when>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	326 <when value="enone">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	327 </when>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	328 </conditional>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	329 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	330 <token name="@CUT@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	331 $cut_ga
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	332 $cut_nc
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	333 $cut_tc
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	334 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	335 <xml name="cut">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	336 <param name="cut_ga" type="boolean" truevalue="--cut_ga" label="use profile's GA gathering cutoffs to set all thresholding" help="(--cut_ga)" falsevalue=""/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	337 <param name="cut_nc" type="boolean" truevalue="--cut_nc" label="use profile's NC gathering cutoffs to set all thresholding" help="(--cut_nc)" falsevalue=""/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	338 <param name="cut_tc" type="boolean" truevalue="--cut_tc" label="use profile's TC gathering cutoffs to set all thresholding" help="(--cut_tc)" falsevalue=""/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	339 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	340 <token name="@MCSS@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	341 --$mcs.model_construction_strategy_select
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	342
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	343 #if $mcs.model_construction_strategy_select == "fast":
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	344 --symfrac $mcs.symfrac
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	345 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	346
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	347 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	348 <xml name="mcss">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	349 <!-- Alternative model construction strategies -->
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	350 <conditional name="mcs">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	351 <param name="model_construction_strategy_select" type="select" label="Model Construction Strategy">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	352 <option value="fast" selected="true">Assign columns with >= symfrac residues as consensus (--fast)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	353 <option value="hand">Manual construction (requires reference annotation) (--hand)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	354 </param>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	355 <when value="fast">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	356 <param name="symfrac" value="0.5" type="float" label="Sets sym fraction controlling --fast construction"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	357 </when>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	358 <when value="hand"></when>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	359 </conditional>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	360 <param name="fragthresh" label="Fraction of alignment length, under which sequences are excluded" help="HMMER infers fragments if the sequence length L is less than or equal to a fraction x times the alignment length in columns (--fragthresh)" value="0.5" optional="True" type="float" />
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	361
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	362 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	363 <token name="@PRIOR@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	364 $aps_select
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	365 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	366 <xml name="prior">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	367 <param name="aps_select" type="select" label="Alternative Prior Strategies">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	368 <option value="" selected="true">Unspecified</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	369 <option value="--pnone">Don't use any prior; parameters are frequencies (--pnone)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	370 <option value="--plaplace">Use a Laplace +1 prior (--plaplace)</option>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	371 </param>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	372 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	373 <xml name="citation">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	374 <citations>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	375 <citation type="doi">10.1093/nar/gkr367</citation>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	376 </citations>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	377 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	378 <token name="@LENGTHS@">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	379 #if $w_beta:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	380 --w_beta $w_beta
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	381 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	382
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	383 #if $w_length:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	384 --w_length $w_length
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	385 #end if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	386
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	387 </token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	388 <xml name="lengths">
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	389 <param name="w_beta" label="Tail mass at which window length is determined"
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	390 help="(--w_beta)" optional="True" type="float"/>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	391 <param name="w_length" label="Window Length"
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	392 help="(--w_length)" optional="True" type="integer" />
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	393 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	394 <xml name="input_hmm">
1 b5066aa77fea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit f7d83adb11624763b9b113f938a1d5f311c8f9fa-dirty iuc parents: 0 diff changeset	395 <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/>
0 62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	396 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	397 <xml name="input_msa">
1 b5066aa77fea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit f7d83adb11624763b9b113f938a1d5f311c8f9fa-dirty iuc parents: 0 diff changeset	398 <param name="msafile" type="data" label="Multiple Sequence Alignment" format="stockholm,clustal,fasta"
b5066aa77fea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit f7d83adb11624763b9b113f938a1d5f311c8f9fa-dirty iuc parents: 0 diff changeset	399 help="in Stockholm, Clustal, or Fasta format. While this tool accepts fasta, please ensure that the sequences are not unaligned"/>
0 62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	400 </xml>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	401
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	402
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	403 <token name="@ACCEL_HEUR_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	404 Acceleration Heuristicts (--F1, --F2, --F3)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	405 -------------------------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	406
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	407 MSV filter
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	408
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	409 The sequence is aligned to the profile using a specialized model that
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	410 allows multiple high-scoring local ungapped segments to match. The
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	411 optimal alignment score (Viterbi score) is calculated under this multi-
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	412 segment model, hence the term MSV, for “multi-segment Viterbi”. This is
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	413 HMMER’s main speed heuristic. The MSV score is comparable to BLAST’s sum
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	414 score (optimal sum of ungapped alignment segments). Roughly speaking,
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	415 MSV is comparable to skipping the heuristic word hit and hit extension
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	416 steps of the BLAST acceleration algorithm.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	417
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	418 The MSV filter is very, very fast. In addition to avoiding indel
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	419 calculations in the dynamic programming table, it uses reduced precision
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	420 scores scaled to 8-bit integers, enabling acceleration via 16-way
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	421 parallel SIMD vector instructions.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	422
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	423 The MSV score is a true log-odds likelihood ratio, so it obeys
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	424 conjectures about the expected score distribution (Eddy, 2008) that
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	425 allow immediate and accurate calculation of the statistical significance
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	426 (P- value) of the MSV bit score.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	427
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	428 By default, comparisons with a P-value of ≤ 0.02 pass this filter,
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	429 meaning that about 2% of nonhomol- ogous sequences are expected to pass.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	430 You can use the --F1 option to change this threshold. For example, --F1
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	431 <0.05> would pass 5% of the comparisons, making a search more sensitive
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	432 but slower. Setting the threshold to ≥ 1.0 (--F1 99 for example) assures
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	433 that all comparisons will pass. Shutting off the MSV filter may be
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	434 worthwhile if you want to make sure you don’t miss comparisons that have
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	435 a lot of scattered insertions and deletions. Alternatively, the --max
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	436 option causes the MSV filter step (and all other filter steps) to be
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	437 bypassed.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	438
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	439 The MSV bit score is calculated as a log-odds score using the null model
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	440 for comparison. No correction for a biased composition or repetitive
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	441 sequence is done at this stage. For comparisons involving biased
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	442 sequences and/or profiles, more than 2% of comparisons will pass the MSV
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	443 filter. At the end of search output, there is a line like:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	444
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	445 Passed MSV filter: 107917 (0.020272); expected 106468.8 (0.02)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	446
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	447 which tells you how many and what fraction of comparisons passed the MSV
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	448 filter, versus how many (and what fraction) were expected.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	449
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	450 Viterbi filter
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	451
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	452 The sequence is now aligned to the profile using a fast Viterbi algorithm for
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	453 optimal gapped alignment.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	454
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	455 This Viterbi implementation is specialized for speed. It is implemented in
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	456 8-way parallel SIMD vector instructions, using reduced precision scores that
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	457 have been scaled to 16-bit integers. Only one row of the dynamic programming
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	458 matrix is stored, so the routine only recovers the score, not the optimal
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	459 alignment itself. The reduced representation has limited range; local alignment
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	460 scores will not underflow, but high scoring comparisons can overflow and return
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	461 infinity, in which case they automatically pass the filter.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	462
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	463 The final Viterbi filter bit score is then computed using the appropriate null
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	464 model log likelihood (by default the biased composition filter model score, or
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	465 if the biased filter is off, just the null model score). If the P-value of this
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	466 score passes the Viterbi filter threshold, the sequence passes on to the next
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	467 step of the pipeline.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	468
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	469 The --F2 <x> option controls the P-value threshold for passing the Viterbi
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	470 filter score. The default is 0.001. The --max option bypasses all filters in
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	471 the pipeline. At the end of a search output, you will see a line like:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	472
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	473 Passed Vit filter: 2207 (0.00443803); expected 497.3 (0.001)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	474
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	475 which tells you how many and what fraction of comparisons passed the Viterbi
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	476 filter, versus how many were expected.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	477
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	478 Forward filter/parser
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	479
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	480 The sequence is now aligned to the profile using the full Forward algorithm,
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	481 which calculates the likelihood of the target sequence given the profile,
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	482 summed over the ensemble of all possible alignments.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	483
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	484 This is a specialized time- and memory-efficient Forward implementation called
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	485 the “Forward parser”. It is implemented in 4-way parallel SIMD vector
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	486 instructions, in full precision (32-bit floating point). It stores just enough
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	487 information that, in combination with the results of the Backward parser
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	488 (below), posterior probabilities of start and stop points of alignments
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	489 (domains) can be calculated in the domain definition step (below), although the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	490 detailed alignments themselves cannot be.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	491
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	492 The Forward filter bit score is calculated by correcting this score using the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	493 appropriate null model log likelihood (by default the biased composition filter
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	494 model score, or if the biased filter is off, just the null model score). If the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	495 P-value of this bit score passes the Forward filter threshold, the sequence
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	496 passes on to the next step of the pipeline.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	497
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	498 The bias filter score has no further effect in the pipeline. It is only used in
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	499 filter stages. It has no effect on final reported bit scores or P-values.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	500 Biased composition compensation for final bit scores is done by a more complex
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	501 domain-specific algorithm, described below.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	502
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	503 The --F3 <x> option controls the P-value threshold for passing the Forward
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	504 filter score. The default is 1e-5. The --max option bypasses all filters in the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	505 pipeline. At the end of a search output, you will see a line like:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	506
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	507 Passed Fwd filter: 1076 (0.00216371); expected 5.0 (1e-05)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	508
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	509 which tells you how many and what fraction of comparisons passed the Forward
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	510 filter, versus how many were expected.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	511
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	512 Bias Filter Options
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	513
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	514 The --max option bypasses all filters in the pipeline, including the bias
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	515 filter.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	516
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	517 The --nobias option turns off (bypasses) the biased composition filter. The
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	518 simple null model is used as a null hypothesis for MSV and in subsequent filter
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	519 steps. The biased composition filter step compromises a small amount of
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	520 sensitivity. Though it is good to have it on by default, you may want to shut
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	521 it off if you know you will have no problem with biased composition hits.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	522
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	523
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	524 Advanced Documentation
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	525
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	526 A more detailed look at the internals of the various filter pipelines was
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	527 posted on the `developer's blog <http://selab.janelia.org/people/eddys/blog/?p=508>`__.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	528 The information posted there may be useful to those who are struggling with
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	529 poor-scoring sequences.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	530
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	531 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	532 <token name="@ADV_OPTS_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	533 Advanced Options
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	534 ----------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	535
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	536 nonull2
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	537
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	538 can be too aggressive sometimes, causing you to miss homologs. You can turn the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	539 biased-composition score correction off with the --nonull2 option (and if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	540 you’re doing that, you may also want to set --nobias, to turn off another
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	541 biased composition step called the bias filter, which affects which sequences
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	542 get scored at all).
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	543
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	544 domZ
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	545
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	546 Assert that the total number of targets in your searches is <x>, for the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	547 purposes of per-domain conditional E-value calculations, rather than the number
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	548 of targets that passed the reporting thresholds.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	549
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	550 Z
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	551
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	552 Assert that the total number of targets in your searches is <x>, for the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	553 purposes of per-sequence E-value calculations, rather than the actual number of
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	554 targets seen.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	555 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	556 <token name="@AEEWS_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	557 Effective Sequence Number
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	558 -------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	559
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	560 After relative weights are determined, they are normalized to sum to a total
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	561 effective sequence number, eff nseq. This number may be the actual number of
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	562 sequences in the alignment, but it is almost always smaller than that. The
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	563 default entropy weighting method (--eent) reduces the effective sequence num-
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	564 ber to reduce the information content (relative entropy, or average expected
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	565 score on true homologs) per consensus position. The target relative entropy is
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	566 controlled by a two-parameter function, where the two parameters are settable
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	567 with --ere and --esigma.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	568
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	569 --eent
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	570
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	571 Adjust effective sequence number to achieve a specific relative entropy per
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	572 position (see --ere). This is the default.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	573
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	574 --eclust
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	575
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	576 Set effective sequence number to the number of single-linkage clusters at a
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	577 specific identity threshold (see --eid). This option is not recommended; it’s
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	578 for experiments evaluating how much better --eent is.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	579
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	580 --enone
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	581
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	582 Turn off effective sequence number determination and just use the actual number
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	583 of sequences. One reason you might want to do this is to try to maximize the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	584 relative entropy/position of your model, which may be useful for short models.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	585
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	586 --eset
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	587
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	588 Explicitly set the effective sequence number for all models to <x>.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	589
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	590 --ere
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	591
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	592 Set the minimum relative entropy/position target to <x>. Requires --eent. Default
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	593 depends on the sequence alphabet. For protein sequences, it is 0.59 bits/position;
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	594 for nucleotide sequences, it is 0.45 bits/position.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	595
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	596 --esigma
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	597
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	598 Sets the minimum relative entropy contributed by an entire model alignment, over
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	599 its whole length. This has the effect of making short models have higher relative
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	600 entropy per position than --ere alone would give. The default is 45.0 bits.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	601
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	602 --eid
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	603
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	604 Sets the fractional pairwise identity cutoff used by single linkage clustering
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	605 with the --eclust option. The default is 0.62.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	606 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	607 <token name="@ARSWS_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	608 Options Controlling Relative Weights
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	609 ------------------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	610
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	611 HMMER uses an ad hoc sequence weighting algorithm to downweight closely related
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	612 sequences and up-weight distantly related ones. This has the effect of making
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	613 models less biased by uneven phylogenetic representation. For example, two
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	614 identical sequences would typically each receive half the weight that one
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	615 sequence would. These options control which algorithm gets used.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	616
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	617
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	618 --wpb
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	619
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	620 Use the Henikoff position-based sequence weighting scheme [Henikoff and
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	621 Henikoff, J. Mol. Biol. 243:574, 1994]. This is the default.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	622
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	623 --wgsc
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	624
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	625 Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Gerstein et al, J.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	626 Mol. Biol. 235:1067, 1994].
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	627
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	628 --wblosum
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	629
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	630 Use the same clustering scheme that was used to weight data in calculating
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	631 BLOSUM subsitution matrices [Henikoff and Henikoff, Proc. Natl. Acad. Sci
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	632 89:10915, 1992]. Sequences are single-linkage clustered at an identity
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	633 threshold (default 0.62; see --wid) and within each cluster of c sequences,
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	634 each sequence gets rela- tive weight 1/c.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	635
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	636 --wnone
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	637
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	638 No relative weights. All sequences are assigned uniform weight.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	639
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	640 --wid
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	641
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	642 Sets the identity threshold used by single-linkage clustering when using
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	643 --wblosum. Invalid with any other weighting scheme. Default is 0.62.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	644 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	645 <token name="@BIAS_COMP_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	646 Bias Composition
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	647 ----------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	648
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	649 The next number, the bias, is a correction term for biased sequence composition
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	650 that has been applied to the sequence bit score.1 For instance, for the top hit
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	651 MYG PHYCA that scored 222.7 bits, the bias of 3.2 bits means that this sequence
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	652 originally scored 225.9 bits, which was adjusted by the slight 3.2 bit biased-
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	653 composition correction. The only time you really need to pay attention to the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	654 bias value is when it’s large, on the same order of magnitude as the sequence
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	655 bit score. Sometimes (rarely) the bias correction isn’t aggressive enough, and
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	656 allows a non-homolog to retain too much score. Conversely, the bias correction
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	657 can be too aggressive sometimes, causing you to miss homologs. You can turn the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	658 biased-composition score correction off with the --nonull2 option (and if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	659 you’re doing that, you may also want to set --nobias, to turn off another
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	660 biased composition step called the bias filter, which affects which sequences
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	661 get scored at all).
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	662
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	663 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	664 <token name="@CUT_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	665 Options for Model-specific Score Thresholding
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	666 ---------------------------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	667
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	668 Curated profile databases may define specific bit score thresholds for each
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	669 profile, superseding any thresholding based on statistical significance alone.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	670 To use these options, the profile must contain the appropriate (GA, TC, and/or
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	671 NC) optional score threshold annotation; this is picked up by hmmbuild from
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	672 Stockholm format alignment files. Each thresholding option has two scores: the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	673 per-sequence threshold <x1> and the per-domain threshold <x2> These act as if
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	674 -T<x1> --incT<x1> --domT<x2> --incdomT<x2> has been applied specifically using
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	675 each model’s curated thresholds.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	676
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	677 --cut_ga
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	678
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	679 Use the GA (gathering) bit scores in the model to set per-sequence (GA1) and
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	680 per-domain (GA2) reporting and inclusion thresholds. GA thresholds are
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	681 generally considered to be the reliable curated thresholds defining family
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	682 membership; for example, in Pfam, these thresholds define what gets included in
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	683 Pfam Full alignments based on searches with Pfam Seed models.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	684
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	685 --cut_nc
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	686
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	687 Use the NC (noise cutoff) bit score thresholds in the model to set
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	688 per-sequence (NC1) and per-domain (NC2) reporting and inclusion thresholds. NC
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	689 thresholds are generally considered to be the score of the highest-scoring
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	690 known false positive.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	691
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	692 --cut_tc
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	693
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	694 Use the NC (trusted cutoff) bit score thresholds in the model to set
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	695 per-sequence (TC1) and per-domain (TC2) reporting and inclusion thresholds. TC
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	696 thresholds are generally considered to be the score of the lowest-scoring known
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	697 true positive that is above all known false positives.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	698 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	699 <token name="@EVAL_CALIB_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	700 Options Controlling H3 Parameter Estimation Methods
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	701 ---------------------------------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	702
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	703 H3 uses three short random sequence simulations to estimating the location
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	704 parameters for the expected score distributions for MSV scores, Viterbi scores,
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	705 and Forward scores. These options allow these simulations to be modified.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	706
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	707 --EmL
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	708
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	709 Sets the sequence length in simulation that estimates the location parameter mu
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	710 for MSV E-values. Default is 200.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	711
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	712 --EmN
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	713
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	714 Sets the number of sequences in simulation that estimates the location parameter
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	715 mu for MSV E-values. Default is 200.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	716
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	717 --EvL
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	718
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	719 Sets the sequence length in simulation that estimates the location parameter mu
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	720 for Viterbi E-values. Default is 200.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	721
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	722 --EvN
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	723
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	724 Sets the number of sequences in simulation that estimates the location parameter
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	725 mu for Viterbi E-values. Default is 200.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	726
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	727
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	728 --EfL
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	729
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	730 Sets the sequence length in simulation that estimates the location parameter tau
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	731 for Forward E-values. Default is 100.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	732
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	733 --EfN
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	734
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	735 Sets the number of sequences in simulation that estimates the location parameter
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	736 tau for Forward E-values. Default is 200.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	737
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	738 --Eft
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	739
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	740 Sets the tail mass fraction to fit in the simulation that estimates the location param-
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	741 eter tau for Forward evalues. Default is 0.04.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	742 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	743 <token name="@FORMAT_SELECTOR_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	744 Options for Specifying the Alphabet
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	745 -----------------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	746
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	747 The alphabet type (amino, DNA, or RNA) is autodetected by default, by looking
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	748 at the composition of the msafile. Autodetection is normally quite reliable,
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	749 but occasionally alphabet type may be ambiguous and autodetection can fail (for
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	750 instance, on tiny toy alignments of just a few residues). To avoid this, or to
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	751 increase robustness in automated analysis pipelines, you may specify the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	752 alphabet type of msafile with these options.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	753 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	754 <token name="@HSSI_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	755 Options Controlling Single Sequence Scoring (first Iteration)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	756 -------------------------------------------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	757
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	758 By default, the first iteration uses a search model constructed from a single
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	759 query sequence. This model is constructed using a standard 20x20 substitution
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	760 matrix for residue probabilities, and two additional pa- rameters for
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	761 position-independent gap open and gap extend probabilities. These options allow
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	762 the default single-sequence scoring parameters to be changed.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	763
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	764 Gap Open (--popen)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	765
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	766 Set the gap open probability for a single sequence query model to <x>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	767
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	768 Gap Extend (--pextend)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	769
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	770 Set the gap extend probability for a single sequence query model to <x>.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	771
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	772
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	773 --mx/--mxfile
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	774
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	775 These options are not currently supported
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	776 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	777 <token name="@LENGTHS_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	778 Tail Mass Options
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	779 -----------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	780
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	781 Window length tail mass (--w_beta)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	782
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	783 The upper bound, W, on the length at which nhmmer expects to find an instance
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	784 of the model is set such that the fraction of all sequences generated by the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	785 model with length >= W is less than <x>. The default is 1e-7.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	786
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	787
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	788 Model instance length upper bound (--w length)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	789
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	790 Override the model instance length upper bound, W, which is otherwise
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	791 controlled by --w beta. It should be larger than the model length. The value of
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	792 W is used deep in the acceleration pipeline, and modest changes are not
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	793 expected to impact results (though larger values of W do lead to longer run
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	794 time).
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	795
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	796 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	797 <token name="@MCSS_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	798 Options Controlling Profile Construction
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	799
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	800 These options control how consensus columns are defined in an alignment.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	801
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	802 --fast
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	803
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	804 Define consensus columns as those that have a fraction >= symfrac of residues
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	805 as opposed to gaps. (See below for the --symfrac option.) This is the default.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	806
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	807 --hand
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	808
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	809 Define consensus columns in next profile using reference annotation to the multiple
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	810 alignment. This allows you to define any consensus columns you like.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	811
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	812
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	813 --symfrac
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	814
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	815 Define the residue fraction threshold necessary to define a consensus column
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	816 when using the --fast option. The default is 0.5. The symbol fraction in each
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	817 column is calculated after taking relative sequence weighting into account, and
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	818 ignoring gap characters corresponding to ends of sequence fragments (as opposed
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	819 to internal insertions/deletions). Setting this to 0.0 means that every
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	820 alignment column will be assigned as consensus, which may be useful in some
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	821 cases. Setting it to 1.0 means that only columns that include 0 gaps (internal
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	822 insertions/deletions) will be assigned as consensus.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	823
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	824 --fragthresh
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	825
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	826 We only want to count terminal gaps as deletions if the aligned sequence is
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	827 known to be full-length, not if it is a fragment (for instance, because only
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	828 part of it was sequenced). HMMER uses a simple rule to infer fragments: if the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	829 sequence length L is less than or equal to a fraction <x> times the alignment
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	830 length in columns, then the sequence is handled as a fragment. The default is
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	831 0.5. Setting --fragthresh0 will define no (nonempty) sequence as a fragment;
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	832 you might want to do this if you know you’ve got a carefully curated alignment
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	833 of full-length sequences. Setting --fragthresh1 will define all sequences as
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	834 fragments; you might want to do this if you know your alignment is entirely
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	835 composed of fragments, such as translated short reads in metagenomic shotgun
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	836 data.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	837
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	838 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	839 <token name="@OFORMAT_WITH_OPTS_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	840 Options for Controlling Output
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	841 ------------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	842
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	843 Table of hits
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	844
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	845 Save a simple tabular (space-delimited) file summarizing the per-target output, with
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	846 one data line per homologous target model found.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	847
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	848 Table of per-domain hits
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	849
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	850 Save a simple tabular (space-delimited) file summarizing the per-domain output,
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	851 with one data line per homologous domain detected in a query sequence for each
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	852 homologous model.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	853
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	854 Table of hits and domains in Pfam Format
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	855
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	856 Save an especially succinct tabular (space-delimited) file summarizing the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	857 per-target output, with one data line per homologous target model found.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	858 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	859 <token name="@OFORMAT_WITH_OPTS_NOPFAM_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	860 Options for Controlling Output
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	861 ------------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	862
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	863 Table of hits
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	864
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	865 Save a simple tabular (space-delimited) file summarizing the per-target output, with
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	866 one data line per homologous target model found.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	867
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	868 Table of per-domain hits
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	869
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	870 Save a simple tabular (space-delimited) file summarizing the per-domain output,
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	871 with one data line per homologous domain detected in a query sequence for each
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	872 homologous model.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	873 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	874 <token name="@OFORMAT_WITH_OPTS_N_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	875 Options for Controlling Output
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	876 ------------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	877
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	878 Table of hits
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	879
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	880 Save a simple tabular (space-delimited) file summarizing the per-target output, with
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	881 one data line per homologous target model found.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	882
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	883 Table of hits (dfam)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	884
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	885 Save a tabular (space-delimited) file summarizing the per-hit output, similar
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	886 to --tblout but more succinct.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	887
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	888
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	889 List of per-position scores for each hit (--aliscoreout)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	890
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	891 Save to file a list of per-position scores for each hit. This is useful, for
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	892 example, in identifying regions of high score density for use in resolving
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	893 overlapping hits from different models.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	894
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	895 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	896 <token name="@PRIOR_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	897 Options Controlling Priors
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	898 --------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	899
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	900 By default, weighted counts are converted to mean posterior probability
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	901 parameter estimates using mixture Dirichlet priors. Default mixture Dirichlet
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	902 prior parameters for protein models and for nucleic acid (RNA and DNA) models
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	903 are built in. The following options allow you to override the default priors.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	904
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	905 No priors (--pnone)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	906
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	907 Don’t use any priors. Probability parameters will simply be the observed
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	908 frequencies, after relative sequence weighting.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	909
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	910 Laplace +1 prior
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	911
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	912 Use a Laplace +1 prior in place of the default mixture Dirichlet prior.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	913 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	914 <token name="@SEED_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	915 Random Seeding
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	916 --------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	917
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	918 Seed the random number generator with <n>, an integer >= 0. If <n> is nonzero,
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	919 any stochastic simulations will be reproducible; the same command will give the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	920 same results. If <n> is 0, the random number generator is seeded arbitrarily,
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	921 and stochastic simulations will vary from run to run of the same command.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	922
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	923 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	924 <token name="@THRESHOLDS_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	925 Options for Reporting Thresholds
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	926 --------------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	927
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	928 Reporting thresholds control which hits are reported in output files (the main
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	929 output, --tblout, and --domtblout).
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	930
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	931 E-value (-E)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	932
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	933 In the per-target output, report target profiles with an E-value of <= <x>. The
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	934 default is 10.0, meaning that on average, about 10 false positives will be
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	935 reported per query, so you can see the top of the noise and decide for yourself
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	936 if it’s really noise.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	937
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	938 Bit score (-T)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	939
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	940 Instead of thresholding per-profile output on E-value, instead report target profiles
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	941 with a bit score of >= <x>.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	942
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	943 domain E-value (--domE)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	944
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	945 In the per-domain output, for target profiles that have already satisfied the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	946 per-profile reporting threshold, report individual domains with a conditional
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	947 E-value of <= <x>. The default is 10.0. A conditional E-value means the
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	948 expected number of additional false positive domains in the smaller search
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	949 space of those comparisons that already satisfied the per-profile reporting
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	950 threshold (and thus must have at least one homologous domain already).
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	951
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	952 domain Bit scores (--domT)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	953
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	954 Instead of thresholding per-domain output on E-value, instead report domains
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	955 with a bit score of >= <x>.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	956
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	957 Options for Inclusion Thresholds
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	958 --------------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	959
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	960 Inclusion thresholds are stricter than reporting thresholds. Inclusion
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	961 thresholds control which hits are considered to be reliable enough to be
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	962 included in an output alignment or a subsequent search round. In hmmscan, which
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	963 does not have any alignment output (like hmmsearch or phmmer) nor any iterative
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	964 search steps (like jackhmmer), inclusion thresholds have little effect. They
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	965 only affect what domains get marked as significant (!) or questionable (?) in
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	966 domain output.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	967
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	968 E-value of per target inclusion threshold
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	969
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	970 Use an E-value of <= <x> as the per-target inclusion threshold. The default is
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	971 0.01, meaning that on average, about 1 false positive would be expected in
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	972 every 100 searches with different query sequences.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	973
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	974 Bit score of per target inclusion threshold
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	975
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	976 Instead of using E-values for setting the inclusion threshold, instead use a
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	977 bit score of >= <x> as the per-target inclusion threshold. It would be unusual
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	978 to use bit score thresholds with hmmscan, because you don’t expect a single
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	979 score threshold to work for different profiles; different profiles have
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	980 slightly different expected score distributions.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	981
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	982 domain E-value per target inclusion treshold
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	983
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	984 Use a conditional E-value of <= <x> as the per-domain inclusion threshold, in
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	985 targets that have already satisfied the overall per-target inclusion threshold.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	986
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	987 domain Bit score per target inclusion treshold
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	988
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	989 Instead of using E-values, instead use a bit score of >= <x> as the per-domain
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	990 inclusion threshold. As with --incT above, it would be unusual to use a single
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	991 bit score threshold in hmmscan.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	992
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	993 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	994 <token name="@THRESHOLDS_NODOM_HELP@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	995 Options for Reporting Thresholds
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	996 --------------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	997
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	998 Reporting thresholds control which hits are reported in output files (the main
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	999 output, --tblout, and --domtblout).
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1000
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1001 E-value (-E)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1002
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1003 In the per-target output, report target profiles with an E-value of <= <x>. The
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1004 default is 10.0, meaning that on average, about 10 false positives will be
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1005 reported per query, so you can see the top of the noise and decide for yourself
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1006 if it’s really noise.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1007
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1008 Bit score (-T)
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1009
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1010 Instead of thresholding per-profile output on E-value, instead report target profiles
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1011 with a bit score of >= <x>.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1012
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1013 Options for Inclusion Thresholds
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1014 --------------------------------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1015
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1016 Inclusion thresholds are stricter than reporting thresholds. Inclusion
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1017 thresholds control which hits are considered to be reliable enough to be
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1018 included in an output alignment or a subsequent search round. In hmmscan, which
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1019 does not have any alignment output (like hmmsearch or phmmer) nor any iterative
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1020 search steps (like jackhmmer), inclusion thresholds have little effect. They
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1021 only affect what domains get marked as significant (!) or questionable (?) in
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1022 domain output.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1023
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1024 E-value of per target inclusion threshold
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1025
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1026 Use an E-value of <= <x> as the per-target inclusion threshold. The default is
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1027 0.01, meaning that on average, about 1 false positive would be expected in
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1028 every 100 searches with different query sequences.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1029
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1030 Bit score of per target inclusion threshold
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1031
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1032 Instead of using E-values for setting the inclusion threshold, instead use a
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1033 bit score of >= <x> as the per-target inclusion threshold. It would be unusual
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1034 to use bit score thresholds with hmmscan, because you don’t expect a single
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1035 score threshold to work for different profiles; different profiles have
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1036 slightly different expected score distributions.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1037
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1038 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1039 <token name="@ATTRIBUTION@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1040
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1041 Attribution
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1042 -----------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1043
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1044 This Galaxy tool relies on HMMER3_ from http://hmmer.janelia.org/
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1045 Internally the software is cited as:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1046
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1047 ::
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1048
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1049 # hmmscan :: search sequence(s) against a profile database
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1050 # HMMER 3.1 (February 2013); http://hmmer.org/
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1051 # Copyright (C) 2011 Howard Hughes Medical Institute.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1052 # Freely distributed under the GNU General Public License (GPLv3).
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1053 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1054
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1055 The wrappers were written by Eric Rasche and is licensed under Apache2_. The
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1056 documentation is copied from the HMMER3 documentation.
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1057
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1058 .. _Apache2: http://www.apache.org/licenses/LICENSE-2.0
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1059 .. _HMMER3: http://hmmer.janelia.org/
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1060
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1061
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1062 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1063 <token name="@HELP_PRE@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1064
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1065 What it does
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1066 ============
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1067 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1068 <token name="@HELP_PRE_OTH@"><![CDATA[
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1069 Options
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1070 =======
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1071 ]]></token>
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569 iuc parents: diff changeset	1072 </macros>

Mercurial > repos > iuc > hmmer3

annotate macros.xml @ 2:54b6b4d0613a draft default tip