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comparison lasttrain.xml @ 0:7f7e48d3b85d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
author iuc
date Wed, 17 Jun 2020 10:20:20 +0000
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children 036d64816c8b
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-1:000000000000 0:7f7e48d3b85d
1 <tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01">
2
3 <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description>
4
5 <macros>
6 <import>macros_last.xml</import>
7 </macros>
8
9 <requirements>
10 <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
11 </requirements>
12
13 <command detect_errors="exit_code"><![CDATA[
14 #if $db_opts.db_opts_input == 'lastdb'
15 ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
16 #end if
17
18 last-train
19
20 -Q $init_options.Q
21
22 -r $init_options.r
23 -q $init_options.q
24
25 -a $init_options.cost_opt.a
26 -b $init_options.cost_opt.b
27 -A $init_options.cost_opt.A
28 -B $init_options.cost_opt.B
29
30 -D $last_train_opt.align_opt.D
31 -E $last_train_opt.align_opt.E
32 -s $last_train_opt.align_opt.s
33 -S $last_train_opt.align_opt.S
34 -T $last_train_opt.align_opt.T
35 -m $last_train_opt.align_opt.m
36 -k $last_train_opt.align_opt.k
37 -X $last_train_opt.align_opt.X
38
39 -P \${GALAXY_SLOTS:-1}
40
41 #if $db_opts.db_opts_input == 'db'
42 '${"' '".join(str($db_opts.database.fields.path).split(","))}'
43 #else if $db_opts.db_opts_input == 'lastdb'
44 'db_files/lastdb'
45 #end if
46
47 '$query_fasta'
48
49 >'$outfile'
50
51 ]]></command>
52
53 <inputs>
54 <expand macro="input_db" />
55 <param name="query_fasta" type="data" format="FASTA" label="Queries input files" />
56 <conditional name="init_options">
57 <param argument="-Q" type="select" multiple="false" label="Input format">
58 <option value="0" selected="true">Fasta or fastq-ignore</option>
59 <option value="1">Fastq-sanger</option>
60 </param>
61 <when value="0">
62 <param argument="-r" type="integer" value="5" label="Match score"/>
63 <param argument="-q" type="integer" value="5" label="Mismatch cost"/>
64 <expand macro="cost_macro" a="15" b="3"/>
65 </when>
66 <when value="1">
67 <param argument="-r" type="integer" value="6" label="Match score"/>
68 <param argument="-q" type="integer" value="18" label="Mismatch cost"/>
69 <expand macro="cost_macro" a="21" b="9"/>
70 </when>
71 </conditional>
72
73 <section name="last_train_opt" title="Last-train options" expanded="false">
74 <!-- Training options missing -->
75 <section name="align_opt" title="Alignment options" expanded="true">
76 <param argument="-D" type="integer" value="1000000" label="Query letters per random alignment"/>
77 <param argument="-E" type="integer" value="10" label="Maximum expected alignments per square giga"/>
78 <param argument="-s" type="select" multiple="false" label="Query strand to use">
79 <option value="0">Reverse</option>
80 <option value="1" selected="true">Forward</option>
81 <option value="2">Both</option>
82 </param>
83 <param argument="-S" type="select" multiple="false" label="Score matrix applies to forward strand of:">
84 <option value="0">Reference</option>
85 <option value="1" selected="true">Query</option>
86 </param>
87 <!--<param name="gapless_align" argument="-C" type="integer" value="" label="Omit gapless alignments in COUNT others with > score-per-length"/>-->
88 <param argument="-T" type="select" multiple="false" label="Type of alignment:">
89 <option value="0" selected="true">Local</option>
90 <option value="1">Overlap</option>
91 </param>
92 <param argument="-m" type="integer" value="10" label="Maximum initial matches per query position"/>
93 <param argument="-k" type="integer" value="1" label="Use initial matches starting at every STEP-th position in each query"/>
94 <param argument="-X" type="select" multiple="false" label="N/X is ambiguous in:">
95 <option value="0" selected="true">Neither sequence</option>
96 <option value="1">Reference</option>
97 <option value="2">Query</option>
98 <option value="3">Both</option>
99 </param>
100 </section>
101 </section>
102 </inputs>
103
104 <outputs>
105 <data name="outfile" format="txt" label="LAST train from ${on_string}" />
106 </outputs>
107
108 <tests>
109 <test>
110 <conditional name="db_opts">
111 <param name="db_opts_input" value="db"/>
112 <param name="database" value="humdb"/>
113 </conditional>
114 <param name="query_fasta" value="fuguMito.fa"/>
115 <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/>
116 </test>
117 </tests>
118
119 <help>@LAST_HELP@</help>
120 <citations><expand macro="citations"/></citations>
121 </tool>