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changeset 7:51f6c6446e69 draft

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Docker support and update for protk 1.4
author iracooke
date Thu, 26 Mar 2015 20:04:12 -0400
parents ac9be1d4885d
children 4294476e3f83
files README README.rst omssa.xml repository_dependencies.xml test-data/AASequences.fasta test-data/mr176-BSA100fmole_BA3_01_8168.d.mgf tool_dependencies.xml
diffstat 7 files changed, 26527 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/README	Sat Jun 14 18:01:42 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Mar 26 20:04:12 2015 -0400
@@ -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
--- a/omssa.xml	Sat Jun 14 18:01:42 2014 -0400
+++ b/omssa.xml	Thu Mar 26 20:04:12 2015 -0400
@@ -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**
 
--- a/repository_dependencies.xml	Sat Jun 14 18:01:42 2014 -0400
+++ b/repository_dependencies.xml	Thu Mar 26 20:04:12 2015 -0400
@@ -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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/AASequences.fasta	Thu Mar 26 20:04:12 2015 -0400
@@ -0,0 +1,204 @@
+>tr|O70238|O70238_MOUSE Homeobox protein PSX OS=Mus musculus GN=Rhox6 PE=2 SV=2
+METPQDSRQSIQKPPSPAAEEDKEEQPGGNAVVSGAPEERIDKKELVLNWLAQGEFDQGE
+GAQGEVAGGEQAQEEPAPLSPAQEATGGEEEGENKEGEMEGRHAGDGASSSEDDSILEEG
+GENIDQQPPQQEAASPDSIRNPHVLNRLAQLRYRRTRFTHSQLHDLERLFQETRYPSLRA
+RRDLARWMGVDECDVQNWFRMRRALFQRNRRVLMFCELPPLPQSDSP
+>sp|P20269|HM05_CAEEL Homeobox protein ceh-5 OS=Caenorhabditis elegans GN=ceh-5 PE=2 SV=4
+MPSADTEFIRVIRIKSANGSEKMLEIPAKLDLERPKRPRTVFTDEQLEKLEESFNTSGYL
+SGSTRAKLAESLGLSDNQVKVWFQNRRTKQKKIDSRDPIKPETLKPAENYQNVYQNYQNY
+WTAAAFLSNNVISS
+>sp|P34663|HM23_CAEEL Homeobox protein ceh-23 OS=Caenorhabditis elegans GN=ceh-23 PE=2 SV=1
+MDTHLPFQTLPVSTPLPVSSSSLTDVLQTIAALQACPTSCIPSTSTGMLSPNLPFSATIP
+RVNLFPPSQPANSLILPTIPAQPFIPNPSLLQANPSAVEALANALFATTSRRASCPEPPA
+SSQATVTLQVPSTGSPERRRYSETNMEVLLREQLAQLMPPTSQLPGMPGCYYQHVPAAGT
+SGIQGSLDAALMGAVPLAMNSMAHSRRAANHRKARTIYGTTQTQQLEDMFKGQMYVVGAE
+RENLAQRLGLSPSQVRIWFQNRRSKHRRKQQEEQQSTTLEEKSEEIGKDEEEDDEEDEDD
+VKVLN
+>sp|P52955|LBX1_MOUSE Transcription factor LBX1 OS=Mus musculus GN=Lbx1 PE=1 SV=2
+MTSKEDGKAAPGEERRRSPLDHLPPPANSNKPLTPFSIEDILNKPSVRRSYSLCGAAHLL
+AAADKHAPGGLPLAGRALLSQTSPLCALEELASKTFKGLEVSVLQAAEGRDGMTIFGQRQ
+TPKKRRKSRTAFTNHQIYELEKRFLYQKYLSPADRDQIAQQLGLTNAQVITWFQNRRAKL
+KRDLEEMKADVESAKKLGPSGQMDIVALAELEQNSEASGGGGGGGCGRAKSRPGSPALPP
+GAPQAPGGGPLQLSPASPLTDQRASSQDCSEDEEDEEIDVDD
+>sp|Q26604|SMOX5_SCHMA Homeobox protein SMOX-5 OS=Schistosoma mansoni GN=SMOX-5 PE=2 SV=1
+MTTSTMQQLKHDGDFSDELNETSTIQFYNKVSQQRKRRKTRTTFSNCQLNELENNFNRQR
+YLTPTDRDRIAKHLGLTNTQVITWFQNRRAKLKREAEELERDVMALRKQKQQKFTCLSLS
+DHDHEETQIDDENEQGDNNNDDDGDDNDVEEDDGEEQEKNHTKYLTQPPSISNILPSSLK
+HFPSSTLNTLEIDNKHETLNMNLFINPFSNEKCLKRNKDLIRQQCYLFNHHINNYCTVNN
+DNNINNNNNNNNRKNSIDGMNKGRSIKKGNKIWCPALELEQEIH
+>tr|O77024|O77024_EPHMU EmH-3 (Fragment) OS=Ephydatia muelleri GN=EmH-3 PE=3 SV=1
+MDNCRGDKKPLLSTNQQSFRIDNLLTRKVIEQQQQPDHYTMYPPSKVENHDILSLTTGPS
+HDDMISDGTEIYEQGRESTSSTSGNDAEDDLLTRRKKARTAFSREQVAELEKKFQDKKYL
+SSAERGELAEKLKLSDMQVKTWFQNRRMKYKRQSEETEMEMKSPKY
+>sp|O93367|TLX3_CHICK T-cell leukemia homeobox protein 3 OS=Gallus gallus GN=TLX3 PE=2 SV=1
+MEPAAGAQGPHQHEPISFGIDQILSGPEQDGAPPPPPPPPPPPPPPPPPPRGPDGAAFLG
+GPRGGAPYPALPGPFPAIAAPFEESGPYGVNLSLAPGGVIRVPAHRPIPGAVPPPVPSAI
+PAVPGLGGLSFPWMESSRRFVKERFTAAAALTPFTVTRRIGHPYQNRTPPKRKKPRTSFS
+RVQICELEKRFHRQKYLASAERAALAKSLKMTDAQVKTWFQNRRTKWRRQTAEEREAERQ
+QASRLMLQLQHDAFQKSLNESIQPDPLCLHNSSLFALQNLQPWEEESAKIPPVTSLV
+>sp|P56407|HM09_CAEEL Homeobox protein ceh-9 OS=Caenorhabditis elegans GN=ceh-9 PE=4 SV=2
+METDLLFQLLQPYFALLTSDVKPQRRTSHLIKDILDLPTVNGEIDEFGRCKSSLDQAKES
+PIEKCQKTKRKKARTTFSGKQVFELEKQFEAKKYLSSSDRSELAKRLDVTETQVKIWFQN
+RRTKWKKIESEKERSGEIPDDQIVKPQ
+>tr|Q24786|Q24786_9METZ Homeobox-containing protein (Fragment) OS=Ephydatia fluviatilis GN=prox1 PE=3 SV=1
+NSDEDKDRYASDLDTDRASSAGGALQMSRHKKRRPRALFSHAQVYELERRFAVQKYLTAH
+EQSKLATVLHLTETQVKIWFQNRRYKSKRQQIEQTRVSPKVVKTSRMVRCSSGYITAI
+>sp|O35767|NKX25_RAT Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1
+MFPSPALTHTPFSVKDILNLEQQQRSLAAGDLSARLEATLAPASCMLAAFKPDGYSGPEA
+AAPGLAELRAELGPAPSPPKCSPAFPTAPTFYPRAYGDPDPAKDPRADKKELCALQKAVE
+LDKAETDGAERRRPRRRRKPRVLFSQAQVYELERRFKQQRYLSPAERDQLASVLKLTSTQ
+VKIWFQNRRYKCKRQRQDQTLELLGPPPPPARRIAVPVLVRDGKPCLGDSAAYAPAYGLG
+LNAYGYNAYPYPGYGGAACSPAYSCAAYPAAPPAAHAPAASANSNFVNFGVGDLNTVQSP
+GMPQGNSGVSTLHGIRAW
+>tr|Q9YH59|Q9YH59_CHICK Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1
+MSMSPKHTTPFSVSDILSPWEESYKKVGMEGSNLGAPLSAYRQSQVSQPAMQQHPMGHNG
+TVTAAYHMTAAGVPQLSHATMGGYCNGNLGNMSELPPYQDTMRNSASATGWYGTNPDPRF
+SSISRFMAPSSGMNMGGMGGLSSLGDVSKSMAPLQSTPRRKRRVLFSQAQVYELERRFKQ
+QKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDKAAHEMQQENGSCQQQQSPR
+RVAVPVLVKDGKPCQAGSNTPTAAIQSHPQQAATTITVATNGNSLGQHQSHQTNSAGQSP
+DMGQHSASPSSLQSQVSSLSHLNSSTSDYGTAMSCSTLLYGRTW
+>tr|O35455|O35455_MOUSE Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1
+VGAPGRQSWRWARILWGSHVKTPPGTISRLGARNPMTDRGVGNLSGDMRRGGPVSTRTRP
+QRKSRVLFSQAQVLALERRFKQQRYLTAPEREHLASALQLTSTQVKIWFQNRRYKSKSQR
+QDQNLELAGHPLAPRPGSSASTGTGRQPLPGSDVAAFLVPTKPPRPIPASVATRALPTTL
+AMRAAAPAPAPAPGRSHHWPALASAQVAKVRLRRAICPLRLRESRPGEKPELTYCHSVPD
+AWSPPLPAGGRGAGKHCPPY
+>sp|P22711|TIN_DROME Muscle-specific homeobox protein tinman OS=Drosophila melanogaster GN=tin PE=2 SV=2
+MLQHHQQQAQSGGYYDHYTQSPSPGSLTNADALNTTPFSVKDILNMVNQTEAYEGSYGHI
+DGAATASALFAAGEYQNPHQYLNHQQHQQSELPIPQQQLHHQHLDDGATTSSSLSPLLPP
+PPHQLYGGYQDYGMPAHMFQHHHGHPHQSFQHSASAYNMSASQFYAGASATAYQTPATYN
+YNYAGSGEVYGGATPSAVGIKSEYIPTPYVTPSPTLDLNSSAEVDSLQAPTQKLCVNPLS
+QRLMETASNSSSLRSIYGSDEGAKKKDNSQVTSSRSELRKNSISGNSNPGSNSGSTKPRM
+KRKPRVLFSQAQVLELECRFRLKKYLTGAEREIIAQKLNLSATQVKIWFQNRRYKSKRGD
+IDCEGIAKHLKLKSEPLDSPTSLPPPIPNHVMWPPTMQQSQQQQQHHAQQQQMQHM
+>tr|O16132|O16132_HYDVU NK-2 class homeobox transcription factor OS=Hydra vulgaris GN=CnNK-2 PE=2 SV=1
+MDFSILPVNSSFLVDDILRRKHYENKIHQSNFSQFSVLSDEISIKTRLSAFPIYNKGMHK
+NKELVNKPFQMNDKNITETERDFNKSSISFDMTSNVEYSFGDKRMNNRHSFQGLSCRVAE
+AEMYARGKREDNSSDENSPKCESPSLTAKTEYHNASGDAMHVTSESLIQQNLLNIKSSRK
+KPRILFSQSQVMELGKKFKDQKYLSASERDQIANKLNLTPTQVKIWFQNKRYKCKKQTIE
+SRTRPPPYEWLHFQHRNVPVLVQNNQVSSDVCLPYCNRPTYLPSNSPVDMNYPPFYPDPY
+NGHNHHYSNSYNTPSQTSTYPNSWPFYK
+>sp|O93590|ZAX_XENLA Homeobox protein zampogna OS=Xenopus laevis GN=zax PE=2 SV=1
+MSLTSFSIQDILARTGGNRGKDTRTDGNNISPPPSPSADEGHNEWPRAENPPLTPEKEKT
+DTDSGTEDFHWERDTETANNGAFTDPSSGDRLADSPKSSKKRSRAAFSHAQVYELERRFS
+LQRYLSGPERADLAASLKLTETQVKIWFQNRRYKTKRKLIATQTAPKSSLVPTRKVAVRV
+LVKDDQRQYCPEDMLSPSLLSLYHAYQYYPYMYCLPAWVPHLPL
+>tr|Q90853|Q90853_CHICK Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1
+MAQDRECLCSAGFQRGDYTQGNTDRSTAAGNCRRRGSGEPRSHPPAEADPPSRSCFTDDA
+GRSDGKRRLHICPRLVLFHRGPAGHRSGGGTRRAAAGGGGGRRTSRCGPHSPLRLGASGC
+PLRDAAVGWYRRAFLGCAAPTPATGTRRSCPEDTERAGGGGRAAGGAAGGRQSSGGREEE
+EERGEEAGEAEQRAAGRKKKTRTVFSRSQVFQLESTFDVKRYLSSSERAGLAASLHLTET
+QVKIWFQNRRNKWKRHVAADLEAANLSHAAQRIVRVPILYHENSPASALGFGLPHMSPPL
+VGFSGGVSYPPGHLPRRLPSLPSLADDGTRLSAHLCRDRGPEPPPLASSFTLGLFLSTFT
+IFRFSTFI
+>tr|O97671|O97671_RABIT Homeobox protein (Fragment) OS=Oryctolagus cuniculus GN=HEX PE=2 SV=1
+GKPLLWSPFLQRPLHKRKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQ
+VKTWFQNRRAKWRRLKQENPQSGKKEQENLDSSCEQRPDLPGDQHKGASLDSSQCSQSPA
+SQEDLESEISEDSDQEVD
+>tr|Q9YHC2|Q9YHC2_CHICK Homeodomain protein (Fragment) OS=Gallus gallus GN=Nkx-6.1 PE=2 SV=1
+PPWRDARIGCAPHQGSILLDKDGKRKHTRPTFSGQQIFALEKTFEQTKYLAGPERARLAY
+SLGMTESQVKVWFQNRRTKWRKKHAAEMATAKKKQDSETERLKGASDNEDDDDDYNKPLD
+PNSDDEKIAQLLKKHKPGAGGLLPHPAEGEASA
+>sp|P28468|HOX1_HALRO Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1
+MEKMHSKSVSPVPFNNSNNTSLGGLRKSSSIPTLAVPECESMGNKHIEEERTNNITTMAM
+KRRLLDPQNKKKQNRFERYSSSNHAQEQSSEENFCRSKKDSTVLKFGIDSILKNKNAEKV
+PKGISNAGRIQDERFTEACTNTSSNVNPLSKYFKPSSNDQLGARRTATSFSSSSEASDSK
+SCCTNNNEEARYKYRVIDKRKSADSDWSEDATGNEADDPDDHINQDNCDLASTLEQSRIV
+ALEILKNKRLRLDSSEALNDLTPYDQLSRTEDQQISRRVEMMNHQAFARENNEWPRSFSS
+GLQDPFAKNLPNAFLPFYMQPYLRAYYNIQKYIYHKKLLNRNDRFYREANVENDNYKTEE
+SLRSPSETKQYSPDASTFYPIRTEDSNGSRNLKVDVEEGDKEANKLFKDLCVSVGDRLSN
+ALSYGRKDYNGLSTSQTSGNRFLNFSDKGIQAGSYYQTGERNDSLAGPLKNSGMSFDFPP
+KFGSNNSSTDKPEQEDNNPQTIGSEYQINTQRSMKDNLLTAKLLENEAKLRYGNIVTQYP
+RPFSWPFAASVRKSYDPALRSYFSRFNNSDAPHYGAAQVNPTAGNNFKSMLPGNFENPYF
+FNELNTLDTTGFLSRQYGHMSSSQNPHSETQNRSEEVRGTVKKRRKWNRAVFSLMQRRGL
+EKSFQSQKYVAKPERRKLADALSLTDAQVKIWFQNRRMKWRQEIKMKNRGLVPVHILGQD
+HEIEKEKTQTPSDEGEVINVD
+>sp|O88181|BARH2_RAT BarH-like 2 homeobox protein OS=Rattus norvegicus GN=Barhl2 PE=2 SV=1
+MTAMEGASGSSFGIDTILSGAGSGSPGMMNGDFRSLGEARTTDFRSQATPSPCSEIDTVG
+TAPSSPISVTLEPPEPHLVTDGPQHHHHLHHGQQPPPPSAPPAQSLQPSPQQQPPPQPQS
+AAQQLGSAAAAPRTSTSSFLIKDILGDSKPLAACAPYSTSVSSPHHTPKQECNAAHESFR
+PKLEQEDSKTKLDKREDSQSDIKCHGTKEEGDREITSSRESPPVRAKKPRKARTAFSDHQ
+LNQLERSFERQKYLSVQDRMDLAAALNLTDTQVKTWYQNRRTKWKRQTAVGLELLAEAGN
+YSALQRMFPSPYFYHPSLLGSMDSTTAAAAAAAMYSSMYRTPPAPHPQLQRPLVPRVLIH
+GLGPGGQPALNPLSNPIPGTPHPR
+>sp|Q24255|BARH1_DROME Homeobox protein B-H1 OS=Drosophila melanogaster GN=B-H1 PE=2 SV=2
+MKDSMSILTQTPSEPNAAHPQLHHHLSTLQQQHHQHHLHYGLQPPAVAHSIHSTTTMSSG
+GSTTTASGIGKPNRSRFMINDILAGSAAAAFYKQQQHHQQLHHHNNNNNSGSSGGSSPAH
+SNNNNNINGDNCEASNVAGVGVLPSALHHPQPHPPTHPHTHPHALMHPHGKLGHFPPTAG
+GNGLNVAQYAAAMQQHYAAAAAAAAARNNAAAAAAAAAAAAAAGVAAPPVDGGVDGGVGL
+APPAGGDLDDSSDYHEENEDCDSGNMDDHSVCSNGGKDDDGNSVKSGSTSDMSGLSKKQR
+KARTAFTDHQLQTLEKSFERQKYLSVQERQELAHKLDLSDCQVKTWYQNRRTKWKRQTAV
+GLELLAEAGNFAAFQRLYGGSPYLGAWPYAAAAGAAHGATPHTNIDIYYRQAAAAAAMQK
+PLPYNLYAGVPSVGVGVGVGVGPAPFSHLSASSSLSSLSSYYQSAAAAASAANPGGPHPV
+APPPSVGGGSPPSGLVKPIPAHSASASPPPRPPSTPSPTLNPGSPPGRSVDSCSQSDDED
+QIQV
+>sp|Q22909|HM30_CAEEL Homeobox protein ceh-30 OS=Caenorhabditis elegans GN=ceh-30 PE=2 SV=2
+MSLLDPRQFLLPAFYLDPTTQALLAQAASTSPCNKISSSSSFRISDILEQSPNNSSHSND
+HDPSPQSIKSDFSTSPRASSPGGDRMGSPGSCKKSRKARTIFTDKQLQELENTFEKQKYL
+SVQDRMDLAHRMGLTDTQVKTWYQNRRTKWKRQATSGMDLLSEPGNLSAVQNLIRSSPYW
+ANYITALPMGTQLPMMGLPMSMIVPPAHAFQPSSSSNSPSTHISSESPQLDVSSNSE
+>sp|P26797|HM19_CAEEL Homeobox protein ceh-19 OS=Caenorhabditis elegans GN=ceh-19 PE=2 SV=2
+MAFNIESLLEKKSNPVEEGNDFEEENDSEKNGEEDEEEEEKNVIDGWTNMATSQLAMFAI
+ANDLRTPTLVELQMLLGVSARKHDYKRSRKSVCERKPRQAYSARQLDRLETEFQTDKYLS
+VNKRIQLSQTLNLTETQIKTWFQNRRTKWKKQLTSSIRQMVKDAPTSTSVGVPFQSLLTP
+PTPPTTLACHVNSLFACEQ
+>sp|P22807|SLOU_DROME Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1
+MVMLQSPAQKASDSASAQNTAVGGLMSPNSNPDSPKSNTSPDVASADSVVSGTGGGSTPP
+AAKIPKFIISANGAAVAGKQEQELRYSLERLKQMSSESGSLLSRLSPLQEDSQDKEKPNH
+NNNNSLTNHNANSNTRRSQSPPASVGSVSFSSPAQQRKLLELNAVRHLARPEPLQHPHAA
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+DLERIKLVAAVAARTTQASSTSALASASNSVSNASISISNSSSGSPSGRDLSDYGFRIQL
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+SSAAANPSSASTSASSDRDAATKRLAFSVENILDPNKFTGNKLPSGPFGHPRQWSYERDE
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+MHCHAELRLSSPGQLKAARRRYKTFMIDEILSKETCDYFEKLSLYSVCPSLVVRPKPLHS
+CTGSPSLRAYPLLSVITRQPTVISHLVPTGSGLTPVLTRHPVAAAEAAAAAAETPGGEAL
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+NLYPILNTDQNHCTYAKEDSLIPEVEEPSTYLQLKQNNAKGSGIKCRKPRTVFSDLQLMV
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+MSGPTYDRKIPGISTDLSGSMSCHPTSKDSPTLPESSATDMGYYSSHHEYYQSPPYPQQM
+NSYHQFNLSGMGATPGAYPTKTEYPYNTYRQYGHFNRDLQTPPQSAVKEEPETEVRMVNG
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+MDPSKGFEYVAGDYYQTSGVAPPTSNGAGSNVSPYFPYHAYPTSSTNGATGGSMYGTPQQ
+TSAYAMYPPGPGSSPEEAFPEHTTTKIVEGCEAKYNVKGKKMRKPRTIYNSSQLQMLQKK
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+>tr|Q24785|Q24785_9METZ Homeobox-containing protein (Fragment) OS=Ephydatia fluviatilis GN=prox3 PE=3 SV=1
+PHSSGSNASTINKQKKDRKPRTPFTSTQLIALERKFRQQKYLSVAERAEFAEYLKLTETQ
+VKIWFQNRRAKEKRLHEAEAERAARSLGFHFHMPMQSKMNTFRHPYCNSQYQTLCLCQFR
+HKIGIGTFPARTTDSISSNSSQPTLPWFLTCNSSTPL
+>sp|P70354|MSX3_MOUSE Homeobox protein MSX-3 OS=Mus musculus GN=Msx3 PE=1 SV=1
+MARATFDMNAAGLEARGGGHTEHGPLPFSVESLLEAERVPGSESGELGVERPLGASKPGA
+WPPPVAHSCPPRAPSPPPCTLRKHKTNRKPRTPFTTAQLLALERKFHQKQYLSIAERAEF
+SSSLSLTETQVKIWFQNRRAKAKRLQEAELEKLKLAAKPLLPAAFALPFPLGTQLHSSAA
+TFGGNAVPGILAGPVAAYGMYYLS
+>tr|Q90263|Q90263_DANRE Empty spiracles homeobox 3 OS=Danio rerio GN=emx3 PE=2 SV=1
+MFQHNKKCFTIESLVGKDSNSSNAAADEPIRPTALRFTESIHPSPFGSCFQNSGRTLYSS
+SPEMMFTDPSTHSTNSGLSLRHLQIPTQPFFSPHQRDTLNFYPWVLRNRYLGHRFQGDDS
+SPENLLLHGPFSRKPKRIRTAFSPSQLLRLERAFEKNHYVVGAERKQLANGLCLTETQVK
+VWFQNRRTKHKRQKLEEESPDPQQKRKGSQHVSRWRVATQQGSPEDIDVISED
--- /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
@@ -0,0 +1,26248 @@
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--- a/tool_dependencies.xml	Sat Jun 14 18:01:42 2014 -0400
+++ b/tool_dependencies.xml	Thu Mar 26 20:04:12 2015 -0400
@@ -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>