hmmer_nhmmer: macros.xml annotate

annotate macros.xml @ 1:d15979968b74 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde

author	iuc
date	Mon, 14 Nov 2016 15:11:53 -0500
parents	f239ab5f45f4
children	c8e81e43bff1

rev	line source
0 f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1 <?xml version="1.0"?>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	2 <macros>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	3 <xml name="requirements">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	4 <requirements>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	5 <requirement type="package" version="3.1b2">hmmer</requirement>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	6 <yield/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	7 </requirements>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	8 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	9 <token name="@WRAPPER_VERSION@">0.1</token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	10 <xml name="stdio">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	11 <stdio>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	12 <!-- Anything other than zero is an error -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	13 <exit_code range="1:"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	14 <exit_code range=":-1"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	15 <!-- In case the return code has not been set propery check stderr too -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	16 <regex match="Error:"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	17 <regex match="Exception:"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	18 </stdio>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	19 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	20 <token name="@THRESHOLDS@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	21 -E $E
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	22 --domE $domE
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	23
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	24 #if $T:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	25 -T $T
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	26 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	27
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	28 #if $domT:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	29 --domT $domT
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	30 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	31
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	32 #if $incE:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	33 --incE $incE
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	34 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	35
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	36 #if $incT:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	37 --incT $incT
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	38 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	39
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	40 #if $incdomE:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	41 --incdomE $incdomE
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	42 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	43
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	44 #if $incdomT:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	45 --incdomT $incdomT
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	46 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	47 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	48 <xml name="thresholds_xml">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	49 <!-- Options controlling reporting thresholds -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	52 <param name="T" label="report sequences >= this score threshold in output" help="(-T)" type="float" optional="True"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	53 <param name="domT" label="report domains >= this score threshold in output" help="(--domT)" type="float" optional="True"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	54 <!-- Options controlling inclusion (significance) thresholds -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	55 <param name="incE" label="consider sequences <= this E-Value threshold as significant" help="(--incE)" type="float" optional="True"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	56 <param name="incdomE" label="consider domains <= this E-Value threshold as significant" help="(--incdomE)" type="float" optional="True"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	57 <param name="incT" label="consider sequences >= this score threshold as significant" help="(--incT)" type="float" optional="True"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	58 <param name="incdomT" label="consider domains >= this score threshold as significant" help="(--incdomT)" type="float" optional="True"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	59 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	60 <token name="@THRESHOLDS_NODOM@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	61 -E $E
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	62
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	63 #if $T:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	64 -T $T
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	65 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	66
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	67 #if $incE:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	68 --incE $incE
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	69 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	70
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	71 #if $incT:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	72 --incT $incT
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	73 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	74 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	75 <xml name="thresholds_nodom">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	76 <!-- Options controlling reporting thresholds -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	78 <param name="T" label="report sequences >= this score threshold in output" help="(-T)" type="float" optional="True"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	79 <!-- Options controlling inclusion (significance) thresholds -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	80 <param name="incE" label="consider sequences <= this E-Value threshold as significant" help="(--incE)" type="float" optional="True"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	81 <param name="incT" label="consider sequences >= this score threshold as significant" help="(--incT)" type="float" optional="True"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	82 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	83 <token name="@ACCEL_HEUR@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	84 $max
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	85 --F1 $F1
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	86 --F2 $F2
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	87 --F3 $F3
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	88 $nobias
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	89
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	90 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	91 <xml name="accel_heur_xml">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	92 <!-- Options controlling acceleration heuristics -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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=""/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	97 <param name="nobias" type="boolean" truevalue="--nobias" label="Turn off composition bias filter" help="(--nobias)" falsevalue=""/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	98 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	99 <token name="@EVAL_CALIB@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	100 --EmL $EmL
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	101 --EmN $EmN
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	102 --EvL $EvL
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	103 --EvN $EvN
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	104 --EfL $EfL
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	105 --EfN $EfN
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	106 --Eft $Eft
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	107 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	108 <xml name="eval_calib_xml">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	109 <!-- Control of E-value calibration -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	117 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	118 <token name="@OFORMAT_WITH_OPTS_NOPFAM@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	119 #if 'tblout' in str($oformat):
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	120 --tblout $tblout
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	121 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	122
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	123 #if 'domtblout' in str($oformat):
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	124 --domtblout $domtblout
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	125 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	126
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	127 $acc $noali $notextw
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	128 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	129 <xml name="oformat_with_opts_nopfam">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	130 <!-- Options directing output -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	131 <param name="oformat" multiple="True" display="checkboxes" label="Output Formats" type="select">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	132 <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	133 <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	134 </param>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	135 <param name="acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" help="(--acc)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	136 <param name="noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" help="(--noali)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	137 <param name="notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" help="(--notextw)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	138 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	139 <token name="@OFORMAT_WITH_OPTS@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	140 #if 'tblout' in str($oformat):
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	141 --tblout $tblout
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	142 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	143
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	144 #if 'domtblout' in str($oformat):
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	145 --domtblout $domtblout
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	146 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	147
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	148 #if 'pfamtblout' in str($oformat):
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	149 --pfamtblout $pfamtblout
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	150 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	151
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	152 $acc $noali $notextw
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	153 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	154 <xml name="oformat_with_opts">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	155 <!-- Options directing output -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	156 <param name="oformat" multiple="True" display="checkboxes" label="Output Formats" type="select">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	157 <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	158 <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	159 <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	160 </param>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	161 <param name="acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" help="(--acc)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	162 <param name="noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" help="(--noali)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	163 <param name="notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" help="(--notextw)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	164 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	165 <xml name="oformat_test">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	166 <param name="notextw" value="True" />
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	167 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	168 <!-- TODO: tblout will match 'pfamtblout,dfamtblout' -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	169 <token name="@OFORMAT_WITH_OPTS_N@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	170 #if 'tblout' in str($oformat):
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	171 --tblout $tblout
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	172 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	173
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	174 #if 'dfamtblout' in str($oformat):
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	175 --dfamtblout $dfamtblout
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	176 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	177
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	178 #if 'aliscoresout' in str($oformat):
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	179 --aliscoresout $aliscoresout
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	180 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	181
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	182 $acc $noali $notextw
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	183 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	184 <xml name="oformat_with_opts_n">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	185 <!-- Options directing output -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	186 <param name="oformat" multiple="True" display="checkboxes" label="Output Formats" type="select">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	187 <option value="tblout" selected="true">Table of hits (--tblout)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	188 <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	189 <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	190 </param>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	191 <param name="acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" help="(--acc)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	192 <param name="noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" help="(--noali)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	193 <param name="notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" help="(--notextw)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	194 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	195 <token name="@HSSI@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	196 #if $hssi.hssi_select == "singlemx":
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	197 --popen $hssi.popen
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	198 --pextend $hssi.pextend
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	199 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	200 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	201 <xml name="hssi">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	202 <!-- Handling single sequence inputs -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	203 <conditional name="hssi">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	204 <param name="hssi_select" type="select" label="Options for handling single sequence inputs">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	205 <option value="false" selected="true">Disable</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	206 <option value="singlemx">Use substitution score matrix for single-sequence inputs</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	207 </param>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	208 <when value="singlemx">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	211 </when>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	212 <when value="false">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	213 </when>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	214 <!-- -mx <s> : substitution score matrix (built-in matrices, with -singlemx)-->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	215 <!-- -mxfile <f> : read substitution score matrix from file <f> (with -singlemx)-->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	216 </conditional>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	217 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	218 <token name="@CPU@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	219 --cpu \${GALAXY_SLOTS:-2}
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	220 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	221 <token name="@SEED@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	222 --seed $seed
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	223 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	224 <xml name="seed">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	225 <param name="seed" label="RNG seed, 0 generates a random seed" value="42" type="integer" help="(--seed)" min="0"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	226 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	227 <xml name="seed_test">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	228 <param name="seed" value="4" />
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	229 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	230 <token name="@ADV_OPTS@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	231 $nonull2
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	232
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	233 #if $Z:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	234 -Z $Z
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	235 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	236
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	237 #if $domZ:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	238 --domZ $domZ
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	239 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	240 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	241 <xml name="adv_opts">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	242 <!-- Other options -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	243 <param name="nonull2" type="boolean" truevalue="--nonull2" label="Turn off biased composition score corrections" help="(--nonull2)" falsevalue=""/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	244 <param name="Z" type="integer" label="# of comparisons done for E-value calculation" help="(-Z)" optional="True"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	245 <param name="domZ" type="integer" label="# of significant sequences, for domain E-value calculation" help="(--domZ)" optional="True"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	246 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	247 <token name="@FORMAT_SELECTOR@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	248 $input_format_select
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	249 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	250 <xml name="format_selector">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	251 <param name="input_format_select" type="select" label="Format of sequence and model">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	252 <option value="--amino">Protein</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	253 <option value="--dna">DNA</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	254 <option value="--rna">RNA</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	255 </param>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	256 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	257 <xml name="format_selector_noprot">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	258 <param name="input_format_select" type="select" label="Format of sequence and model">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	259 <option value="--dna">DNA</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	260 <option value="--rna">RNA</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	261 </param>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	262 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	263 <token name="@ARSWS@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	264 $arsws.arsws_select
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	265
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	266 #if $arsws.arsws_select == "--wblosum":
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	267 --wid $arsws.wid
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	268 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	269 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	270 <xml name="arsws">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	271 <!-- Alternative relative sequence weighting strategies -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	272 <conditional name="arsws">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	273 <param name="arsws_select" type="select" label="Alternative relative sequence weighting strategies">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	274 <option value="--wpb" selected="true">Henikoff position-based weights (--wpb)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	275 <option value="--wgsc">Gerstein/Sonnhammer/Chothia tree weights (--wgsc)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	276 <option value="--wblosum">Henikoff simple filter weights (--wblosum)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	277 <option value="--wnone">don't do any relative weighting; set all to 1 (--wnnoe)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	278 <option value="--wgiven">use weights as given in MSA file (--wgiven)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	279 </param>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	280 <when value="--wpb">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	281 </when>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	282 <when value="--wgsc">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	283 </when>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	284 <when value="--wblosum">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	285 <param name="wid" label="Set identity cutoff" value="0.62" type="float" help="(--wid)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	286 </when>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	287 <when value="--wnone">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	288 </when>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	289 <when value="--wgiven">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	290 </when>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	291 </conditional>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	292 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	293 <token name="@AEEWS@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	294 #if $aeews.aeews_select != "":
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	295 --$aeews.aeews_select
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	296 #if $aeews.aeews_select == "eent":
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	297 --eset $aeews.eset
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	298 --ere $aeews.ere
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	299 --esigma $aeews.esigma
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	300 #elif $aeews.aeews_select == "eclust":
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	301 --eset $aeews.eset
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	302 --eid $aeews.eid
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	303 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	304 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	305 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	306 <xml name="aeews">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	307 <!-- Alternative effective sequence weighting strategies -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	308 <conditional name="aeews">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	309 <param name="aeews_select" type="select" label="Alternative effective sequence weighting strategies">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	310 <option value="">Disabled</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	311 <option value="eent">Adjust eff seq # to achieve relative entropy target (--eent)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	312 <option value="eclust">Eff seq # is the # of single linkage clusters (--eclust)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	313 <option value="enone">No effective seq # weighting: just use nseq (--enone)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	314 </param>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	315 <when value="">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	316 </when>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	317 <when value="eent">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	318 <param name="eset" type="float" value="0" label="set eff seq # for all models" help="(--eset)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	319 <param name="ere" type="float" value="0" label="set minimum rel entropy/position" help="(--ere)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	320 <param name="esigma" type="float" value="45" label="set sigma param" help="(--esigma)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	321 </when>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	322 <when value="eclust">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	323 <param name="eset" type="float" value="0" label="set eff seq # for all models" help="(--eset)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	324 <param name="eid" type="float" value="0.62" label="set fractional identity cutoff" min="0" max="1" help="(--eid)"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	325 </when>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	326 <when value="enone">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	327 </when>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	328 </conditional>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	329 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	330 <token name="@CUT@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	331 $cut_ga
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	332 $cut_nc
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	333 $cut_tc
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	334 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	335 <xml name="cut">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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=""/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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=""/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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=""/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	339 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	340 <token name="@MCSS@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	341 --$mcs.model_construction_strategy_select
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	342
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	343 #if $mcs.model_construction_strategy_select == "fast":
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	344 --symfrac $mcs.symfrac
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	345 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	346
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	347 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	348 <xml name="mcss">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	349 <!-- Alternative model construction strategies -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	350 <conditional name="mcs">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	351 <param name="model_construction_strategy_select" type="select" label="Model Construction Strategy">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	352 <option value="fast" selected="true">Assign columns with >= symfrac residues as consensus (--fast)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	353 <option value="hand">Manual construction (requires reference annotation) (--hand)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	354 </param>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	355 <when value="fast">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	356 <param name="symfrac" value="0.5" type="float" label="Sets sym fraction controlling --fast construction"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	357 </when>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	358 <when value="hand"></when>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	359 </conditional>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 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" />
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	361
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	362 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	363 <token name="@PRIOR@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	364 $aps_select
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	365 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	366 <xml name="prior">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	367 <param name="aps_select" type="select" label="Alternative Prior Strategies">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	368 <option value="" selected="true">Unspecified</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	369 <option value="--pnone">Don't use any prior; parameters are frequencies (--pnone)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	370 <option value="--plaplace">Use a Laplace +1 prior (--plaplace)</option>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	371 </param>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	372 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	373 <xml name="citation">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	374 <citations>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	375 <citation type="doi">10.1093/nar/gkr367</citation>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	376 </citations>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	377 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	378 <token name="@LENGTHS@">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	379 #if $w_beta:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	380 --w_beta $w_beta
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	381 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	382
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	383 #if $w_length:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	384 --w_length $w_length
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	385 #end if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	386
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	387 </token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	388 <xml name="lengths">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	389 <param name="w_beta" label="Tail mass at which window length is determined"
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	390 help="(--w_beta)" optional="True" type="float"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	391 <param name="w_length" label="Window Length"
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	392 help="(--w_length)" optional="True" type="integer" />
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	393 </xml>
1 d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	394 <token name="@INPUTHMMCHOICE@">
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	395 #if $input_hmm_conditional.input_hmm_source == "history":
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	396 '$input_hmm_conditional.hmmfile'
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	397 #else:
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	398 '$input_hmm_conditional.index.fields.db_path'
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	399 #end if
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	400 </token>
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	401 <xml name="input_hmm_choice">
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	402 <conditional name="input_hmm_conditional">
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	403 <param name="input_hmm_source" type="select" label="Use a built-in HMM model database or own from your history" >
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	404 <option value="indexed" selected="True">Use a built-in HMM model database</option>
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	405 <option value="history">Use a HMM database from history</option>
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	406 </param>
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	407 <when value="indexed">
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	408 <param name="index" type="select" label="Select a HMM model database" help="If your database of interest is not listed, contact the Galaxy administrator">
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	409 <options from_data_table="hmm_database">
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	410 <filter type="sort_by" column="2"/>
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	411 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	412 </options>
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	413 </param>
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	414 </when>
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	415 <when value="history">
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	416 <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/>
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	417 </when> <!-- history -->
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	418 </conditional> <!-- input_hmm_conditional -->
d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	419 </xml>
0 f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	420 <xml name="input_hmm">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	421 <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	422 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	423 <xml name="input_msa">
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	424 <param name="msafile" type="data" label="Multiple Sequence Alignment" format="stockholm,clustal,fasta"
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	425 help="in Stockholm, Clustal, or Fasta format. While this tool accepts fasta, please ensure that the sequences are not unaligned"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	426 </xml>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	427
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	428
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	429 <token name="@ACCEL_HEUR_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	430 Acceleration Heuristicts (--F1, --F2, --F3)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	431 -------------------------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	432
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	433 MSV filter
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	434
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	435 The sequence is aligned to the profile using a specialized model that
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	436 allows multiple high-scoring local ungapped segments to match. The
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	437 optimal alignment score (Viterbi score) is calculated under this multi-
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	438 segment model, hence the term MSV, for “multi-segment Viterbi”. This is
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	439 HMMER’s main speed heuristic. The MSV score is comparable to BLAST’s sum
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	440 score (optimal sum of ungapped alignment segments). Roughly speaking,
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	441 MSV is comparable to skipping the heuristic word hit and hit extension
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	442 steps of the BLAST acceleration algorithm.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	443
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	444 The MSV filter is very, very fast. In addition to avoiding indel
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	445 calculations in the dynamic programming table, it uses reduced precision
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	446 scores scaled to 8-bit integers, enabling acceleration via 16-way
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	447 parallel SIMD vector instructions.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	448
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	449 The MSV score is a true log-odds likelihood ratio, so it obeys
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	450 conjectures about the expected score distribution (Eddy, 2008) that
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	451 allow immediate and accurate calculation of the statistical significance
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	452 (P- value) of the MSV bit score.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	453
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	454 By default, comparisons with a P-value of ≤ 0.02 pass this filter,
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	455 meaning that about 2% of nonhomol- ogous sequences are expected to pass.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	456 You can use the --F1 option to change this threshold. For example, --F1
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	457 <0.05> would pass 5% of the comparisons, making a search more sensitive
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	458 but slower. Setting the threshold to ≥ 1.0 (--F1 99 for example) assures
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	459 that all comparisons will pass. Shutting off the MSV filter may be
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	460 worthwhile if you want to make sure you don’t miss comparisons that have
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	461 a lot of scattered insertions and deletions. Alternatively, the --max
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	462 option causes the MSV filter step (and all other filter steps) to be
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	463 bypassed.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	464
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	465 The MSV bit score is calculated as a log-odds score using the null model
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	466 for comparison. No correction for a biased composition or repetitive
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	467 sequence is done at this stage. For comparisons involving biased
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	468 sequences and/or profiles, more than 2% of comparisons will pass the MSV
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	469 filter. At the end of search output, there is a line like:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	470
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	471 Passed MSV filter: 107917 (0.020272); expected 106468.8 (0.02)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	472
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	473 which tells you how many and what fraction of comparisons passed the MSV
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	474 filter, versus how many (and what fraction) were expected.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	475
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	476 Viterbi filter
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	477
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	478 The sequence is now aligned to the profile using a fast Viterbi algorithm for
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	479 optimal gapped alignment.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	480
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	481 This Viterbi implementation is specialized for speed. It is implemented in
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	482 8-way parallel SIMD vector instructions, using reduced precision scores that
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	483 have been scaled to 16-bit integers. Only one row of the dynamic programming
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	484 matrix is stored, so the routine only recovers the score, not the optimal
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	485 alignment itself. The reduced representation has limited range; local alignment
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	486 scores will not underflow, but high scoring comparisons can overflow and return
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	487 infinity, in which case they automatically pass the filter.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	488
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	489 The final Viterbi filter bit score is then computed using the appropriate null
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	490 model log likelihood (by default the biased composition filter model score, or
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	491 if the biased filter is off, just the null model score). If the P-value of this
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	492 score passes the Viterbi filter threshold, the sequence passes on to the next
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	493 step of the pipeline.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	494
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	495 The --F2 <x> option controls the P-value threshold for passing the Viterbi
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	496 filter score. The default is 0.001. The --max option bypasses all filters in
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	497 the pipeline. At the end of a search output, you will see a line like:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	498
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	499 Passed Vit filter: 2207 (0.00443803); expected 497.3 (0.001)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	500
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	501 which tells you how many and what fraction of comparisons passed the Viterbi
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	502 filter, versus how many were expected.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	503
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	504 Forward filter/parser
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	505
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	506 The sequence is now aligned to the profile using the full Forward algorithm,
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	507 which calculates the likelihood of the target sequence given the profile,
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	508 summed over the ensemble of all possible alignments.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	509
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	510 This is a specialized time- and memory-efficient Forward implementation called
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	511 the “Forward parser”. It is implemented in 4-way parallel SIMD vector
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	512 instructions, in full precision (32-bit floating point). It stores just enough
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	513 information that, in combination with the results of the Backward parser
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	514 (below), posterior probabilities of start and stop points of alignments
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	515 (domains) can be calculated in the domain definition step (below), although the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	516 detailed alignments themselves cannot be.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	517
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	518 The Forward filter bit score is calculated by correcting this score using the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	519 appropriate null model log likelihood (by default the biased composition filter
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	520 model score, or if the biased filter is off, just the null model score). If the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	521 P-value of this bit score passes the Forward filter threshold, the sequence
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	522 passes on to the next step of the pipeline.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	523
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	524 The bias filter score has no further effect in the pipeline. It is only used in
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	525 filter stages. It has no effect on final reported bit scores or P-values.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	526 Biased composition compensation for final bit scores is done by a more complex
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	527 domain-specific algorithm, described below.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	528
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	529 The --F3 <x> option controls the P-value threshold for passing the Forward
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	530 filter score. The default is 1e-5. The --max option bypasses all filters in the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	531 pipeline. At the end of a search output, you will see a line like:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	532
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	533 Passed Fwd filter: 1076 (0.00216371); expected 5.0 (1e-05)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	534
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	535 which tells you how many and what fraction of comparisons passed the Forward
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	536 filter, versus how many were expected.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	537
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	538 Bias Filter Options
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	539
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	540 The --max option bypasses all filters in the pipeline, including the bias
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	541 filter.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	542
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	543 The --nobias option turns off (bypasses) the biased composition filter. The
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	544 simple null model is used as a null hypothesis for MSV and in subsequent filter
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	545 steps. The biased composition filter step compromises a small amount of
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	546 sensitivity. Though it is good to have it on by default, you may want to shut
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	547 it off if you know you will have no problem with biased composition hits.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	548
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	549
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	550 Advanced Documentation
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	551
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	552 A more detailed look at the internals of the various filter pipelines was
1 d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	553 posted on the `developer's blog <https://cryptogenomicon.org/2011/09/19/hmmer3-is-stubborn/>`__.
0 f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	554 The information posted there may be useful to those who are struggling with
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	555 poor-scoring sequences.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	556
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	557 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	558 <token name="@ADV_OPTS_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	559 Advanced Options
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	560 ----------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	561
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	562 nonull2
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	563
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	564 can be too aggressive sometimes, causing you to miss homologs. You can turn the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	565 biased-composition score correction off with the --nonull2 option (and if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	566 you’re doing that, you may also want to set --nobias, to turn off another
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	567 biased composition step called the bias filter, which affects which sequences
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	568 get scored at all).
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	569
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	570 domZ
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	571
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	572 Assert that the total number of targets in your searches is <x>, for the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	573 purposes of per-domain conditional E-value calculations, rather than the number
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	574 of targets that passed the reporting thresholds.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	575
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	576 Z
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	577
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	578 Assert that the total number of targets in your searches is <x>, for the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	579 purposes of per-sequence E-value calculations, rather than the actual number of
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	580 targets seen.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	581 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	582 <token name="@AEEWS_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	583 Effective Sequence Number
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	584 -------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	585
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	586 After relative weights are determined, they are normalized to sum to a total
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	587 effective sequence number, eff nseq. This number may be the actual number of
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	588 sequences in the alignment, but it is almost always smaller than that. The
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	589 default entropy weighting method (--eent) reduces the effective sequence num-
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	590 ber to reduce the information content (relative entropy, or average expected
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	591 score on true homologs) per consensus position. The target relative entropy is
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	592 controlled by a two-parameter function, where the two parameters are settable
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	593 with --ere and --esigma.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	594
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	595 --eent
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	596
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	597 Adjust effective sequence number to achieve a specific relative entropy per
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	598 position (see --ere). This is the default.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	599
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	600 --eclust
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	601
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	602 Set effective sequence number to the number of single-linkage clusters at a
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	603 specific identity threshold (see --eid). This option is not recommended; it’s
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	604 for experiments evaluating how much better --eent is.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	605
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	606 --enone
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	607
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	608 Turn off effective sequence number determination and just use the actual number
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	609 of sequences. One reason you might want to do this is to try to maximize the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	610 relative entropy/position of your model, which may be useful for short models.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	611
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	612 --eset
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	613
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	614 Explicitly set the effective sequence number for all models to <x>.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	615
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	616 --ere
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	617
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	618 Set the minimum relative entropy/position target to <x>. Requires --eent. Default
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	619 depends on the sequence alphabet. For protein sequences, it is 0.59 bits/position;
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	620 for nucleotide sequences, it is 0.45 bits/position.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	621
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	622 --esigma
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	623
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	624 Sets the minimum relative entropy contributed by an entire model alignment, over
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	625 its whole length. This has the effect of making short models have higher relative
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	626 entropy per position than --ere alone would give. The default is 45.0 bits.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	627
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	628 --eid
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	629
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	630 Sets the fractional pairwise identity cutoff used by single linkage clustering
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	631 with the --eclust option. The default is 0.62.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	632 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	633 <token name="@ARSWS_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	634 Options Controlling Relative Weights
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	635 ------------------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	636
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	637 HMMER uses an ad hoc sequence weighting algorithm to downweight closely related
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	638 sequences and up-weight distantly related ones. This has the effect of making
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	639 models less biased by uneven phylogenetic representation. For example, two
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	640 identical sequences would typically each receive half the weight that one
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	641 sequence would. These options control which algorithm gets used.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	642
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	643
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	644 --wpb
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	645
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	646 Use the Henikoff position-based sequence weighting scheme [Henikoff and
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	647 Henikoff, J. Mol. Biol. 243:574, 1994]. This is the default.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	648
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	649 --wgsc
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	650
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	651 Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Gerstein et al, J.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	652 Mol. Biol. 235:1067, 1994].
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	653
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	654 --wblosum
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	655
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	656 Use the same clustering scheme that was used to weight data in calculating
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	657 BLOSUM subsitution matrices [Henikoff and Henikoff, Proc. Natl. Acad. Sci
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	658 89:10915, 1992]. Sequences are single-linkage clustered at an identity
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	659 threshold (default 0.62; see --wid) and within each cluster of c sequences,
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	660 each sequence gets rela- tive weight 1/c.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	661
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	662 --wnone
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	663
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	664 No relative weights. All sequences are assigned uniform weight.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	665
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	666 --wid
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	667
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	668 Sets the identity threshold used by single-linkage clustering when using
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	669 --wblosum. Invalid with any other weighting scheme. Default is 0.62.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	670 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	671 <token name="@BIAS_COMP_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	672 Bias Composition
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	673 ----------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	674
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	675 The next number, the bias, is a correction term for biased sequence composition
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	676 that has been applied to the sequence bit score.1 For instance, for the top hit
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	677 MYG PHYCA that scored 222.7 bits, the bias of 3.2 bits means that this sequence
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	678 originally scored 225.9 bits, which was adjusted by the slight 3.2 bit biased-
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	679 composition correction. The only time you really need to pay attention to the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	680 bias value is when it’s large, on the same order of magnitude as the sequence
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	681 bit score. Sometimes (rarely) the bias correction isn’t aggressive enough, and
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	682 allows a non-homolog to retain too much score. Conversely, the bias correction
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	683 can be too aggressive sometimes, causing you to miss homologs. You can turn the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	684 biased-composition score correction off with the --nonull2 option (and if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	685 you’re doing that, you may also want to set --nobias, to turn off another
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	686 biased composition step called the bias filter, which affects which sequences
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	687 get scored at all).
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	688
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	689 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	690 <token name="@CUT_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	691 Options for Model-specific Score Thresholding
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	692 ---------------------------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	693
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	694 Curated profile databases may define specific bit score thresholds for each
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	695 profile, superseding any thresholding based on statistical significance alone.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	696 To use these options, the profile must contain the appropriate (GA, TC, and/or
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	697 NC) optional score threshold annotation; this is picked up by hmmbuild from
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	698 Stockholm format alignment files. Each thresholding option has two scores: the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	699 per-sequence threshold <x1> and the per-domain threshold <x2> These act as if
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	700 -T<x1> --incT<x1> --domT<x2> --incdomT<x2> has been applied specifically using
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	701 each model’s curated thresholds.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	702
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	703 --cut_ga
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	704
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	705 Use the GA (gathering) bit scores in the model to set per-sequence (GA1) and
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	706 per-domain (GA2) reporting and inclusion thresholds. GA thresholds are
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	707 generally considered to be the reliable curated thresholds defining family
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	708 membership; for example, in Pfam, these thresholds define what gets included in
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	709 Pfam Full alignments based on searches with Pfam Seed models.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	710
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	711 --cut_nc
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	712
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	713 Use the NC (noise cutoff) bit score thresholds in the model to set
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	714 per-sequence (NC1) and per-domain (NC2) reporting and inclusion thresholds. NC
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	715 thresholds are generally considered to be the score of the highest-scoring
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	716 known false positive.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	717
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	718 --cut_tc
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	719
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	720 Use the NC (trusted cutoff) bit score thresholds in the model to set
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	721 per-sequence (TC1) and per-domain (TC2) reporting and inclusion thresholds. TC
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	722 thresholds are generally considered to be the score of the lowest-scoring known
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	723 true positive that is above all known false positives.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	724 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	725 <token name="@EVAL_CALIB_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	726 Options Controlling H3 Parameter Estimation Methods
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	727 ---------------------------------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	728
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	729 H3 uses three short random sequence simulations to estimating the location
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	730 parameters for the expected score distributions for MSV scores, Viterbi scores,
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	731 and Forward scores. These options allow these simulations to be modified.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	732
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	733 --EmL
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	734
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	735 Sets the sequence length in simulation that estimates the location parameter mu
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	736 for MSV E-values. Default is 200.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	737
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	738 --EmN
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	739
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	740 Sets the number of sequences in simulation that estimates the location parameter
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	741 mu for MSV E-values. Default is 200.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	742
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	743 --EvL
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	744
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	745 Sets the sequence length in simulation that estimates the location parameter mu
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	746 for Viterbi E-values. Default is 200.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	747
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	748 --EvN
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	749
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	750 Sets the number of sequences in simulation that estimates the location parameter
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	751 mu for Viterbi E-values. Default is 200.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	752
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	753
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	754 --EfL
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	755
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	756 Sets the sequence length in simulation that estimates the location parameter tau
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	757 for Forward E-values. Default is 100.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	758
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	759 --EfN
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	760
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	761 Sets the number of sequences in simulation that estimates the location parameter
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	762 tau for Forward E-values. Default is 200.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	763
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	764 --Eft
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	765
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	766 Sets the tail mass fraction to fit in the simulation that estimates the location param-
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	767 eter tau for Forward evalues. Default is 0.04.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	768 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	769 <token name="@FORMAT_SELECTOR_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	770 Options for Specifying the Alphabet
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	771 -----------------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	772
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	773 The alphabet type (amino, DNA, or RNA) is autodetected by default, by looking
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	774 at the composition of the msafile. Autodetection is normally quite reliable,
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	775 but occasionally alphabet type may be ambiguous and autodetection can fail (for
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	776 instance, on tiny toy alignments of just a few residues). To avoid this, or to
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	777 increase robustness in automated analysis pipelines, you may specify the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	778 alphabet type of msafile with these options.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	779 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	780 <token name="@HSSI_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	781 Options Controlling Single Sequence Scoring (first Iteration)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	782 -------------------------------------------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	783
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	784 By default, the first iteration uses a search model constructed from a single
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	785 query sequence. This model is constructed using a standard 20x20 substitution
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	786 matrix for residue probabilities, and two additional pa- rameters for
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	787 position-independent gap open and gap extend probabilities. These options allow
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	788 the default single-sequence scoring parameters to be changed.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	789
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	790 Gap Open (--popen)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	791
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	792 Set the gap open probability for a single sequence query model to <x>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	793
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	794 Gap Extend (--pextend)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	795
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	796 Set the gap extend probability for a single sequence query model to <x>.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	797
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	798
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	799 --mx/--mxfile
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	800
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	801 These options are not currently supported
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	802 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	803 <token name="@LENGTHS_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	804 Tail Mass Options
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	805 -----------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	806
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	807 Window length tail mass (--w_beta)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	808
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	809 The upper bound, W, on the length at which nhmmer expects to find an instance
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	810 of the model is set such that the fraction of all sequences generated by the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	811 model with length >= W is less than <x>. The default is 1e-7.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	812
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	813
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	814 Model instance length upper bound (--w length)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	815
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	816 Override the model instance length upper bound, W, which is otherwise
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	817 controlled by --w beta. It should be larger than the model length. The value of
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	818 W is used deep in the acceleration pipeline, and modest changes are not
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	819 expected to impact results (though larger values of W do lead to longer run
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	820 time).
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	821
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	822 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	823 <token name="@MCSS_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	824 Options Controlling Profile Construction
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	825
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	826 These options control how consensus columns are defined in an alignment.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	827
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	828 --fast
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	829
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	830 Define consensus columns as those that have a fraction >= symfrac of residues
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	831 as opposed to gaps. (See below for the --symfrac option.) This is the default.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	832
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	833 --hand
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	834
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	835 Define consensus columns in next profile using reference annotation to the multiple
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	836 alignment. This allows you to define any consensus columns you like.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	837
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	838
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	839 --symfrac
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	840
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	841 Define the residue fraction threshold necessary to define a consensus column
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	842 when using the --fast option. The default is 0.5. The symbol fraction in each
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	843 column is calculated after taking relative sequence weighting into account, and
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	844 ignoring gap characters corresponding to ends of sequence fragments (as opposed
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	845 to internal insertions/deletions). Setting this to 0.0 means that every
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	846 alignment column will be assigned as consensus, which may be useful in some
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	847 cases. Setting it to 1.0 means that only columns that include 0 gaps (internal
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	848 insertions/deletions) will be assigned as consensus.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	849
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	850 --fragthresh
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	851
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	852 We only want to count terminal gaps as deletions if the aligned sequence is
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	853 known to be full-length, not if it is a fragment (for instance, because only
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	854 part of it was sequenced). HMMER uses a simple rule to infer fragments: if the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	855 sequence length L is less than or equal to a fraction <x> times the alignment
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	856 length in columns, then the sequence is handled as a fragment. The default is
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	857 0.5. Setting --fragthresh0 will define no (nonempty) sequence as a fragment;
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	858 you might want to do this if you know you’ve got a carefully curated alignment
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	859 of full-length sequences. Setting --fragthresh1 will define all sequences as
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	860 fragments; you might want to do this if you know your alignment is entirely
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	861 composed of fragments, such as translated short reads in metagenomic shotgun
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	862 data.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	863
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	864 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	865 <token name="@OFORMAT_WITH_OPTS_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	866 Options for Controlling Output
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	867 ------------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	868
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	869 Table of hits
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	870
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	871 Save a simple tabular (space-delimited) file summarizing the per-target output, with
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	872 one data line per homologous target model found.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	873
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	874 Table of per-domain hits
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	875
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	876 Save a simple tabular (space-delimited) file summarizing the per-domain output,
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	877 with one data line per homologous domain detected in a query sequence for each
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	878 homologous model.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	879
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	880 Table of hits and domains in Pfam Format
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	881
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	882 Save an especially succinct tabular (space-delimited) file summarizing the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	883 per-target output, with one data line per homologous target model found.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	884 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	885 <token name="@OFORMAT_WITH_OPTS_NOPFAM_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	886 Options for Controlling Output
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	887 ------------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	888
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	889 Table of hits
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	890
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	891 Save a simple tabular (space-delimited) file summarizing the per-target output, with
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	892 one data line per homologous target model found.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	893
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	894 Table of per-domain hits
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	895
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	896 Save a simple tabular (space-delimited) file summarizing the per-domain output,
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	897 with one data line per homologous domain detected in a query sequence for each
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	898 homologous model.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	899 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	900 <token name="@OFORMAT_WITH_OPTS_N_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	901 Options for Controlling Output
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	902 ------------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	903
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	904 Table of hits
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	905
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	906 Save a simple tabular (space-delimited) file summarizing the per-target output, with
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	907 one data line per homologous target model found.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	908
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	909 Table of hits (dfam)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	910
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	911 Save a tabular (space-delimited) file summarizing the per-hit output, similar
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	912 to --tblout but more succinct.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	913
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	914
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	915 List of per-position scores for each hit (--aliscoreout)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	916
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	917 Save to file a list of per-position scores for each hit. This is useful, for
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	918 example, in identifying regions of high score density for use in resolving
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	919 overlapping hits from different models.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	920
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	921 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	922 <token name="@PRIOR_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	923 Options Controlling Priors
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	924 --------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	925
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	926 By default, weighted counts are converted to mean posterior probability
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	927 parameter estimates using mixture Dirichlet priors. Default mixture Dirichlet
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	928 prior parameters for protein models and for nucleic acid (RNA and DNA) models
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	929 are built in. The following options allow you to override the default priors.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	930
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	931 No priors (--pnone)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	932
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	933 Don’t use any priors. Probability parameters will simply be the observed
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	934 frequencies, after relative sequence weighting.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	935
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	936 Laplace +1 prior
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	937
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	938 Use a Laplace +1 prior in place of the default mixture Dirichlet prior.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	939 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	940 <token name="@SEED_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	941 Random Seeding
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	942 --------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	943
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	944 Seed the random number generator with <n>, an integer >= 0. If <n> is nonzero,
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	945 any stochastic simulations will be reproducible; the same command will give the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	946 same results. If <n> is 0, the random number generator is seeded arbitrarily,
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	947 and stochastic simulations will vary from run to run of the same command.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	948
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	949 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	950 <token name="@THRESHOLDS_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	951 Options for Reporting Thresholds
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	952 --------------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	953
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	954 Reporting thresholds control which hits are reported in output files (the main
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	955 output, --tblout, and --domtblout).
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	956
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	957 E-value (-E)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	958
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	959 In the per-target output, report target profiles with an E-value of <= <x>. The
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	960 default is 10.0, meaning that on average, about 10 false positives will be
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	961 reported per query, so you can see the top of the noise and decide for yourself
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	962 if it’s really noise.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	963
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	964 Bit score (-T)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	965
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	966 Instead of thresholding per-profile output on E-value, instead report target profiles
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	967 with a bit score of >= <x>.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	968
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	969 domain E-value (--domE)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	970
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	971 In the per-domain output, for target profiles that have already satisfied the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	972 per-profile reporting threshold, report individual domains with a conditional
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	973 E-value of <= <x>. The default is 10.0. A conditional E-value means the
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	974 expected number of additional false positive domains in the smaller search
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	975 space of those comparisons that already satisfied the per-profile reporting
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	976 threshold (and thus must have at least one homologous domain already).
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	977
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	978 domain Bit scores (--domT)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	979
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	980 Instead of thresholding per-domain output on E-value, instead report domains
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	981 with a bit score of >= <x>.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	982
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	983 Options for Inclusion Thresholds
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	984 --------------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	985
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	986 Inclusion thresholds are stricter than reporting thresholds. Inclusion
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	987 thresholds control which hits are considered to be reliable enough to be
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	988 included in an output alignment or a subsequent search round. In hmmscan, which
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	989 does not have any alignment output (like hmmsearch or phmmer) nor any iterative
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	990 search steps (like jackhmmer), inclusion thresholds have little effect. They
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	991 only affect what domains get marked as significant (!) or questionable (?) in
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	992 domain output.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	993
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	994 E-value of per target inclusion threshold
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	995
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	996 Use an E-value of <= <x> as the per-target inclusion threshold. The default is
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	997 0.01, meaning that on average, about 1 false positive would be expected in
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	998 every 100 searches with different query sequences.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	999
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1000 Bit score of per target inclusion threshold
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1001
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1002 Instead of using E-values for setting the inclusion threshold, instead use a
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1003 bit score of >= <x> as the per-target inclusion threshold. It would be unusual
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1004 to use bit score thresholds with hmmscan, because you don’t expect a single
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1005 score threshold to work for different profiles; different profiles have
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1006 slightly different expected score distributions.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1007
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1008 domain E-value per target inclusion treshold
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1009
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1010 Use a conditional E-value of <= <x> as the per-domain inclusion threshold, in
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1011 targets that have already satisfied the overall per-target inclusion threshold.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1012
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1013 domain Bit score per target inclusion treshold
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1014
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1015 Instead of using E-values, instead use a bit score of >= <x> as the per-domain
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1016 inclusion threshold. As with --incT above, it would be unusual to use a single
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1017 bit score threshold in hmmscan.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1018
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1019 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1020 <token name="@THRESHOLDS_NODOM_HELP@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1021 Options for Reporting Thresholds
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1022 --------------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1023
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1024 Reporting thresholds control which hits are reported in output files (the main
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1025 output, --tblout, and --domtblout).
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1026
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1027 E-value (-E)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1028
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1029 In the per-target output, report target profiles with an E-value of <= <x>. The
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1030 default is 10.0, meaning that on average, about 10 false positives will be
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1031 reported per query, so you can see the top of the noise and decide for yourself
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1032 if it’s really noise.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1033
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1034 Bit score (-T)
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1035
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1036 Instead of thresholding per-profile output on E-value, instead report target profiles
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1037 with a bit score of >= <x>.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1038
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1039 Options for Inclusion Thresholds
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1040 --------------------------------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1041
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1042 Inclusion thresholds are stricter than reporting thresholds. Inclusion
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1043 thresholds control which hits are considered to be reliable enough to be
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1044 included in an output alignment or a subsequent search round. In hmmscan, which
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1045 does not have any alignment output (like hmmsearch or phmmer) nor any iterative
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1046 search steps (like jackhmmer), inclusion thresholds have little effect. They
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1047 only affect what domains get marked as significant (!) or questionable (?) in
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1048 domain output.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1049
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1050 E-value of per target inclusion threshold
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1051
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1052 Use an E-value of <= <x> as the per-target inclusion threshold. The default is
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1053 0.01, meaning that on average, about 1 false positive would be expected in
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1054 every 100 searches with different query sequences.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1055
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1056 Bit score of per target inclusion threshold
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1057
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1058 Instead of using E-values for setting the inclusion threshold, instead use a
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1059 bit score of >= <x> as the per-target inclusion threshold. It would be unusual
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1060 to use bit score thresholds with hmmscan, because you don’t expect a single
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1061 score threshold to work for different profiles; different profiles have
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1062 slightly different expected score distributions.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1063
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1064 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1065 <token name="@ATTRIBUTION@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1066
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1067 Attribution
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1068 -----------
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1069
1 d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	1070 This Galaxy tool relies on HMMER3_
0 f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1071 Internally the software is cited as:
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1072
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1073 ::
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1074
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1075 # hmmscan :: search sequence(s) against a profile database
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1076 # HMMER 3.1 (February 2013); http://hmmer.org/
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1077 # Copyright (C) 2011 Howard Hughes Medical Institute.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1078 # Freely distributed under the GNU General Public License (GPLv3).
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1079 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1080
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1081 The wrappers were written by Eric Rasche and is licensed under Apache2_. The
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1082 documentation is copied from the HMMER3 documentation.
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1083
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1084 .. _Apache2: http://www.apache.org/licenses/LICENSE-2.0
1 d15979968b74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde iuc parents: 0 diff changeset	1085 .. _HMMER3: http://hmmer.org/
0 f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1086
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1087
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1088 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1089 <token name="@HELP_PRE@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1090
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1091 What it does
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1092 ============
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1093 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1094 <token name="@HELP_PRE_OTH@"><![CDATA[
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1095 Options
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1096 =======
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1097 ]]></token>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47 iuc parents: diff changeset	1098 </macros>

Mercurial > repos > iuc > hmmer_nhmmer

annotate macros.xml @ 1:d15979968b74 draft