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comparison lastsplit.xml @ 0:9a7e91fc6562 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
author iuc
date Wed, 17 Jun 2020 14:50:21 -0400
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children 8705e0d74a0f
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-1:000000000000 0:9a7e91fc6562
1 <tool id="last_split" name="LAST-split" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01">
2
3 <description>finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA).</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-split
19
20 -f $output_format
21 #if $db_opts.db_opts_input == 'db'
22 -g '${"'" "'".join(str($db_opts.database.fields.path).split(","))}'
23 #else if $db_opts.db_opts_input == 'lastdb'
24 -g 'db_files/lastdb'
25 #end if
26
27 -d $lastsplit_opt.d
28 -c $lastsplit_opt.c
29 -t $lastsplit_opt.t
30 -M $lastsplit_opt.M
31 -S $lastsplit_opt.S
32 -m $lastsplit_opt.m
33 $lastsplit_opt.no_split
34 -b \${GALAXY_MEMORY_MB:-2G}
35
36 '$last_align'
37
38 >'$outfile'
39 ]]></command>
40
41 <inputs>
42 <expand macro="input_db" />
43 <param name="last_align" type="data" format="maf" label="LASTal data file" />
44 <param name="output_format" argument="-f" type="select" multiple="false" label="Output format">
45 <option value="MAF">MAF</option>
46 <option value="MAF+" selected="true">MAF+</option>
47 </param>
48 <section name="lastsplit_opt" title="Last-split options" expanded="false">
49 <param argument="-d" type="select" multiple="false" label="RNA direction">
50 <option value="0">Reverse</option>
51 <option value="1" selected="true">Forward</option>
52 <option value="2">Mixed</option>
53 </param>
54 <param argument="-c" type="float" value="0.004" label="Cis-splice probability per base"/>
55 <param argument="-t" type="float" value="0.00001" label="Trans-splice probability per base"/>
56 <param argument="-M" type="float" value="7" label="Mean of ln[intron length]"/>
57 <param argument="-S" type="float" value="1.7" label="Standard deviation of ln[intron length]"/>
58 <param argument="-m" type="float" value="1" label="Maximum mismap probability"/>
59 <!--<param name="score" argument="-s" type="int" value="lastal e" label="Minimum alignement score"/>-->
60 <param name="no_split" argument="-n" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Write original, not split, alignement."/>
61 </section>
62 </inputs>
63
64 <outputs>
65 <data name="outfile" format="maf" label="LAST split from ${on_string}" />
66 </outputs>
67
68 <tests>
69 <test>
70 <conditional name="db_opts">
71 <param name="db_opts_input" value="db"/>
72 <param name="database" value="humdb"/>
73 </conditional>
74 <param name="last_align" ftype="maf" value="last_align_gen.maf"/>
75 <output name="outfile" ftype="maf" file="last_split.maf"/>
76 </test>
77 </tests>
78
79 <help>@LAST_HELP@</help>
80 <citations><expand macro="citations"/></citations>
81 </tool>