| Previous changeset 6:ac9be1d4885d (2014-06-14) Next changeset 8:4294476e3f83 (2015-10-20) |
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Commit message:
Docker support and update for protk 1.4 |
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modified:
omssa.xml repository_dependencies.xml tool_dependencies.xml |
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added:
README.rst test-data/AASequences.fasta test-data/mr176-BSA100fmole_BA3_01_8168.d.mgf |
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removed:
README |
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| diff -r ac9be1d4885d -r 51f6c6446e69 README --- a/README Sat Jun 14 18:01:42 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -This package installs wrapper scripts for running OMSSA MS/MS searches - -Requirements: -This package depends on the galaxy_protk, protk_omssa and protk_blast packages -Please see instructions for those packages before installing |
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| diff -r ac9be1d4885d -r 51f6c6446e69 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Mar 26 20:04:12 2015 -0400 |
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| @@ -0,0 +1,42 @@ +OMSSA +===== + +Galaxy wrapper for the OMSSA tandem ms search tool + +Requirements +------------ + +This package uses protk_, omssa_ and blast_ which need to be present in order for the tool to work. + +.. _protk: https://github.com/iracooke/protk +.. _omssa: http://www.ncbi.nlm.nih.gov/pubmed/15473683 +.. _blast: https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus + + +When installing this package, if you instruct galaxy to install dependencies it will automatically install blast_ but installation of protk_ and omssa_ may require additional steps (see below). + +There are two ways you can satify these dependencies (choose one): + +1. **Manual Install:** Details on how to install protk_ and omssa_ manually are available here_. + +2. **Use Docker:** These tools are designed to run inside a docker_ container. If your galaxy supports `running tools within a docker container`__ you don't need to worry about dependencies. Simply install and things should just work. The docker container itself is versioned and new versions of this tool will automatically download an update to the container if needed. + +.. _docker: https://www.docker.com/ +.. _here: https://github.com/iracooke/protk/#galaxy-integration +.. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker +__ container_ + + +Further Info +------------ + +The source code for this tool and other protk galaxy tools is on github_. Please visit the github page to contribute to the project or to `report an issue`__ + +.. _github: https://github.com/iracooke/protk-galaxytools +.. _issue: https://github.com/iracooke/protk-galaxytools/issues +__ issue_ + +Unfortunately the omssa_ search tool itself is `no longer actively developed`__ but it remains a useful tool. This wrapper uses the last released omssa_ binary. + +.. _developed: http://pubchem.ncbi.nlm.nih.gov/omssa/ +__ developed_ \ No newline at end of file |
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| diff -r ac9be1d4885d -r 51f6c6446e69 omssa.xml --- a/omssa.xml Sat Jun 14 18:01:42 2014 -0400 +++ b/omssa.xml Thu Mar 26 20:04:12 2015 -0400 |
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| @@ -1,7 +1,8 @@ -<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.1"> +<tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.1.0"> <requirements> - <requirement type="package" version="1.3">protk</requirement> + <container type="docker">iracooke/protk-1.4.1</container> + <requirement type="package" version="1.4">protk</requirement> <requirement type="package" version="2.1.9">omssa</requirement> <requirement type="package" version="2.2.29">blast+</requirement> </requirements> @@ -59,7 +60,7 @@ <conditional name="database"> <param name="source_select" type="select" label="Database source"> <option value="built_in">Built-In</option> - <option value="input_ref">Uploaded fasta file</option> + <option selected="true" value="input_ref">Uploaded fasta file</option> </param> <when value="built_in"> <param name="dbkey" type="select" format="text" > @@ -98,7 +99,7 @@ <label>Missed Cleavages Allowed</label> <option value="0">0</option> <option value="1">1</option> - <option value="2">2</option> + <option selected="true" value="2">2</option> </param> <param name="enzyme" type="select" format="text"> @@ -130,12 +131,12 @@ <option value="24">Semi-Glu-C</option> </param> - <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/> - <param name="max_hit_expect" help="Expect values less than this are considered to be hits. Use a large value, eg 10000 when results will be processed downstream with Peptide Prophet" type="float" value="1.0" min="0" max="10000000" label="Maximum Expect value allowed in the hit list"/><!-- -he--> + <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/> + <param name="max_hit_expect" help="Expect values less than this are considered to be hits. Use a large value, eg 10000 when results will be processed downstream with Peptide Prophet" type="float" value="10000.0" min="0" max="10000000" label="Maximum Expect value allowed in the hit list"/><!-- -he--> <param name="intensity_cut_off" help="Peak intensity cut-off as a fraction of maximum peak intensity" type="float" value="0.0005" min="0" max="1" label="Peak intensity cut-off"/><!-- -ci--> - <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/> + <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/> <param name="precursor_tolu" type="select" format="text"> <label>Precursor Ion Tolerance Units</label> <option value="ppm">ppm</option> @@ -155,10 +156,10 @@ </param> <param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help=""> - <option selected="true" value="0">a</option> + <option value="0">a</option> <option selected="true" value="1">b</option> <option value="2">c</option> - <option selected="true" value="3">x</option> + <option value="3">x</option> <option selected="true" value="4">y</option> <option value="5">zdot</option> <option value="10">adot</option> @@ -172,6 +173,27 @@ <data format="raw_pepxml" name="output" metadata_source="input_file" label="omssa_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.pepXML"/> </outputs> + <tests> + <!-- Just test that the tool runs and produces vaguely correct output --> + <test> + <param name="source_select" value="input_ref"/> + <param name="fasta_file" value="AASequences.fasta" format="fasta"/> + <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d.mgf" format="mgf"/> + <param name="max_hit_expect" value="1000"/> + <param name="precursor_ion_tol" value="1.2"/> + <param name="precursor_tolu" value="Da"/> + <param name="fix_mods" value="3"/> + <param name="variable_mods" value="1"/> + + + <output name="output" format="raw_pepxml"> + <assert_contents> + <has_text text="VLFSQAQVYELERRFK" /> + </assert_contents> + </output> + </test> + </tests> + <help> **What it does** |
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| diff -r ac9be1d4885d -r 51f6c6446e69 repository_dependencies.xml --- a/repository_dependencies.xml Sat Jun 14 18:01:42 2014 -0400 +++ b/repository_dependencies.xml Thu Mar 26 20:04:12 2015 -0400 |
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| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="Proteomics datatypes"> - <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ac51d9dbfb4d" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |
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| diff -r ac9be1d4885d -r 51f6c6446e69 test-data/AASequences.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AASequences.fasta Thu Mar 26 20:04:12 2015 -0400 |
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| b'@@ -0,0 +1,204 @@\n+>tr|O70238|O70238_MOUSE Homeobox protein PSX OS=Mus musculus GN=Rhox6 PE=2 SV=2\n+METPQDSRQSIQKPPSPAAEEDKEEQPGGNAVVSGAPEERIDKKELVLNWLAQGEFDQGE\n+GAQGEVAGGEQAQEEPAPLSPAQEATGGEEEGENKEGEMEGRHAGDGASSSEDDSILEEG\n+GENIDQQPPQQEAASPDSIRNPHVLNRLAQLRYRRTRFTHSQLHDLERLFQETRYPSLRA\n+RRDLARWMGVDECDVQNWFRMRRALFQRNRRVLMFCELPPLPQSDSP\n+>sp|P20269|HM05_CAEEL Homeobox protein ceh-5 OS=Caenorhabditis elegans GN=ceh-5 PE=2 SV=4\n+MPSADTEFIRVIRIKSANGSEKMLEIPAKLDLERPKRPRTVFTDEQLEKLEESFNTSGYL\n+SGSTRAKLAESLGLSDNQVKVWFQNRRTKQKKIDSRDPIKPETLKPAENYQNVYQNYQNY\n+WTAAAFLSNNVISS\n+>sp|P34663|HM23_CAEEL Homeobox protein ceh-23 OS=Caenorhabditis elegans GN=ceh-23 PE=2 SV=1\n+MDTHLPFQTLPVSTPLPVSSSSLTDVLQTIAALQACPTSCIPSTSTGMLSPNLPFSATIP\n+RVNLFPPSQPANSLILPTIPAQPFIPNPSLLQANPSAVEALANALFATTSRRASCPEPPA\n+SSQATVTLQVPSTGSPERRRYSETNMEVLLREQLAQLMPPTSQLPGMPGCYYQHVPAAGT\n+SGIQGSLDAALMGAVPLAMNSMAHSRRAANHRKARTIYGTTQTQQLEDMFKGQMYVVGAE\n+RENLAQRLGLSPSQVRIWFQNRRSKHRRKQQEEQQSTTLEEKSEEIGKDEEEDDEEDEDD\n+VKVLN\n+>sp|P52955|LBX1_MOUSE Transcription factor LBX1 OS=Mus musculus GN=Lbx1 PE=1 SV=2\n+MTSKEDGKAAPGEERRRSPLDHLPPPANSNKPLTPFSIEDILNKPSVRRSYSLCGAAHLL\n+AAADKHAPGGLPLAGRALLSQTSPLCALEELASKTFKGLEVSVLQAAEGRDGMTIFGQRQ\n+TPKKRRKSRTAFTNHQIYELEKRFLYQKYLSPADRDQIAQQLGLTNAQVITWFQNRRAKL\n+KRDLEEMKADVESAKKLGPSGQMDIVALAELEQNSEASGGGGGGGCGRAKSRPGSPALPP\n+GAPQAPGGGPLQLSPASPLTDQRASSQDCSEDEEDEEIDVDD\n+>sp|Q26604|SMOX5_SCHMA Homeobox protein SMOX-5 OS=Schistosoma mansoni GN=SMOX-5 PE=2 SV=1\n+MTTSTMQQLKHDGDFSDELNETSTIQFYNKVSQQRKRRKTRTTFSNCQLNELENNFNRQR\n+YLTPTDRDRIAKHLGLTNTQVITWFQNRRAKLKREAEELERDVMALRKQKQQKFTCLSLS\n+DHDHEETQIDDENEQGDNNNDDDGDDNDVEEDDGEEQEKNHTKYLTQPPSISNILPSSLK\n+HFPSSTLNTLEIDNKHETLNMNLFINPFSNEKCLKRNKDLIRQQCYLFNHHINNYCTVNN\n+DNNINNNNNNNNRKNSIDGMNKGRSIKKGNKIWCPALELEQEIH\n+>tr|O77024|O77024_EPHMU EmH-3 (Fragment) OS=Ephydatia muelleri GN=EmH-3 PE=3 SV=1\n+MDNCRGDKKPLLSTNQQSFRIDNLLTRKVIEQQQQPDHYTMYPPSKVENHDILSLTTGPS\n+HDDMISDGTEIYEQGRESTSSTSGNDAEDDLLTRRKKARTAFSREQVAELEKKFQDKKYL\n+SSAERGELAEKLKLSDMQVKTWFQNRRMKYKRQSEETEMEMKSPKY\n+>sp|O93367|TLX3_CHICK T-cell leukemia homeobox protein 3 OS=Gallus gallus GN=TLX3 PE=2 SV=1\n+MEPAAGAQGPHQHEPISFGIDQILSGPEQDGAPPPPPPPPPPPPPPPPPPRGPDGAAFLG\n+GPRGGAPYPALPGPFPAIAAPFEESGPYGVNLSLAPGGVIRVPAHRPIPGAVPPPVPSAI\n+PAVPGLGGLSFPWMESSRRFVKERFTAAAALTPFTVTRRIGHPYQNRTPPKRKKPRTSFS\n+RVQICELEKRFHRQKYLASAERAALAKSLKMTDAQVKTWFQNRRTKWRRQTAEEREAERQ\n+QASRLMLQLQHDAFQKSLNESIQPDPLCLHNSSLFALQNLQPWEEESAKIPPVTSLV\n+>sp|P56407|HM09_CAEEL Homeobox protein ceh-9 OS=Caenorhabditis elegans GN=ceh-9 PE=4 SV=2\n+METDLLFQLLQPYFALLTSDVKPQRRTSHLIKDILDLPTVNGEIDEFGRCKSSLDQAKES\n+PIEKCQKTKRKKARTTFSGKQVFELEKQFEAKKYLSSSDRSELAKRLDVTETQVKIWFQN\n+RRTKWKKIESEKERSGEIPDDQIVKPQ\n+>tr|Q24786|Q24786_9METZ Homeobox-containing protein (Fragment) OS=Ephydatia fluviatilis GN=prox1 PE=3 SV=1\n+NSDEDKDRYASDLDTDRASSAGGALQMSRHKKRRPRALFSHAQVYELERRFAVQKYLTAH\n+EQSKLATVLHLTETQVKIWFQNRRYKSKRQQIEQTRVSPKVVKTSRMVRCSSGYITAI\n+>sp|O35767|NKX25_RAT Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1\n+MFPSPALTHTPFSVKDILNLEQQQRSLAAGDLSARLEATLAPASCMLAAFKPDGYSGPEA\n+AAPGLAELRAELGPAPSPPKCSPAFPTAPTFYPRAYGDPDPAKDPRADKKELCALQKAVE\n+LDKAETDGAERRRPRRRRKPRVLFSQAQVYELERRFKQQRYLSPAERDQLASVLKLTSTQ\n+VKIWFQNRRYKCKRQRQDQTLELLGPPPPPARRIAVPVLVRDGKPCLGDSAAYAPAYGLG\n+LNAYGYNAYPYPGYGGAACSPAYSCAAYPAAPPAAHAPAASANSNFVNFGVGDLNTVQSP\n+GMPQGNSGVSTLHGIRAW\n+>tr|Q9YH59|Q9YH59_CHICK Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1\n+MSMSPKHTTPFSVSDILSPWEESYKKVGMEGSNLGAPLSAYRQSQVSQPAMQQHPMGHNG\n+TVTAAYHMTAAGVPQLSHATMGGYCNGNLGNMSELPPYQDTMRNSASATGWYGTNPDPRF\n+SSISRFMAPSSGMNMGGMGGLSSLGDVSKSMAPLQSTPRRKRRVLFSQAQVYELERRFKQ\n+QKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKAAHEMQQENGSCQQQQSPR\n+RVAVPVLVKDGKPCQAGSNTPTAAIQSHPQQAATTITVATNGNSLGQHQSHQTNSAGQSP\n+DMGQHSASPSSLQSQVSSLSHLNSSTSDYGTAMSCSTLLYGRTW\n+>tr|O35455|O35455_MOUSE Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1\n+VGAPGRQSWRWARILWGSHVKTPPGTISRLGARNPMTDRGVGNLSGDMRRGGPVSTRTRP\n+QRKSRVLFSQAQVLALERRFKQQRYLTAPEREHLASALQLTSTQVKIWFQNRRYKSKSQR\n+QDQNLELAGHPLAPRPGSSASTGTGRQPLPGSDVAAFLVPTKPPRPIPASV'..b'aenorhabditis elegans GN=ceh-19 PE=2 SV=2\n+MAFNIESLLEKKSNPVEEGNDFEEENDSEKNGEEDEEEEEKNVIDGWTNMATSQLAMFAI\n+ANDLRTPTLVELQMLLGVSARKHDYKRSRKSVCERKPRQAYSARQLDRLETEFQTDKYLS\n+VNKRIQLSQTLNLTETQIKTWFQNRRTKWKKQLTSSIRQMVKDAPTSTSVGVPFQSLLTP\n+PTPPTTLACHVNSLFACEQ\n+>sp|P22807|SLOU_DROME Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1\n+MVMLQSPAQKASDSASAQNTAVGGLMSPNSNPDSPKSNTSPDVASADSVVSGTGGGSTPP\n+AAKIPKFIISANGAAVAGKQEQELRYSLERLKQMSSESGSLLSRLSPLQEDSQDKEKPNH\n+NNNNSLTNHNANSNTRRSQSPPASVGSVSFSSPAQQRKLLELNAVRHLARPEPLQHPHAA\n+LLQQHPHLLQNPQFLAAAQQHMHHHQHQHHQHPAHPHSHQHPHPHPHPHPHPHPSAVFHL\n+RAPSSSSTAPPSPATSPLSPPTSPAMHSDQQMSPPIAPPQNPPHSSQPPQQQQVAAPSDM\n+DLERIKLVAAVAARTTQASSTSALASASNSVSNASISISNSSSGSPSGRDLSDYGFRIQL\n+GGLAAAAAAAAATSRQIAAATYARSDTSEELNVDGNDEDSNDGSHSTPSVCPVDLTRSVN\n+SSAAANPSSASTSASSDRDAATKRLAFSVENILDPNKFTGNKLPSGPFGHPRQWSYERDE\n+EMQERLDDDQSEDMSAQDLNDMDQDDMCDDGSDIDDPSSETDSKKGGSRNGDGKSGGGGG\n+GGSKPRRARTAFTYEQLVSLENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKW\n+KKQNPGMDVNSPTIPPPGGGSFGPGAYASGLLYSHAVPYPPYGPYFHPLGAHHLSHSHS\n+>sp|Q04787|BSH_DROME Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5\n+MAMLNEASLSPADAHAHANATTPTHSKAAAMASATTMLTTKTPFSIEHILFQNLNSASNN\n+NNSSDTNGIAANTNNYAPKSSRNAVKSARSAFAHDNNPHKHPSQHSHPPQSHPPASASAS\n+ATATARSNQAASGYAGEDYGKSMHSTPRSNHHSRHGTSHYNGDQISQQLGSGAAQHPPVP\n+TTQPQPPPPPPLNGGSGASNGVLYPNAPYTDHGFLQMTLGYLSPSSGTYKSVDPYFLSQA\n+SLFGGAPFFGAPGCVPELALGLGMGVNALRHCRRRKARTVFSDPQLSGLEKRFEGQRYLS\n+TPERVELATALGLSETQVKTWFQNRRMKHKKQLRRRDNANEPVDFSRSEPGKQPGEATSS\n+SGDSKHGKLNPGSVGGTPTQPTSEQQLQMCLMQQGYSTDDYSDLEADSGDEDNSSDVDIV\n+GDAKLYQLT\n+>sp|O08686|BARX2_MOUSE Homeobox protein BarH-like 2 OS=Mus musculus GN=Barx2 PE=2 SV=2\n+MHCHAELRLSSPGQLKAARRRYKTFMIDEILSKETCDYFEKLSLYSVCPSLVVRPKPLHS\n+CTGSPSLRAYPLLSVITRQPTVISHLVPTGSGLTPVLTRHPVAAAEAAAAAAETPGGEAL\n+ASSESETEQPTPRQKKPRRSRTIFTELQLMGLEKKFQKQKYLSTPDRLDLAQSLGLTQLQ\n+VKTWYQNRRMKWKKMVLKGGQEAPTKPKGRPKKNSIPTSEEIEAEEKMNSQAQSQELLES\n+SERQEEPCDTQEPKACLVPLEVAEPIHQPQELSEASSEPPPLS\n+>tr|Q23819|Q23819_HYDVD Cnox3 protein (Fragment) OS=Hydra viridissima GN=cnox3 PE=2 SV=1\n+NLYPILNTDQNHCTYAKEDSLIPEVEEPSTYLQLKQNNAKGSGIKCRKPRTVFSDLQLMV\n+LEREFNNRKYLSTPQRTNLADRLGLNQTQVKTWYQNRRMKWKKETFESEDKEPKIS\n+>sp|Q01702|DLX3B_DANRE Homeobox protein Dlx3b OS=Danio rerio GN=dlx3b PE=2 SV=1\n+MSGPTYDRKIPGISTDLSGSMSCHPTSKDSPTLPESSATDMGYYSSHHEYYQSPPYPQQM\n+NSYHQFNLSGMGATPGAYPTKTEYPYNTYRQYGHFNRDLQTPPQSAVKEEPETEVRMVNG\n+KPKKIRKPRTIYSSYQLAALQRRFQKAQYLALPERAELAAQLGLTQTQVKIWFQNRRSKF\n+KKLYKNGEVPLEHSPNASDSMACNSPPSPAVWDNNAHSSQVNRGQIPQPPLSSTPPYMED\n+YSNHWYQQGSHLQHPVHHPGPPQSVGAVY\n+>sp|Q18273|HM43_CAEEL Homeobox protein ceh-43 OS=Caenorhabditis elegans GN=ceh-43 PE=2 SV=1\n+MDPSKGFEYVAGDYYQTSGVAPPTSNGAGSNVSPYFPYHAYPTSSTNGATGGSMYGTPQQ\n+TSAYAMYPPGPGSSPEEAFPEHTTTKIVEGCEAKYNVKGKKMRKPRTIYNSSQLQMLQKK\n+FQKTQYLALPDRAALAHELGLSQTQVKIWFQNRRSKQKKQKGGSSDHASDEEDDDTEESK\n+PESPPMGESVMIQESSEPRTLVSSSIKTEMKEEYPPMTLNEQYASPYLYGSDFSTILPPS\n+QGFPNNALYNTAGAYPSIDYTNGVYQNTLYKYV\n+>tr|Q23824|Q23824_HYDVD Msh protein (Fragment) OS=Hydra viridissima GN=msh PE=2 SV=1\n+EFQFDLSKCFLRKHKANRKPRTPFSVNQLLTLEQKFKRKQYLSISERAELSELLRLTETQ\n+IKIWFQNRRAKQKRSKEAEIEESVRNRLPLSAADYRSLDHLTLLSSFIAFIPIEYEVKIF\n+MNVQRGIE\n+>tr|Q24785|Q24785_9METZ Homeobox-containing protein (Fragment) OS=Ephydatia fluviatilis GN=prox3 PE=3 SV=1\n+PHSSGSNASTINKQKKDRKPRTPFTSTQLIALERKFRQQKYLSVAERAEFAEYLKLTETQ\n+VKIWFQNRRAKEKRLHEAEAERAARSLGFHFHMPMQSKMNTFRHPYCNSQYQTLCLCQFR\n+HKIGIGTFPARTTDSISSNSSQPTLPWFLTCNSSTPL\n+>sp|P70354|MSX3_MOUSE Homeobox protein MSX-3 OS=Mus musculus GN=Msx3 PE=1 SV=1\n+MARATFDMNAAGLEARGGGHTEHGPLPFSVESLLEAERVPGSESGELGVERPLGASKPGA\n+WPPPVAHSCPPRAPSPPPCTLRKHKTNRKPRTPFTTAQLLALERKFHQKQYLSIAERAEF\n+SSSLSLTETQVKIWFQNRRAKAKRLQEAELEKLKLAAKPLLPAAFALPFPLGTQLHSSAA\n+TFGGNAVPGILAGPVAAYGMYYLS\n+>tr|Q90263|Q90263_DANRE Empty spiracles homeobox 3 OS=Danio rerio GN=emx3 PE=2 SV=1\n+MFQHNKKCFTIESLVGKDSNSSNAAADEPIRPTALRFTESIHPSPFGSCFQNSGRTLYSS\n+SPEMMFTDPSTHSTNSGLSLRHLQIPTQPFFSPHQRDTLNFYPWVLRNRYLGHRFQGDDS\n+SPENLLLHGPFSRKPKRIRTAFSPSQLLRLERAFEKNHYVVGAERKQLANGLCLTETQVK\n+VWFQNRRTKHKRQKLEEESPDPQQKRKGSQHVSRWRVATQQGSPEDIDVISED\n' |
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| diff -r ac9be1d4885d -r 51f6c6446e69 test-data/mr176-BSA100fmole_BA3_01_8168.d.mgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mr176-BSA100fmole_BA3_01_8168.d.mgf Thu Mar 26 20:04:12 2015 -0400 |
| b |
| b'@@ -0,0 +1,26248 @@\n+BEGIN IONS\n+TITLE=Cmpd 1, +MSn(722.3522), 33.5 min\n+PEPMASS=722.35225000000003\n+CHARGE=2+\n+198.13402 12.0\n+204.14855 50.0\n+215.14924 16.0\n+216.14697 52.0\n+226.09713 12.0\n+230.07293 101.0\n+232.14589 13.0\n+234.15667 228.0\n+243.12353 30.0\n+244.1095 25.0\n+246.13836 23.0\n+248.08086 40.0\n+249.17284 2164.0\n+257.11062 19.0\n+258.06895 17.0\n+259.05306 18.0\n+268.14012 15.0\n+274.13079 64.0\n+276.07752 164.0\n+277.16652 291.0\n+282.08022 14.0\n+284.17195 15.0\n+285.17172 14.0\n+286.15293 14.0\n+294.19124 16.0\n+302.17391 17.0\n+303.18008 66.0\n+312.16842 24.0\n+313.16574 12.0\n+321.19043 828.0\n+327.1396 22.0\n+328.12684 14.0\n+341.12552 30.0\n+345.14196 24.0\n+346.16906 13.0\n+358.14899 71.0\n+362.12886 18.0\n+372.11454 34.0\n+373.0946 33.0\n+389.16458 44.0\n+390.12438 168.0\n+407.14623 83.0\n+409.19069 21.0\n+414.21115 10.0\n+416.26685 16.0\n+419.1978 11.0\n+424.16828 21.0\n+429.21492 28.0\n+429.71536 23.0\n+430.21559 11.0\n+434.27836 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13.0\n+873.33147 12.0\n+874.46002 30.0\n+875.44423 131.0\n+881.36032 11.0\n+892.47057 665.0\n+898.36261 12.0\n+899.35735 22.0\n+900.35113 15.0\n+916.38949 24.0\n+917.3777 34.0\n+918.37069 14.0\n+934.39336 23.0\n+935.39897 16.0\n+936.3935 12.0\n+972.46907 13.0\n+973.4597 18.0\n+974.4341 12.'..b'.0\n+651.56008 11.0\n+652.55494 16.0\n+663.25675 7.0\n+663.56082 11.0\n+664.60856 46.0\n+665.57787 19.0\n+666.62814 1110.0\n+668.06434 6.0\n+668.34314 7.0\n+670.4486 7.0\n+670.82298 6.0\n+671.53988 8.0\n+715.91104 7.0\n+961.66916 6.0\n+END IONS\n+BEGIN IONS\n+TITLE=Cmpd 117, +MSn(666.6268), 78.2 min\n+PEPMASS=666.6268\n+CHARGE=1+\n+199.11787 8.0\n+202.02003 16.0\n+203.18849 9.0\n+205.37949 23.0\n+206.13461 11.0\n+207.05227 10.0\n+208.19718 9.0\n+209.13293 12.0\n+211.22177 15.0\n+213.19376 12.0\n+217.2048 17.0\n+220.07549 12.0\n+221.19821 11.0\n+223.16276 19.0\n+224.02837 10.0\n+227.14643 14.0\n+227.20741 15.0\n+229.11602 9.0\n+229.19308 8.0\n+232.22619 14.0\n+233.213 10.0\n+233.24911 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12.0\n+454.4011 16.0\n+455.37991 15.0\n+457.31264 9.0\n+457.41713 10.0\n+458.38319 12.0\n+459.40721 10.0\n+461.70679 10.0\n+466.43465 18.0\n+467.42383 12.0\n+473.99569 14.0\n+475.3938 10.0\n+477.22395 22.0\n+481.40895 35.0\n+491.70977 9.0\n+492.39201 15.0\n+493.42755 14.0\n+494.47387 9.0\n+495.28352 593.0\n+496.45737 21.0\n+498.08145 11.0\n+506.62345 11.0\n+508.48933 16.0\n+509.4511 30.0\n+510.46935 14.0\n+519.39734 10.0\n+521.43055 9.0\n+522.34524 15.0\n+522.46115 9.0\n+523.48411 61.0\n+524.55162 10.0\n+525.47612 9.0\n+527.89179 10.0\n+533.48995 13.0\n+536.50765 22.0\n+537.49288 142.0\n+549.51265 16.0\n+550.30584 17.0\n+551.34954 192.0\n+551.49872 39.0\n+552.48288 19.0\n+554.01025 10.0\n+564.58669 9.0\n+581.61267 10.0\n+593.16063 13.0\n+607.4135 35.0\n+608.38074 14.0\n+609.41496 10.0\n+611.63767 9.0\n+615.18233 15.0\n+629.56203 10.0\n+630.62641 12.0\n+631.50591 11.0\n+641.54067 9.0\n+646.58063 14.0\n+648.60084 20.0\n+649.24139 11.0\n+649.4769 9.0\n+650.59822 9.0\n+652.55235 11.0\n+662.8894 10.0\n+663.47551 15.0\n+663.64326 12.0\n+664.61517 93.0\n+665.48958 11.0\n+666.62395 502.0\n+666.77299 33.0\n+667.43293 23.0\n+668.40657 11.0\n+668.63958 310.0\n+686.30957 10.0\n+856.14597 19.0\n+END IONS\n+BEGIN IONS\n+TITLE=Cmpd 118, +MSn(668.6319), 78.7 min\n+PEPMASS=668.63189\n+CHARGE=1+\n+283.27515 1834.0\n+309.28924 1667.0\n+311.30461 752.0\n+383.33607 66.0\n+425.37707 32.0\n+439.35868 33.0\n+453.3673 57.0\n+509.4289 70.0\n+523.45287 62.0\n+537.49546 110.0\n+539.48344 46.0\n+666.62265 409.0\n+671.61589 34.0\n+875.78553 20.0\n+1142.68411 11.0\n+END IONS\n' |
| b |
| diff -r ac9be1d4885d -r 51f6c6446e69 tool_dependencies.xml --- a/tool_dependencies.xml Sat Jun 14 18:01:42 2014 -0400 +++ b/tool_dependencies.xml Thu Mar 26 20:04:12 2015 -0400 |
| b |
| @@ -2,7 +2,7 @@ <tool_dependency> <package name="blast+" version="2.2.29"> - <repository changeset_revision="a2ec897aac2c" name="package_blast_plus_2_2_29" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a2ec897aac2c" name="package_blast_plus_2_2_29" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |