Mercurial > repos > iuc > last

annotate lasttrain.xml @ 10:a07c62dc88f9 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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_train" name="LAST-train" version="@TOOL_VERSION@+galaxy0" 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 the rates (probabilities) of insertion, deletion, and substitutions between two sets of 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: 6
diff changeset
14 set -e -o pipefail;
0
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
15 #if $db_opts.db_opts_input == 'lastdb'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
16 ln -s '$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
17 #end if
7
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
iuc
parents: 6
diff changeset
18 #if $query_fasta.ext.endswith('.gz')
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
iuc
parents: 6
diff changeset
19 zcat
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
iuc
parents: 6
diff changeset
20 #else
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
iuc
parents: 6
diff changeset
21 cat
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
iuc
parents: 6
diff changeset
22 #end if
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
iuc
parents: 6
diff changeset
23 '$query_fasta' | last-train
0
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
24
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
25 -Q $init_options.Q
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
26 -r $init_options.r
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
27 -q $init_options.q
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
28 -a $init_options.cost_opt.a
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
29 -b $init_options.cost_opt.b
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
30 -A $init_options.cost_opt.A
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
31 -B $init_options.cost_opt.B
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
32 -D $last_train_opt.align_opt.D
6
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
33 #if $last_train_opt.align_opt.E != ""
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
34 -E $last_train_opt.align_opt.E
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
35 #end if
0
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
36 -s $last_train_opt.align_opt.s
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
37 -S $last_train_opt.align_opt.S
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
38 -T $last_train_opt.align_opt.T
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
39 -m $last_train_opt.align_opt.m
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
40 -k $last_train_opt.align_opt.k
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
41 -X $last_train_opt.align_opt.X
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
42
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
43 -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
44
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
45 #if $db_opts.db_opts_input == 'db'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
46 '${"' '".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
47 #else if $db_opts.db_opts_input == 'lastdb'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
48 'db_files/lastdb'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
49 #end if
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
50
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
51 >'$outfile'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
52
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
53 ]]></command>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
54
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
55 <inputs>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
56 <expand macro="input_db" />
7
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
iuc
parents: 6
diff changeset
57 <param name="query_fasta" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Queries input files" />
0
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
58 <conditional name="init_options">
4
036d64816c8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 67b8e5adffa4015ee60b1b4a0cd220f632ba1082"
iuc
parents: 0
diff changeset
59 <param argument="-Q" type="select" multiple="false" label="Query input format">
036d64816c8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 67b8e5adffa4015ee60b1b4a0cd220f632ba1082"
iuc
parents: 0
diff changeset
60 <option value="0" selected="true">FASTA</option>
0
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
61 <option value="1">Fastq-sanger</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
62 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
63 <when value="0">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
64 <param argument="-r" type="integer" value="5" label="Match score"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
65 <param argument="-q" type="integer" value="5" label="Mismatch cost"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
66 <expand macro="cost_macro" a="15" b="3"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
67 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
68 <when value="1">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
69 <param argument="-r" type="integer" value="6" label="Match score"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
70 <param argument="-q" type="integer" value="18" label="Mismatch cost"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
71 <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
72 </when>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
73 </conditional>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
74
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
75 <section name="last_train_opt" title="Last-train options" expanded="false">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
76 <!-- Training options missing -->
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
77 <section name="align_opt" title="Alignment options" expanded="true">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
78 <param argument="-D" type="integer" value="1000000" label="Query letters per random alignment"/>
6
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
79 <param argument="-E" type="integer" value="" optional="true" label="Maximum expected alignments per square giga"/>
0
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
80 <param argument="-s" type="select" multiple="false" label="Query strand to use">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
81 <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
82 <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
83 <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
84 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
85 <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
86 <option value="0">Reference</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
87 <option value="1" selected="true">Query</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
88 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
89 <!--<param name="gapless_align" argument="-C" type="integer" value="" label="Omit gapless alignments in COUNT 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
90 <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
91 <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
92 <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
93 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
94 <param argument="-m" type="integer" value="10" 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
95 <param argument="-k" type="integer" value="1" label="Use initial matches starting at every STEP-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
96 <param argument="-X" type="select" multiple="false" label="N/X is ambiguous in:">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
97 <option value="0" selected="true">Neither sequence</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
98 <option value="1">Reference</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
99 <option value="2">Query</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="3">Both</option>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
101 </param>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
102 </section>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
103 </section>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
104 </inputs>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
105
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
106 <outputs>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
107 <data name="outfile" format="txt" label="LAST train from ${on_string}" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
108 </outputs>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
109
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
110 <tests>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
111 <test>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
112 <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
113 <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
114 <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
115 </conditional>
6
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
116 <section name="last_train_opt">
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
117 <section name="align_opt">
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
118 <param name="E" value="10"/>
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
119 </section>
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
120 </section>
7
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
iuc
parents: 6
diff changeset
121 <param name="query_fasta" value="fuguMito.fa.gz" ftype="fasta.gz"/>
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
iuc
parents: 6
diff changeset
122 <output name="outfile" file="last_train_E.txt" ftype="txt" lines_diff="28"/>
6
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
123 </test>
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
124 <test>
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
125 <conditional name="db_opts">
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
126 <param name="db_opts_input" value="db"/>
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
127 <param name="database" value="humdb"/>
713be4796767 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
iuc
parents: 4
diff changeset
128 </conditional>
7
657fb614ee81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
iuc
parents: 6
diff changeset
129 <param name="query_fasta" value="fuguMito.fq.gz" ftype="fastqsanger.gz"/>
0
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
130 <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
131 </test>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
132 </tests>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
133
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
iuc
parents:
diff changeset
134 <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
135 <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
136 </tool>