Mercurial > repos > fernando > protein_funcional_analysis_similarities
comparison interpro/paso2.xml @ 0:c342ebb50f0b draft default tip
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author | fernando |
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date | Thu, 22 May 2014 05:09:07 -0400 |
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-1:000000000000 | 0:c342ebb50f0b |
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1 <tool id="BLaGiFer_2" name="Sequences assortment" version="1.0.0"> | |
2 <description> Select the most similar sequences</description> | |
3 <command interpreter="bash"> | |
4 ./paso2.sh "$infile" "$outfile" "$numsequences" | |
5 </command> | |
6 | |
7 <inputs> | |
8 <param name="infile" type="data" format="txt" label="ids file"/> | |
9 | |
10 <param name="numsequences" type="select" label="Select number of sequences" help=""> | |
11 <option value="1">1</option> | |
12 <option value="2">2</option> | |
13 <option value="3">3</option> | |
14 <option value="4">4</option> | |
15 <option value="5" selected="true">5</option> | |
16 </param> | |
17 </inputs> | |
18 <outputs> | |
19 <data format="fasta" name="outfile"/> | |
20 </outputs> | |
21 | |
22 <stdio><exit_code range="1:" level="fatal" description="Error" /></stdio> | |
23 <help> | |
24 | |
25 **What it does** | |
26 | |
27 From the output text file generated in RemoteBlast wrapper, the user may choose from the five first sequences. The result is stored in a fasta file. | |
28 | |
29 **Dependencies** | |
30 | |
31 This tool only runs UNIX commands, awk is necessary to be installed. | |
32 | |
33 | |
34 ##### | |
35 Input | |
36 ##### | |
37 | |
38 The input text file generated by RemoteBlast is necessary. | |
39 | |
40 ###### | |
41 | |
42 The Blast results are saved on an output text file. | |
43 | |
44 | |
45 | |
46 Example Output | |
47 -------------- | |
48 | |
49 >sp|Q09443|ARP6_CAEEL Actin-like protein C08B11.6 OS=Caenorhabditis elegans GN=arp-6 PE=2 SV=3 | |
50 MSLTTIIFDNGGHNMKIGTIDSESPRLVPNSIVKAKHEKKRVFVAHEQEECSDKFSLFYV | |
51 RPIERGYVVNWDTQQQIWEKTFGSMDVEASTSRIALTDNNYLIPALPDVSSEILFDYFGF | |
52 TEVHKTSASTLVAKHSNKINNEKCAVVVDSGFSWTTVASFVNGMLIQDSVIRIDVGGKAL | |
53 TNKLKDWVSYRQLNVSEETYVINECKEDLCFVSQNFDESMKEARNRFQENTTMKRYIMPD | |
54 FHSTFRGVVKDVKEPHDPQIPSIHLGVERFAIPEILFNPSDIDIDQCGVAEAVIESICQC | |
55 PEALRPALAENIIVIGGSSCFPGFRERLEREVRSMLPAEYGLNVSNDVINPQTHSWHCGQ | |
56 ELLTASKVPWINRKDWDERGDSLEFSNFFQTLVQSDELKGTRNFDDQREKSPKEDEDF | |
57 >sp|Q9D864|ARP6_MOUSE Actin-related protein 6 OS=Mus musculus GN=Actr6 PE=1 SV=2 | |
58 MTTLVLDNGAYNAKIGYSHDSVSVIPNCQFRSKTARLKTFTANQIDEIKDPSGLFYILPF | |
59 QKGYLVNWDVQRQVWDYLFGKEMYQVDFLDTNIIITEPYFNFTSIQESMNEILFEEYQFQ | |
60 AVLRVNAGALSAHRYFRDNPSELCCIIVDSGYSFTHIVPYCRSKKKKEAIIRINVGGKLL | |
61 TNHLKEIISYRQLHVMDETHVINQVKEDVCYVSQDFYRDMDIAKLKGEDNTVMIDYVLPD | |
62 FSTIKKGFCKPREEMVLSGKYKSGEQILRLANERFAVPEILFNPSDIGIQEMGIPEAIVY | |
63 SIQNLPEEMQPHFFKNIVLTGGNSLFPGFRERVYSEVRCLTPTDYDVSVVLPENPITYSW | |
64 EGGKLISENDDFEDMVVTREDYEENGHSVCEEKFDI | |
65 >sp|Q9GZN1|ARP6_HUMAN Actin-related protein 6 OS=Homo sapiens GN=ACTR6 PE=1 SV=1 | |
66 MTTLVLDNGAYNAKIGYSHENVSVIPNCQFRSKTARLKTFTANQIDEIKDPSGLFYILPF | |
67 QKGYLVNWDVQRQVWDYLFGKEMYQVDFLDTNIIITEPYFNFTSIQESMNEILFEEYQFQ | |
68 AVLRVNAGALSAHRYFRDNPSELCCIIVDSGYSFTHIVPYCRSKKKKEAIIRINVGGKLL | |
69 TNHLKEIISYRQLHVMDETHVINQVKEDVCYVSQDFYRDMDIAKLKGEENTVMIDYVLPD | |
70 FSTIKKGFCKPREEMVLSGKYKSGEQILRLANERFAVPEILFNPSDIGIQEMGIPEAIVY | |
71 SIQNLPEEMQPHFFKNIVLTGGNSLFPGFRDRVYSEVRCLTPTDYDVSVVLPENPITYAW | |
72 EGGKLISENDDFEDMVVTREDYEENGHSVCEEKFDI | |
73 >sp|Q9DEE9|ARP6_CHICK Actin-related protein 6 OS=Gallus gallus GN=ACTR6 PE=2 SV=1 | |
74 MATLVLDNGAYNAKIGYSHAHVSVIPNCQFRSKTARLKTFTANQLDEIKDPSGLFYILPF | |
75 QKGYLVNWDVQRQVWDYLFGKEMYQVDFVDTNIIITEPYFNFSSIQESMNEILFEEYQFQ | |
76 AVLRVNAGALSAHRYFRDNPSELCCIIVDSGYSFTHIVPYCRSKKKKEAIIRINVGGKLL | |
77 TNHLKEIISYRQLHVMDETHVINQVKEDVCYVSQDFYKDMEIAKLKGEENTVMVDYVLPD | |
78 FSTIKKGFCKPREEMVLSGKYKTGEQILRLTNERFAVPEILFHPSDIGIQEMGIPEAIVD | |
79 SIQNLPEEMQPHFFKNIVLTGGNTLFPGFRDRVYSEVRCLTPTDYDVSVVLPENPITYSW | |
80 EGGKLISENDDFEDLVVTREDYEEHGHNICEEKFDI | |
81 | |
82 **Galaxy Wrapper Authors**:: | |
83 | |
84 * Ginés Almagro | |
85 * Laura Entrambasaguas | |
86 * Fernando Pérez | |
87 </help> | |
88 </tool> |