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