last: lastal.xml annotate

annotate lastal.xml @ 10:a07c62dc88f9 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 88d7f81768f05f490f444b646f47241cf2547b44"

author	iuc
date	Sat, 27 Nov 2021 10:11:58 +0000
parents	18ff8319181f
children

rev	line source
10 a07c62dc88f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 88d7f81768f05f490f444b646f47241cf2547b44" iuc parents: 9 diff changeset	1 <tool id="last_al" name="LASTal" version="@TOOL_VERSION@+galaxy1" profile="20.01">
0 7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	2
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	3 <description>finds local alignments between query sequences, and reference sequences.</description>
9 18ff8319181f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 7 diff changeset	4 <expand macro="bio_tools"/>
0 7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	5 <macros>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	6 <import>macros_last.xml</import>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	7 </macros>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	8
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	9 <requirements>
10 a07c62dc88f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 88d7f81768f05f490f444b646f47241cf2547b44" iuc parents: 9 diff changeset	10 <requirement type="package" version="@TOOL_VERSION@">last</requirement>
0 7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	11 </requirements>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	12
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	13 <command detect_errors="exit_code"><![CDATA[
7 657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	14 set -e -o pipefail;
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	15
0 7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	16 #if $db_opts.db_opts_input == 'lastdb'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	17 ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	18 #end if
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	19
7 657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	20 #if $query_seq.ext.endswith('.gz')
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	21 zcat
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	22 #else
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	23 cat
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	24 #end if
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	25 '$query_seq' \| lastal
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	26
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	27 #if $query_seq.ext.startswith('fasta')
5 187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	28 -Q 0
7 657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	29 #else if $query_seq.ext.startswith('fastqsanger')
5 187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	30 -Q 1
7 657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	31 #else if $query_seq.ext.startswith('fastqsolexa')
5 187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	32 -Q 2
7 657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	33 #else if $query_seq.ext.startswith('fastqillumina')
5 187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	34 -Q 3
7 657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	35 #else if $query_seq.ext.startswith('pssm')
5 187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	36 -Q 5
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	37 #end if
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	38
0 7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	39 -f $lastal.f
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	40 -j $lastal.j
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	41
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	42 -R $lastal.repeats_misc.uppercase_misc$lastal.repeats_misc.simple_repeat_misc
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	43
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	44 #if $lastal.isprotein.schoring_schemes.score_matrix != 'scoreFile'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	45 -p $lastal.isprotein.schoring_schemes.score_matrix
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	46
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	47 -X $lastal.isprotein.schoring_schemes.score_opt.X
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	48 -x $lastal.isprotein.schoring_schemes.score_opt.x
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	49 -y $lastal.isprotein.schoring_schemes.score_opt.y
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	50 -z $lastal.isprotein.schoring_schemes.score_opt.z
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	51 -d $lastal.isprotein.schoring_schemes.score_opt.d
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	52 -e $lastal.isprotein.schoring_schemes.score_opt.e
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	53
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	54 -a $lastal.isprotein.schoring_schemes.cost_opt.a
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	55 -b $lastal.isprotein.schoring_schemes.cost_opt.b
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	56 -A $lastal.isprotein.schoring_schemes.cost_opt.A
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	57 -B $lastal.isprotein.schoring_schemes.cost_opt.B
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	58
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	59 -s $lastal.isprotein.s
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	60 #else if $lastal.isprotein.schoring_schemes.score_matrix == 'scoreFile'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	61 -p $lastal.isprotein.schoring_schemes.scoreMatrixFile
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	62 #end if
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	63
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	64 -D $lastal.evalue_opt.D
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	65
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	66 -m $lastal.init_match_opt.m
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	67 -l $lastal.init_match_opt.l
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	68 -L $lastal.init_match_opt.L
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	69 -k $lastal.init_match_opt.k
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	70 -W $lastal.init_match_opt.W
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	71
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	72 -S $lastal.misc_opt.S
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	73 -K $lastal.misc_opt.K
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	74 -C $lastal.misc_opt.C
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	75 -T $lastal.misc_opt.T
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	76 -n $lastal.misc_opt.n
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	77 -w $lastal.misc_opt.w
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	78 -u $lastal.misc_opt.u
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	79 -g $lastal.misc_opt.g
10 a07c62dc88f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 88d7f81768f05f490f444b646f47241cf2547b44" iuc parents: 9 diff changeset	80 -G $lastal.misc_opt.G
0 7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	81
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	82 -P \${GALAXY_SLOTS:-1}
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	83
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	84 #if $db_opts.db_opts_input == 'db'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	85 '${"'" "'".join(str($db_opts.database.fields.path).split(","))}'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	86 #else if $db_opts.db_opts_input == 'lastdb'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	87 'db_files/lastdb'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	88 #end if
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	89
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	90 >'$outfile'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	91 ]]></command>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	92
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	93 <inputs>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	94 <expand macro="input_db"/>
7 657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	95 <param name="query_seq" type="data" format="fasta,fasta.gz,fastq,fastq.gz,tabular" label="Query sequences"/>
0 7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	96
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	97 <section name="lastal" title="Lastal arguments" expanded="true">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	98 <param argument="-f" type="select" multiple="false" label="Output format">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	99 <option value="MAF" selected="true">MAF</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	100 <option value="TAB">TAB</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	101 <option value="BlastTab">BlastTab</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	102 <option value="BlastTab+">BlastTab+</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	103 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	104 <param argument="-j" type="select" multiple="false" label="Output type">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	105 <option value="0">Match counts</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	106 <option value="1">Gapless</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	107 <option value="2">Redundant gapped</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	108 <option value="3" selected="true">Gapped</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	109 <option value="4">Column ambiguity estimates</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	110 <option value="5">Gamma-centroid</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	111 <option value="6">LAMA</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	112 <option value="7">Expected counts</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	113 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	114
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	115 <conditional name="isprotein">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	116 <param name="lastal_protein" type="select" multiple="false" label="The sequences are :">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	117 <option value="dna" selected="true">DNA</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	118 <option value="prot">Proteins (-p)</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	119 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	120 <when value="dna">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	121 <conditional name="schoring_schemes">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	122 <param name="score_matrix" argument="-p" type="select" multiple="false" label="Match/mismatch score matrix.">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	123 <option value="AT77">AT77</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	124 <option value="ATMAP">ATMAP</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	125 <option value="BISF">BISF</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	126 <option value="BISR">BISR</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	127 <option value="BL62">BLOSUM62</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	128 <option value="BL80" selected="true">BLOSUM80</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	129 <option value="HOXD70">HOXD70</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	130 <option value="MIQS">MIQS</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	131 <option value="PAM10">PAM10</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	132 <option value="PAM30">PAM30</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	133 <option value="scoreFile">Other score matrix</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	134 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	135 <when value="AT77">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	136 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	137 <expand macro="cost_macro" a="15" b="2"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	138 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	139 <when value="ATMAP">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	140 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	141 <expand macro="cost_macro" a="24" b="6"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	142 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	143 <when value="BISF">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	144 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	145 <expand macro="cost_macro" a="21" b="9"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	146 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	147 <when value="BISR">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	148 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	149 <expand macro="cost_macro" a="21" b="9"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	150 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	151 <when value="BL62">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	152 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	153 <expand macro="cost_macro" a="11" b="2"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	154 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	155 <when value="BL80">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	156 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	157 <expand macro="cost_macro" a="7" b="1"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	158 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	159 <when value="HOXD70">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	160 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	161 <expand macro="cost_macro" a="400" b="30"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	162 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	163 <when value="MIQS">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	164 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	165 <expand macro="cost_macro" a="13" b="2"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	166 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	167 <when value="PAM10">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	168 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	169 <expand macro="cost_macro" a="20" b="3"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	170 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	171 <when value="PAM30">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	172 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	173 <expand macro="cost_macro" a="13" b="3"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	174 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	175 <when value="scoreFile">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	176 <param name="scoreMatrixFile" type="data" format="txt" label="Score matrix file" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	177 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	178 </conditional>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	179 <param argument="-s" type="select" multiple="false" label="Strand">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	180 <option value="0">Reverse</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	181 <option value="1">Forward</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	182 <option value="2" selected="true">Both</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	183 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	184 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	185 <when value="prot">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	186 <conditional name="schoring_schemes">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	187 <param name="score_matrix" argument="-p" type="select" multiple="false" label="Match/mismatch score matrix.">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	188 <option value="AT77">AT77</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	189 <option value="ATMAP">ATMAP</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	190 <option value="BISF">BISF</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	191 <option value="BISR">BISR</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	192 <option value="BL62" selected="true">BLOSUM62</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	193 <option value="BL80">BLOSUM80</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	194 <option value="HOXD70">HOXD70</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	195 <option value="MIQS">MIQS</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	196 <option value="PAM10">PAM10</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	197 <option value="PAM30">PAM30</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	198 <option value="scoreFile">Other score matrix</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	199 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	200 <when value="AT77">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	201 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	202 <expand macro="cost_macro" a="15" b="2"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	203 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	204 <when value="ATMAP">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	205 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	206 <expand macro="cost_macro" a="24" b="6"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	207 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	208 <when value="BISF">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	209 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	210 <expand macro="cost_macro" a="21" b="9"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	211 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	212 <when value="BISR">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	213 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	214 <expand macro="cost_macro" a="21" b="9"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	215 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	216 <when value="BL62">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	217 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	218 <expand macro="cost_macro" a="11" b="2"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	219 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	220 <when value="BL80">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	221 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	222 <expand macro="cost_macro" a="7" b="1"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	223 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	224 <when value="HOXD70">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	225 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	226 <expand macro="cost_macro" a="400" b="30"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	227 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	228 <when value="MIQS">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	229 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	230 <expand macro="cost_macro" a="13" b="2"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	231 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	232 <when value="PAM10">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	233 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	234 <expand macro="cost_macro" a="20" b="3"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	235 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	236 <when value="PAM30">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	237 <expand macro="score_macro"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	238 <expand macro="cost_macro" a="13" b="3"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	239 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	240 <when value="scoreFile">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	241 <param name="scoreMatrixFile" type="data" format="txt" label="Score matrix file" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	242 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	243 </conditional>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	244 <param argument="-s" type="select" multiple="false" label="Strand">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	245 <option value="0">Reverse</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	246 <option value="1" selected="true">Forward</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	247 <option value="2">Both</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	248 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	249 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	250 </conditional>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	251
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	252 <section name="repeats_misc" title="Specify lowercase-marking of repeats. (-R)" expanded="false">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	253 <param name="uppercase_misc" type="select" multiple="false" label="Input sequences to uppercase.">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	254 <option value="0">Convert the input sequences to uppercase while reading them.(0)</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	255 <option value="1" selected="true">Keep any lowercase in the input sequences.(1)</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	256 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	257 <param name="simple_repeat_misc" type="select" multiple="false" label="Check for simple repeats.">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	258 <option value="0" selected="true">Do not check for simple repeats.(0)</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	259 <option value="1">Convert simple repeats to lowercase.(1)</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	260 <option value="2">Convert simple DNA repeats to lowercase.(2)</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	261 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	262 </section>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	263
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	264 <section name="evalue_opt" title="E-value options" expanded="false">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	265 <param argument="-D" type="integer" value="1000000" label="Query letters per random alignment (-D)"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	266 <!--<param argument="-E" type="integer" value="1e+18" label="Maximum expected alignments per square giga"/>-->
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	267 </section>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	268
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	269 <section name="init_match_opt" title="Initial-match options" expanded="false">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	270 <param argument="-m" type="integer" value="10" min="1" label="Maximum initial matches per query position"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	271 <param argument="-l" type="integer" value="1" min="1" label="Minimum length for initial matches"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	272 <!-- Infinity -->
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	273 <param argument="-L" type="integer" value="999999999" min="1" label="Maximum length for initial matches"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	274 <param argument="-k" type="integer" value="1" min="1" label="Use initial matches starting at every k-th position in each query"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	275 <param argument="-W" type="integer" value="1" min="1" label="Use minimum positions in sliding windows of W consecutive positions"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	276 </section>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	277
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	278 <section name="misc_opt" title="Miscellaneous options" expanded="false">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	279 <param argument="-S" type="select" multiple="false" label="Score matrix applies to forward strand of :">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	280 <option value="0" selected="true">Reference</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	281 <option value="1">Query</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	282 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	283 <param argument="-K" type="integer" value="0" min="0" label="Omit alignments whose query range lies in >= K others with > score"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	284 <param argument="-C" type="integer" value="0" min="0" label="Omit gapless alignments in >= C others with > score-per-length"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	285 <!--<param name="omit_gap" argument="-M" type="integer" value="" label="Find minimum-difference alignments (faster but cruder)"/>-->
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	286
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	287 <param argument="-T" type="select" multiple="false" label="Type of alignment">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	288 <option value="0" selected="true">Local</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	289 <option value="1">Overlap</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	290 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	291 <param argument="-n" type="integer" value="10" min="0" label="Maximum gapless alignments per query position" help="Infinity if m=0"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	292 <!--<param name="max_gap_align" argument="-N" type="integer" value="0" label="Stop after the first N alignments per query strand"/>-->
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	293
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	294 <!-- Condition lastdb : 2 if lastdb -c and Q<5 -->
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	295 <param argument="-u" type="select" multiple="false" label="Mask lowercase during extensions.">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	296 <option value="0" selected="true">Never.(0)</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	297 <option value="1">Gapless.(1)</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	298 <option value="2">Gapless+postmask.(2)</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	299 <option value="3">Always.(3)</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	300 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	301 <param argument="-w" type="integer" value="1000" min="0" label="Suppress repeats inside exact matches, offset by less or equal this distance. Use 0 to set this off" help="Use 0 to turn this off"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	302
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	303 <!-- https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi -->
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	304 <!-- Condition if ADN vs prot and -F -->
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	305 <param argument="-G" type="select" multiple="false" label="Genetic code.">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	306 <option value="1" selected="true">Standard Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	307 <option value="2">Vertebrate Mitochondrial Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	308 <option value="3">Yeast Mitochondrial Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	309 <option value="4">Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	310 <option value="5">Invertebrate Mitochondrial Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	311 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	312 <option value="9">Echinoderm and Flatworm Mitochondrial Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	313 <option value="10">Euplotid Nuclear Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	314 <option value="11">Bacterial, Archaeal and Plant Plastid Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	315 <option value="12">Alternative Yeast Nuclear Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	316 <option value="13">Ascidian Mitochondrial Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	317 <option value="14">Alternative Flatworm Mitochondrial Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	318 <option value="16">Chlorophycean Mitochondrial Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	319 <option value="21">Trematode Mitochondrial Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	320 <option value="22">Scenedesmus obliquus Mitochondrial Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	321 <option value="23">Thraustochytrium Mitochondrial Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	322 <option value="24">Pterabranchia Mitochondrial Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	323 <option value="25">Candidate Division SR1 and Gracilibacteria Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	324 <option value="26">Pachysolen tannophilus Nuclear Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	325 <option value="27">Karyorelict Nuclear Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	326 <option value="28">Condylostoma Nuclear Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	327 <option value="29">Mesodinium Nuclear Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	328 <option value="30">Peritrich Nuclear Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	329 <option value="31">Blastocrithidia Nuclear Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	330 <option value="33">Cephalodiscidae Mitochondrial UAA-Tyr Code</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	331 <!-- Add filename option with <repeat> -->
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	332 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	333
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	334 <!--<param name="temperature" argument="-t" type="integer" value="1/lambda" label="Temperature for calculating probabilities"/>-->
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	335 <param argument="-g" type="integer" value="1" min="0" label="Gamma parameter for gamma-centroid and LAMA"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	336 </section>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	337 </section>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	338 </inputs>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	339
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	340 <outputs>
5 187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	341 <data name="outfile" format="maf" label="LAST align from ${on_string}" >
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	342 <change_format>
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	343 <when input="f" value="MAF" format="maf" />
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	344 <when input="f" value="TAB" format="tabular" />
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	345 <when input="f" value="BlastTab" format="tabular" />
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	346 <when input="f" value="BlastTab+" format="tabular" />
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	347 </change_format>
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	348 </data>
0 7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	349 </outputs>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	350
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	351 <tests>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	352 <test>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	353 <conditional name="db_opts">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	354 <param name="db_opts_input" value="db"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	355 <param name="database" value="humdb"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	356 </conditional>
7 657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	357 <param name="query_seq" value="fuguMito.fa.gz" ftype="fasta.gz"/>
0 7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	358 <output name="outfile" ftype="maf" file="last_align_gen.maf" lines_diff="2"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	359 </test>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	360 <test>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	361 <conditional name="db_opts">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	362 <param name="db_opts_input" value="db"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	363 <param name="database" value="hedgdb"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	364 </conditional>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	365 <section name="lastal">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	366 <conditional name="isprotein">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	367 <param name="lastal_protein" value="prot"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	368 </conditional>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	369 </section>
5 187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	370 <param name="query_seq" value="hedgehog_prot_drosophila.fa" ftype="fasta"/>
0 7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	371 <output name="outfile" ftype="maf" file="last_align_prot.maf" lines_diff="2"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	372 </test>
5 187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	373 <test>
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	374 <conditional name="db_opts">
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	375 <param name="db_opts_input" value="db"/>
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	376 <param name="database" value="humdb-sanger"/>
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	377 </conditional>
7 657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba" iuc parents: 5 diff changeset	378 <param name="query_seq" value="fuguMito.fq.gz" ftype="fastqsanger.gz"/>
5 187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	379 <section name="lastal">
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	380 <param name="Q" value="1"/>
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	381 </section>
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	382 <output name="outfile" ftype="maf" file="last_align_fastq.maf" lines_diff="2"/>
187b3c87902b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db" iuc parents: 4 diff changeset	383 </test>
0 7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	384 </tests>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	385
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	386 <help>@LAST_HELP@</help>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	387 <citations><expand macro="citations"/></citations>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8" iuc parents: diff changeset	388 </tool>

Mercurial > repos > iuc > last

annotate lastal.xml @ 10:a07c62dc88f9 draft default tip