Mercurial > repos > eremeeva > sibelia
comparison tools/sibelia/init_sibelia.xml @ 5:7b5e87542bd8 draft default tip
Coming to conclusion. Testing.
author | eremeevaaa94@mail.ru |
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date | Sun, 13 Apr 2014 07:02:26 -0700 |
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2:74df95d8152a | 5:7b5e87542bd8 |
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1 <tool id="Sibelia" name="sibelia"> | |
2 <command interpreter="python"> | |
3 #if $p_s.p_s_select == "-s" #Sibelia_wrapper.py -s $p_s.simplification $ram -m $b_size $single_ou $postprocess -i $iter $fasta | |
4 #else #Sibelia_wrapper.py -k $p_s.cpfile $ram -m $b_size $single_ou $postprocess -i $iter $fasta | |
5 #end if# | |
6 </command> | |
7 <inputs> | |
8 <conditional name="p_s"> | |
9 <param name="p_s_select" type="select" label="Parameters set"> | |
10 <option value="-s">Select parameters set</option> | |
11 <option value="-k">Custom parameteres set</option> | |
12 </param> | |
13 <when value="-k"> | |
14 <param name="cpfile" size="50" type="text" label="File of custom parameters set" /> | |
15 </when> | |
16 <when value="-s"> | |
17 <param name="simplification" type="select" label="Simplification"> | |
18 <option value="loose">Loose</option> | |
19 <option value="fine">Fine</option> | |
20 </param> | |
21 </when> | |
22 </conditional> | |
23 <param name="ram" type="boolean" truevalue="-r" falsevalue="" label="Store temporary files in RAM?" /> | |
24 <param name="single_ou" type="boolean" truevalue="-a" falsevalue="" label="Find blocks that occur exactly once in each input sequence" /> | |
25 <param name="postprocess" type="boolean" truevalue="--nopostprocess" falsevalue="" label="Turn off postprocessing?" /> | |
26 <param name="iter" type="integer" value="4" label="Number of iterations" /> | |
27 <param name="b_size" type="integer" value="2000" label="Minimum block size" /> | |
28 <param name="fasta" size="50" type="text" label="Path to input fasta file" /> | |
29 </inputs> | |
30 <outputs> | |
31 <data format="txt" name="outperm" label="Genomes permutations" from_work_dir="genomes_permutations.txt" /> | |
32 <data format="txt" name="outblc" label="Blocks coords" from_work_dir="blocks_coords.txt" /> | |
33 <data format="txt" name="outcov" label="Coverage report" from_work_dir="coverage_report.txt" /> | |
34 <data format="html" name="outbld" label="Blocks diagram" from_work_dir="d3_blocks_diagram.html" /> | |
35 </outputs> | |
36 <!-- <tests> | |
37 <test> | |
38 <param name="p_s_select" value="-s" /> | |
39 <param name="simplification" value="loose" /> | |
40 <param name="ram" value="0" /> | |
41 <param name="single_ou" value="0" /> | |
42 <param name="postprocess" value="0" /> | |
43 <param name="fasta" value="Helicobacter_pylori.fasta" /> | |
44 </test> | |
45 <test> | |
46 <param name="p_s_select" value="-k" /> | |
47 <param name="cpfile" value="CPFile.txt" /> | |
48 <param name="ram" value="0" /> | |
49 <param name="single_ou" value="0" /> | |
50 <param name="postprocess" value="0" /> | |
51 <param name="fasta" value="Helicobacter_pylori.fasta" /> | |
52 </test> | |
53 </tests> --> | |
54 <help> | |
55 .. class:: infomark | |
56 Sibelia -- "Sibelia" is a tool for finding synteny blocks in closely related genomes, like different strains of the same bacterial species. It takes a set of FASTA files with genomes and locates coordinates of the synteny blocks in these sequences. It also represents genomes as permutations of the blocks. | |
57 </help> | |
58 </tool> |