|
2
|
1 <tool id="extract_proteic_seq_from_coordinates" name="Extract protein sequences">
|
|
|
2 <description>using coordinates</description>
|
|
|
3 <command interpreter="perl">extract_proteic_seq_using_coordinates.pl -i $input -o $output -c $coordinates</command>
|
|
|
4 <inputs>
|
|
|
5 <param format="fasta" name="input" type="data" label="Protein FASTA file"/>
|
|
|
6 <param format="tabular" name="coordinates" type="data" label="Coordinates for extraction (tabular)"/>
|
|
|
7 </inputs>
|
|
|
8 <outputs>
|
|
|
9 <data format="fasta" name="output" label="Extracted proteins"/>
|
|
|
10 </outputs>
|
|
|
11 <help>
|
|
|
12
|
|
|
13 .. class:: infomark
|
|
|
14
|
|
|
15 **Program encapsulated in Galaxy by Southgreen**
|
|
|
16
|
|
|
17 .. class:: infomark
|
|
|
18
|
|
|
19 **extract_proteic_seq_using_coordinates.pl version 1.0, 2012**
|
|
|
20
|
|
|
21 -----
|
|
|
22
|
|
|
23 ==========
|
|
|
24 Authors:
|
|
|
25 ==========
|
|
|
26
|
|
|
27 **Dereeper A**
|
|
|
28
|
|
|
29 -----
|
|
|
30
|
|
|
31 ===========
|
|
|
32 Overview:
|
|
|
33 ===========
|
|
|
34
|
|
|
35 Extract sequences from a protein FASTA file using coordinates.
|
|
|
36
|
|
|
37
|
|
|
38 -----
|
|
|
39
|
|
|
40 **Example**
|
|
|
41
|
|
|
42 If the input dataset is::
|
|
|
43
|
|
|
44 >MCCS00001-0.9-1
|
|
|
45 MRLQLGLRRLHFLRRRDHCNHHRRGFATKYSGRVVVETDNGRSFAVEVDNPILQTDVRGY
|
|
|
46 PLPRRDLICKVVSILQSPPSTASSSSFDDLFMDLSDYLETLNVMITPSEASEILKSLKSP
|
|
|
47 NLALKFFQFCSSEIPDFRHNSFTYNRILLILSKAYLPNRLDLVRNILNEMDQSATGGSIS
|
|
|
48 TVNILIGIFSDGQEYGGIDELEKCLGLVKKWELSLNCYTYKCLMQGYLRLNDSKKALEVY
|
|
|
49 REMTRRGYKLDIFAYNMLLDALAKDEK
|
|
|
50 >MCCS00001-0.1-1
|
|
|
51 MRLNSRFGTSSLIHVSLVLLLCFKASGGSAERSSAFFIFGDSTVDPGNNNYIKTTPENQA
|
|
|
52 NYKPYGQNGFFKEPTGRFSDGRIIVDYIAEYAKLPIIPPYLQPSADYSHGVNFASGGAGI
|
|
|
53 LSTTNPGVVIDLKTQLEYFHKVQRSLAEKLGTAEAEEIISNAVYFISMGSNDYMGGYLGN
|
|
|
54 PEMQQLHPPEDYVRMVIGNLTQGIQELYDRGARKFGFLSLCPLGCLPALRVLNPKGHDAG
|
|
|
55 CFEQASALALAHSNALQAVLPNLELLLPKGFKYCNSNFYDWLLDRINDPTKYGFKEGESA
|
|
|
56 CCGAGPYRGIFTCGGTKKDPNYELCDNPSDYVWFDSFHPTERIHEQFAKALWDGLSPSVG
|
|
|
57 PYNLEGLFFNKQTIADVVDNPETQQIF
|
|
|
58
|
|
|
59 Interval file must be in the form::
|
|
|
60
|
|
|
61 MCCS00001-0.9-1 2 6
|
|
|
62 MCCS00001-0.1-1 5 132
|
|
|
63
|
|
|
64 Extracting sequences returns::
|
|
|
65
|
|
|
66 >MCCS00001-0.9-1
|
|
|
67 RLQLG
|
|
|
68 >MCCS00001-0.1-1
|
|
|
69 SRFGTSSLIHVSLVLLLCFKASGGSAERSSAFFIFGDSTVDPGNNNYIKTTPENQANYKP
|
|
|
70 YGQNGFFKEPTGRFSDGRIIVDYIAEYAKLPIIPPYLQPSADYSHGVNFASGGAGILSTT
|
|
|
71 NPGVVIDL
|
|
|
72
|
|
|
73
|
|
|
74 </help>
|
|
|
75 </tool>
|
