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comparison interpro/paso2.xml @ 0:c342ebb50f0b draft default tip

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author fernando
date Thu, 22 May 2014 05:09:07 -0400
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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>