| Previous changeset 0:b8be455c27d1 (2011-08-02) Next changeset 2:d1aebb0acee7 (2013-05-30) |
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Commit message:
Uploaded v0.0.4, which adds a unit test |
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modified:
tools/protein_analysis/clinod.txt tools/protein_analysis/clinod.xml |
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added:
test-data/four_human_proteins.clinod-1.3.tabular test-data/four_human_proteins.fasta |
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| diff -r b8be455c27d1 -r 221d7dca03a5 test-data/four_human_proteins.clinod-1.3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins.clinod-1.3.tabular Tue Apr 16 13:01:54 2013 -0400 |
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| @@ -0,0 +1,4 @@ +#ID Start End NOLS +sp|Q9NSY1|BMP2K_HUMAN 965 998 SQQQKVKQRSLQKLSSRQRRTKQDMSKSNGKRHH +sp|Q9NSY1|BMP2K_HUMAN 1000 1035 TPTSTKKTLKPTYRTPERARRHKKVGRRDSQSSNEF +sp|P06213|INSR_HUMAN 286 307 CQDLHHKCKNSRRQGCHQYVIH |
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| diff -r b8be455c27d1 -r 221d7dca03a5 test-data/four_human_proteins.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins.fasta Tue Apr 16 13:01:54 2013 -0400 |
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| @@ -0,0 +1,61 @@ +>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 +MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRF +SQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMK +REYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFER +VANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK +CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHAD +CDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREF +HHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL +>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 +MKKFSRMPKSEGGSGGGAAGGGAGGAGAGAGCGSGGSSVGVRVFAVGRHQVTLEESLAEG +GFSTVFLVRTHGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSIS +DNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRD +LKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGG +KPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEP +DPEHRPDIFQVSYFAFKFAKKDCPVSNINNSSIPSALPEPMTASEAAARKSQIKARITDT +IGPTETSIAPRQRPKANSATTATPSVLTIQSSATPVKVLAPGEFGNHRPKGALRPGNGPE +ILLGQGPPQQPPQQHRVLQQLQQGDWRLQQLHLQHRHPHQQQQQQQQQQQQQQQQQQQQQ +QQQQQQHHHHHHHHLLQDAYMQQYQHATQQQQMLQQQFLMHSVYQPQPSASQYPTMMPQY +QQAFFQQQMLAQHQPSQQQASPEYLTSPQEFSPALVSYTSSLPAQVGTIMDSSYSANRSV +ADKEAIANFTNQKNISNPPDMSGWNPFGEDNFSKLTEEELLDREFDLLRSNRLEERASSD +KNVDSLSAPHNHPPEDPFGSVPFISHSGSPEKKAEHSSINQENGTANPIKNGKTSPASKD +QRTGKKTSVQGQVQKGNDESESDFESDPPSPKSSEEEEQDDEEVLQGEQGDFNDDDTEPE +NLGHRPLLMDSEDEEEEEKHSSDSDYEQAKAKYSDMSSVYRDRSGSGPTQDLNTILLTSA +QLSSDVAVETPKQEFDVFGAVPFFAVRAQQPQQEKNEKNLPQHRFPAAGLEQEEFDVFTK +APFSKKVNVQECHAVGPEAHTIPGYPKSVDVFGSTPFQPFLTSTSKSESNEDLFGLVPFD +EITGSQQQKVKQRSLQKLSSRQRRTKQDMSKSNGKRHHGTPTSTKKTLKPTYRTPERARR +HKKVGRRDSQSSNEFLTISDSKENISVALTDGKDRGNVLQPEESLLDPFGAKPFHSPDLS +WHPPHQGLSDIRADHNTVLPGRPRQNSLHGSFHSADVLKMDDFGAVPFTELVVQSITPHQ +SQQSQPVELDPFGAAPFPSKQ +>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 +MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHL +QILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYAL +VIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNE +ECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECL +GNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQG +CHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGC +TVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETL +EIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQE +RNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQ +NVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFS +DERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWE +RQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQIL +KELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAF +PNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYV +SARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCV +SRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIG +PLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSR +EKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKG +FTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAENNPGRPPPTLQEMIQMA +AEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPV +RWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDN +CPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPESEELEME +FEDMENVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIPYTHMNGGKKNGRILTLPRSN +PS +>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY +VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG +GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP +EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES +ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI +YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA |
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| diff -r b8be455c27d1 -r 221d7dca03a5 tools/protein_analysis/clinod.txt --- a/tools/protein_analysis/clinod.txt Tue Aug 02 06:51:52 2011 -0400 +++ b/tools/protein_analysis/clinod.txt Tue Apr 16 13:01:54 2013 -0400 |
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| @@ -39,6 +39,9 @@ ======= v0.0.1 - Initial public release +v0.0.2 - Treat non-zero return codes as errors +v0.0.3 - Describe output table in help +v0.0.4 - Added unit test Developers @@ -47,16 +50,18 @@ This script and related tools are being developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools -For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: -$ tar -czf clinod.tar.gz tools/protein_analysis/clinod.xml tools/protein_analysis/clinod.txt +$ tar -czf clinod.tar.gz tools/protein_analysis/clinod.xml tools/protein_analysis/clinod.txt test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular Check this worked: $ tar -tzf clinod.tar.gz tools/protein_analysis/clinod.xml tools/protein_analysis/clinod.txt +test-data/four_human_proteins.fasta +test-data/four_human_proteins.clinod-1.3.tabular Licence (MIT/BSD style) |
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| diff -r b8be455c27d1 -r 221d7dca03a5 tools/protein_analysis/clinod.xml --- a/tools/protein_analysis/clinod.xml Tue Aug 02 06:51:52 2011 -0400 +++ b/tools/protein_analysis/clinod.xml Tue Apr 16 13:01:54 2013 -0400 |
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| @@ -1,10 +1,15 @@ -<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.1"> +<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.4"> <description>Find nucleolar localization signals (NoLSs) in protein sequences</description> <command> java -jar /opt/clinod/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=8 -f=MEDIUM_TAB -nonols -clean_sequence ##I want the number of threads to be a Galaxy config option... - ##TODO - Make the -clean_sequece argument a parameter? + ##TODO - Make the -clean_sequence argument a parameter? </command> + <stdio> + <!-- Assume anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> <inputs> <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> </inputs> @@ -14,8 +19,14 @@ <requirements> <requirement type="binary">java</requirement> </requirements> + <tests> + <test> + <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" /> + <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" /> + </test> + </tests> <help> - + **What it does** This calls the command line version of the NoD tool from the Barton Group for @@ -28,14 +39,19 @@ The input is a FASTA file of protein sequences, and the output is tabular with four columns (multiple rows per protein): - * Sequence identifier - * Start of NoLS - * End of NoLS - * NoLS sequence +====== =================== +Column Description +------ ------------------- + 1 Sequence identifier + 2 Start of NoLS + 3 End of NoLS + 4 NoLS sequence +====== =================== If a sequence has no predicted NoLS, then there is no line in the output file for it. + **References** M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton. @@ -45,7 +61,8 @@ M. S. Scott, P. V. Troshin and G. J. Barton. NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. -BMC Bioinformatics, in press, 2011. +BMC Bioinformatics, 12:317, 2011. +http://dx.doi.org/10.1186/1471-2105-12-317 http://www.compbio.dundee.ac.uk/www-nod/ |