Mercurial > repos > edward-kirton > minimus2
comparison minimus2/minimus2.xml @ 0:937ba44abdb7 default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | edward-kirton |
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date | Tue, 07 Jun 2011 17:29:43 -0400 |
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1 <tool id="minimus2" name="Minimus2" version='1.0.1'> | |
2 <description>Merge two sets of assembled contig sequences</description> | |
3 <command interpreter='perl'>minimus2_wrapper.pl -tmpdir $contigs_outfile.extra_files_path $infile1 $infile2 $contigs_outfile $singletons_outfile | |
4 #if $prefix1.select == 'y': | |
5 -prefix1 $prefix1.prefix | |
6 #end if | |
7 #if $prefix2.select == 'y': | |
8 -prefix2 $prefix2.prefix | |
9 #end if | |
10 </command> | |
11 <inputs> | |
12 <param name="infile1" type="data" format="fasta" label="Contig sequences file 1"/> | |
13 <conditional name='prefix1'> | |
14 <param name='select' type='select' label='Rename contigs in file 1 by adding prefix?'> | |
15 <option value='y'>yes, add prefix</option> | |
16 <option value='n'>no, contig IDs are unique</option> | |
17 </param> | |
18 <when value='y'> | |
19 <param name="prefix" type="text" value="1" label="Prefix for sequences in file 1" /> | |
20 </when> | |
21 <when value='n'> | |
22 </when> | |
23 </conditional> | |
24 <param name="infile2" type="data" format="fasta" label="Contig sequences file 2"/> | |
25 <conditional name='prefix2'> | |
26 <param name='select' type='select' label='Rename contigs in file 2 by adding prefix?'> | |
27 <option value='y'>yes, add prefix</option> | |
28 <option value='n'>no, contig IDs are unique</option> | |
29 </param> | |
30 <when value='y'> | |
31 <param name="prefix" type="text" value="2" label="Prefix for sequences in file 2" /> | |
32 </when> | |
33 <when value='n'> | |
34 </when> | |
35 </conditional> | |
36 </inputs> | |
37 <outputs> | |
38 <data name="contigs_outfile" format="fasta" label="contigs" /> | |
39 <data name="singletons_outfile" format="fasta" label="singletons" /> | |
40 </outputs> | |
41 <help> | |
42 **What it does** | |
43 | |
44 minimus2 is part of the AMOS assembler package, designed for merging one or two sets of contig sequences. | |
45 | |
46 This tool preprocesses the Fasta input files prior to coassembly with minimus2 and separately returns the new contigs | |
47 and the sequences which did not co-assemble (singletons). | |
48 | |
49 The input sequences in each dataset must have unique IDs; use of the optional rename with prefix option avoids this. | |
50 | |
51 **Documentation** | |
52 | |
53 http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus2 | |
54 </help> | |
55 </tool> |