Mercurial > repos > dereeper > subseq_protein

diff extract_proteic_seq_using_coordinates.xml @ 0:60507a6de56c draft

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author dereeper
date Sun, 16 Sep 2012 09:26:09 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_proteic_seq_using_coordinates.xml	Sun Sep 16 09:26:09 2012 -0400
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+<tool id="extract_proteic_seq_from_coordinates" name="Extract protein sequences">
+	<description>using coordinates</description>
+	<command interpreter="bash">./extract_proteic_seq_using_coordinates.sh $input $output $coordinates</command>
+	<inputs>
+		<param format="fasta" name="input" type="data" label="Protein FASTA file"/>	
+		<param format="txt" name="coordinates" type="data" label="Coordinates for extraction"/>
+	</inputs>
+	<outputs>
+		<data format="fasta" name="output" label="Extracted proteins"/>
+	</outputs>
+	<help>
+	
+.. class:: infomark
+
+**Program encapsulated in Galaxy by Southgreen**
+
+.. class:: infomark
+
+**extract_proteic_seq_using_coordinates.pl version 1.0, 2012**
+
+-----
+
+==========
+ Authors:
+==========
+
+**Dereeper A**
+
+-----
+
+===========
+ Overview:
+===========
+
+Extract sequences from a protein FASTA file using coordinates.  
+
+
+-----
+
+**Example**
+
+If the input dataset is::
+
+	>MCCS00001-0.9-1
+	MRLQLGLRRLHFLRRRDHCNHHRRGFATKYSGRVVVETDNGRSFAVEVDNPILQTDVRGY
+	PLPRRDLICKVVSILQSPPSTASSSSFDDLFMDLSDYLETLNVMITPSEASEILKSLKSP
+	NLALKFFQFCSSEIPDFRHNSFTYNRILLILSKAYLPNRLDLVRNILNEMDQSATGGSIS
+	TVNILIGIFSDGQEYGGIDELEKCLGLVKKWELSLNCYTYKCLMQGYLRLNDSKKALEVY
+	REMTRRGYKLDIFAYNMLLDALAKDEK
+	>MCCS00001-0.1-1
+	MRLNSRFGTSSLIHVSLVLLLCFKASGGSAERSSAFFIFGDSTVDPGNNNYIKTTPENQA
+	NYKPYGQNGFFKEPTGRFSDGRIIVDYIAEYAKLPIIPPYLQPSADYSHGVNFASGGAGI
+	LSTTNPGVVIDLKTQLEYFHKVQRSLAEKLGTAEAEEIISNAVYFISMGSNDYMGGYLGN
+	PEMQQLHPPEDYVRMVIGNLTQGIQELYDRGARKFGFLSLCPLGCLPALRVLNPKGHDAG
+	CFEQASALALAHSNALQAVLPNLELLLPKGFKYCNSNFYDWLLDRINDPTKYGFKEGESA
+	CCGAGPYRGIFTCGGTKKDPNYELCDNPSDYVWFDSFHPTERIHEQFAKALWDGLSPSVG
+	PYNLEGLFFNKQTIADVVDNPETQQIF
+
+Interval file must be in the form::
+
+	MCCS00001-0.9-1	2	6
+	MCCS00001-0.1-1	5	132
+
+Extracting sequences returns::
+
+	>MCCS00001-0.9-1
+	RLQLG
+	>MCCS00001-0.1-1
+	SRFGTSSLIHVSLVLLLCFKASGGSAERSSAFFIFGDSTVDPGNNNYIKTTPENQANYKP
+	YGQNGFFKEPTGRFSDGRIIVDYIAEYAKLPIIPPYLQPSADYSHGVNFASGGAGILSTT
+	NPGVVIDL
+
+
+	</help>
+</tool>