changeset 14:f419359341ff draft

Uploaded

--- a/README.md	Fri May 09 04:11:23 2014 -0400
+++ b/README.md	Mon Jun 09 06:32:28 2014 -0400
@@ -57,6 +57,8 @@
 
 Authors and contributors:
 
+* Bjoern Gruening <[e-mail]>
+* Ira Cooke
 * Cody Wang
 * Fred Sadler
 * John Chilton <[e-mail]>

--- a/peptide_shaker.xml	Fri May 09 04:11:23 2014 -0400
+++ b/peptide_shaker.xml	Mon Jun 09 06:32:28 2014 -0400
@@ -1,14 +1,15 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.18.3.0">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.19.1.0">
     <description>
         Perform protein identification using various search engines (using SearchGUI) and combine results with PeptideShaker.
     </description>
     <requirements>
-        <requirement type="package" version="0.28.0">peptide_shaker</requirement>
-        <requirement type="package" version="1.18.0">searchgui</requirement>
+        <requirement type="package" version="0.30.1">peptide_shaker</requirement>
+        <requirement type="package" version="1.19.1">searchgui</requirement>
         <!--<requirement type="package" version="2.2.29">blast+</requirement>-->
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Job Failed" />
+        <regex match="Error" level="fatal" description="Error encounterd!"/> 
     </stdio>
     <command>
 
@@ -109,7 +110,7 @@
         ################
         ## Search CLI ##
         ################
-        (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI
+        (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI 
             -temp_folder `pwd`
             -spectrum_files \$cwd
             -output_folder \$cwd/output
@@ -117,12 +118,13 @@
 
             -threads "\${GALAXY_SLOTS:-12}"
             -correct_titles "${correct_titles}"
+            $missing_titles
             -mgf_splitting "${mgf_splitting}"
             -mgf_spectrum_count "${mgf_spectrum_count}"
 
             ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
             ## the tree is generated afterwards in PeptideShaker
-            -protein_tree 0
+            -protein_index 0
 
             ##-makeblastdb_folder \$BLAST_ROOT_DIR
 
@@ -250,6 +252,19 @@
         2>> $temp_stderr)
         &amp;&amp;
 
+        #if 'mzidentML' in str($outputs).split(','):
+            java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.MzidCLI
+                -in \$cwd/peptide_shaker_output.cps
+                -output_file output.mzid
+                -contact_first_name 'Proteomics'
+                -contact_last_name 'Galaxy'
+                -contact_email '[e-mail]'
+                -contact_address '[e-mail]'
+                -organization_name 'University of Minnesota'
+                -organization_email '[e-mail]'
+                -organization_address 'Minneapolis, MN 55455, Vereinigte Staaten'
+                ;
+        #end if
         #if '0' in str($outputs).split(','):
             find \$cwd/output_reports -name '*Certificate*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
             ;
@@ -329,6 +344,8 @@
             <option value="2">delete spectra</option>
         </param>
 
+        <param name="missing_titles" label="Add missing spectrum titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" help="(-missing_titles)"/>
+
         <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
             help="Choose a smaller value if you are running on a machine with limited memory"/>
         <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
@@ -592,8 +609,6 @@
             </param>
             <when value="basic" />
             <when value="advanced">
-                <param name="xtandem" label="Run X! Tandem" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-
                 <conditional name="xtandem">
                     <param name="xtandem_selector" type="select" label="Run X!Tandem search">
                         <option value="yes" selected="True">Search with X!Tandem</option>
@@ -601,30 +616,27 @@
                     </param>
                     <when value="no" />
                     <when value="yes">
-
-
-                            <param name="xtandem_npeaks" label="X!Tandem: Total Peaks" type="integer" value="50" help="Maximum number of peaks to be used from a spectrum"/>
-                            <param name="xtandem_min_peaks" label="X!Tandem: Min Peaks" type="integer" value="15" help="Minimum number of peaks required for a spectrum to be considered"/>
-                            <param name="xtandem_min_frag_mz" label="X!Tandem: Min Frag m/z" type="integer" value="200" help="Fragment mass peaks with m/z less than this value will be discarded"/>
-                            <param name="xtandem_min_prec_mass" label="X!Tandem: Min Precursor Mass" type="integer" value="200" help="Minimum mass of 1+ mass of parent ion to be considered"/>
-                            <param name="xtandem_noise_suppr" label="X!Tandem: Noise Suppression" type="boolean" checked="true" truevalue="1" falsevalue="0" help="Use noise suppression"/>
-
+                        <param name="xtandem_npeaks" label="X!Tandem: Total Peaks" type="integer" value="50" help="Maximum number of peaks to be used from a spectrum"/>
+                        <param name="xtandem_min_peaks" label="X!Tandem: Min Peaks" type="integer" value="15" help="Minimum number of peaks required for a spectrum to be considered"/>
+                        <param name="xtandem_min_frag_mz" label="X!Tandem: Min Frag m/z" type="integer" value="200" help="Fragment mass peaks with m/z less than this value will be discarded"/>
+                        <param name="xtandem_min_prec_mass" label="X!Tandem: Min Precursor Mass" type="integer" value="200" help="Minimum mass of 1+ mass of parent ion to be considered"/>
+                        <param name="xtandem_noise_suppr" label="X!Tandem: Noise Suppression" type="boolean" checked="true" truevalue="1" falsevalue="0" help="Use noise suppression"/>
 
-                            <conditional name="xtandem_refine"><!-- -xtandem_refine -->
-                                <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
-                                    <option value="no" selected="True">Don't refine</option>
-                                    <option value="yes" >Use refinement</option>
-                                </param>
-                                <when value="no"/>
-                                <when value="yes">
-                                    <param name="xtandem_refine_unc" label="X!Tandem: Unanticipated cleavage, refinement" type="boolean" truevalue="1" falsevalue="0" help="Allow for unanticipated cleavage during refinement"/>
-                                    <param name="xtandem_refine_semi" label="X!Tandem: Cleavage semi, refinement" type="boolean" truevalue="1" falsevalue="0" help="Search for semi-tryptic peptides during refinement"/>
-                                    <param name="xtandem_refine_p_mut" label="X!Tandem: Point mutations, refinement" type="boolean" truevalue="1" falsevalue="0" help="Allow for point mutations during refinement"/>
-                                    <param name="xtandem_refine_snaps" label="X!Tandem: snAPs, refinement" type="boolean" truevalue="1" falsevalue="0" help="Search for known single amino acid polymorphisms during refinement"/>
-                                    <param name="xtandem_refine_spec_synt" label="X!Tandem: Spectrum synthesis, refinement" type="boolean" truevalue="1" falsevalue="0" help="Use spectrum synthesis scoring"/>
-                                </when>
-                            </conditional>
-                        </when>
+                        <conditional name="xtandem_refine"><!-- -xtandem_refine -->
+                            <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
+                                <option value="no" selected="True">Don't refine</option>
+                                <option value="yes" >Use refinement</option>
+                            </param>
+                            <when value="no"/>
+                            <when value="yes">
+                                <param name="xtandem_refine_unc" label="X!Tandem: Unanticipated cleavage, refinement" type="boolean" truevalue="1" falsevalue="0" help="Allow for unanticipated cleavage during refinement"/>
+                                <param name="xtandem_refine_semi" label="X!Tandem: Cleavage semi, refinement" type="boolean" truevalue="1" falsevalue="0" help="Search for semi-tryptic peptides during refinement"/>
+                                <param name="xtandem_refine_p_mut" label="X!Tandem: Point mutations, refinement" type="boolean" truevalue="1" falsevalue="0" help="Allow for point mutations during refinement"/>
+                                <param name="xtandem_refine_snaps" label="X!Tandem: snAPs, refinement" type="boolean" truevalue="1" falsevalue="0" help="Search for known single amino acid polymorphisms during refinement"/>
+                                <param name="xtandem_refine_spec_synt" label="X!Tandem: Spectrum synthesis, refinement" type="boolean" truevalue="1" falsevalue="0" help="Use spectrum synthesis scoring"/>
+                            </when>
+                        </conditional>
+                    </when>
                 </conditional>
 
                 <conditional name="omssa">
@@ -648,15 +660,15 @@
                     </param>
                     <when value="no" />
                     <when value="yes">
-                        <param name="msgf_decoy" label="MS-GF+: Search Decoys" type="boolean" truevalue="1" falsevalue="0" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
-                        <param name="msgf_min_pep_length" label="MS-GF+: Minimum Peptide Length" type="integer" value="6" help="Minimum length for a peptide to be considered"/>
-                        <param name="msgf_max_pep_length" label="MS-GF+: Maximum Peptide Length" type="integer" value="30" help="Maximum length for a peptide to be considered"/>
-                        <param name="msgf_termini" label="MS-GF+: Number of tolerable termini" type="select" format="text" help="Searches will take much longer if selecting a value other than 2">
+                        <param name="msgf_decoy" label="Search Decoys" type="boolean" truevalue="1" falsevalue="0" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
+                        <param name="msgf_min_pep_length" label="Minimum Peptide Length" type="integer" value="6" help="Minimum length for a peptide to be considered"/>
+                        <param name="msgf_max_pep_length" label="Maximum Peptide Length" type="integer" value="30" help="Maximum length for a peptide to be considered"/>
+                        <param name="msgf_termini" label="Number of tolerable termini" type="select" format="text" help="Searches will take much longer if selecting a value other than 2">
                             <option value="0">0 (ie non-specific cleavage)</option>
                             <option value="1">1 (ie semi-tryptic cleavage)</option>
                             <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
                         </param>
-                        <param name="msgf_num_ptms" label="MS-GF+: Max PTMs per peptide" type="integer" value="2"/>
+                        <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/>
                     </when>
                 </conditional>
 
@@ -721,6 +733,7 @@
         </conditional>
 
         <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
+            <option value="mzidentML" selected="True">mzidentML File</option>
             <option value="3" selected="True">Peptide Report</option>
             <option value="4" selected="True">Protein Report</option>
             <option value="2">PSM Report</option>
@@ -731,6 +744,9 @@
         </param>
     </inputs>
     <outputs>
+        <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
+            <filter>'mzidentML' in outputs</filter>
+        </data>
         <data format="cps" name="output" from_work_dir="peptide_shaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
             <filter>'cps' in outputs</filter>
         </data>
@@ -763,7 +779,10 @@
             <param name="species_type_selector" value="no_species_type"/>
             <param name="processing_options_selector" value="no"/>
             <param name="filtering_options_selector" value="no"/>
+            <!--param name="xtandem_selector" value="no"/>-->
             <param name="xtandem_selector" value="yes"/>
+            <param name="xtandem_selector.xtandem_refine_selector" value="yes"/>
+
             <param name="omssa_selector" value="no"/>
             <param name="msgf_selector" value="yes"/>
             <param name="ms_amanda_selector" value="no"/>

--- a/repository_dependencies.xml	Fri May 09 04:11:23 2014 -0400
+++ b/repository_dependencies.xml	Mon Jun 09 06:32:28 2014 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="Required proteomics dependencies.">
-    <repository changeset_revision="25f42af5b73d" name="proteomics_datatypes" owner="iracooke" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="a1b29f86bdbf" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>

--- a/test-data/tinydb.fasta	Fri May 09 04:11:23 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
->cds.comp107265_c0_seq1|m.36816 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.94 EValue:9.0e-68
-LKSSFESSFSIKSRDVTFGNSMNITMVPPELEFFKDNRHKEKSEMQDLNTRLESYLSVGKDDSDANLKLMQELEEIKNGIKTETNNIKATFEAELGQLKNLLDDIDHDKNQVIVIGDNNDEMYKDLEQRIKNYNDMEMIHLSKIRQLDNLLSNYGLKMNQLQKKIGFLCEEKDRDIESINKLRADIDVAKNDLSNEILLRTDAQNRCQSLEEDIEFTKEVHQRELSNMIALADYDPVSQSMDWWNDEFARCIKEIQDEYEDRLNNIQYDMDSHYNSKIQDVETTILQSSAKSEMLDQCSMLENSNAEIEDQTSELEKKNAMLKEQNDLLNRGIREIQSQFETLITEKQSEMLEIRKHFEQSLADLQAIVDDNLSLQMEIMSYKKLLECEELRVGIYPESNANENQGDQGQRQNEQITEPITETIPKRKKPERKISYQRSSKGPLTISECKSDGSYILIENMDQYDGQNLGGWRLVQNVDGMEEYDYTFSRYYLGPGESVKIWAENAGPKGVNDLVWDDLKCLGIGEKVITSLMNQKGKEKSSYTQKAIYKV
->cds.comp307584_c0_seq2|m.40556 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 39.47 EValue:1.0e-14
-DDNYDSLQYSFPKSDHQRKTTYQRSAKGPITITRVQPDGSYIEIENTNIAVNEDISGWKMVQCTDDKIYEYIFDDHVLNGGTCVKIWANGLSGKEENDLVWIDRTCLTTGSVVTTTLMDYNGNEKATFTQ
->cds.comp376950_c0_seq1|m.42080 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 41.38 EValue:1.0e-32
-KELEDINEDNLGRLRRQDEDVSNYEAQNASLRRKCDNLQADKDRDRNNVEKLKGEVTSLRNDLMMETVSRIDSQNKCQTLREELEFLKDIHSQELKELSPTLGKDPFAKSKEWWSSEFSNCIREIQEEYDNRLDSIKTDMDNYYTLKVQEIQTGAAR
->cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67
-METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
->cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67
-METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
->cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10
-SGLAGDSDTMRASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT
->cds.comp41890_c0_seq1|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20
-YQSPTPALVKGELQEHSTYRKNNKGPVAISETDRDGSFILLENTSNSHTVDLSGWKIMQNSDNIDISEYEIENLVLKPGGFAKVWANGMGDPNSGDLVWHNKSRLGVGAKVNTVLLNTRGDEKATYNLETTYNL
->cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91
-MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGTTSITTGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF
->cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92
-MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF
->cds.comp55448_c0_seq1|m.24261 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 96.04 EValue:0.0
-MRRIKKKITLDVRVTELIDQLERQQKELEESRTYHQIDQEQIARQNQQLADLEGEISMLRRSIESLEKEKMRQSNILAKMNDELEKLRMDLNNETINHLDAENRRQTLEEELEFQKDVHAQELKELAALAYRDTTAENREFWRNELAQAIRDIQQEYDAKCDQMRGDIEAYYNLKVQEFRTGATKQNMEVTRNKEENTKLRSNMNEVRNRLADLEARNAQLERTNQDLLRDLEEKDRQNELESCQYKEEITKLRGEMESILKELQDLMDIKLSLELEIAAYRKLLEGEESRVGMKQIVEQVVGARPNEAEVLSSILTRSEGGYEATGDSQISMKMMRGELAAKTTYQRTSKGPVSIKEADSQGQFIALETKKEENITGWKIVRKVDDNMVYSYEIPNVVLKTGTVIKIWSKSHQAQARGDDIVSRENDTWGTGSNVVTILQNEKGEEKANYTQNTVYQ
->cds.comp55448_c0_seq1|m.24262 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 91.49 EValue:5.0e-87
-MSGGFSYSAKIHPRTGYVSRTSQSPYRSSMGSNAAFTRSYEFNYGATAMPGAYANISSTGVNHVKANREREKQDMRDLNERFANYIEKVRFLEAQNKKLAGELEELKSKWGKETSAIKEMYETELEEARKLIDATNKEKNYLGRESN
->cds.comp8310_c0_seq2|m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16
-FKDTCIRDKTDMKGLNERLSEFIEVARYNAILAKKLEKTIKRFHSQEIPEDVERIYEATIKKLRKLLVVFENERDNERAKNLKLQTECAKLKESLEDLKAKEIENRDRLISKFKILEDLQSKAIRIEKNIEIVAEENVLKNNKIEKLKKHFENLKSKITSERRNRSTHKESYDEVKEDFGIFKELKNQQLSSVRFPKYKDSIKYLRKQWSNEFSKCIKELQNEYESRVSSVKEELESNYCTKTEEIQNYVLKSNYESDFLKNRNLVAEESMNMLKNKFKEAKKENVLLNHEKEELEIEFNKSKNEYDHLAEEKNNEILNFKEYAEKILIQLTEILEINNHLQFEIEYYKTVITSGETKIDFDFDGLDDECMTSINSELP

Binary file test-data/tinyoutput.cps has changed

--- a/test-data/tinyspectra.mgf	Fri May 09 04:11:23 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6153 +0,0 @@
-BEGIN IONS
-TITLE= Cmpd 636, +MSn(730.3981), 66.9 min
-PEPMASS=730.39814	92569
-CHARGE=2+
-156.06738	122	
-175.10440	1049	
-186.08322	120	
-187.12501	241	
-188.06515	494	1+
-193.09503	180	
-197.12522	208	
-199.17309	1374	1+
-204.08687	454	1+
-213.14347	128	
-215.11998	747	1+
-227.17167	1524	1+
-229.12416	156	
-233.09327	3574	1+
-236.99586	113	
-243.14264	571	1+
-244.07481	236	
-245.12901	240	
-246.12647	275	
-256.20038	432	1+
-258.12496	133	
-260.19976	423	
-261.09190	17853	1+
-270.16206	114	
-274.12614	207	
-283.15366	136	
-284.18559	406	1+
-286.14626	237	
-287.10013	105	
-301.15759	131	
-303.17924	2962	1+
-310.21264	944	1+
-315.13250	122	
-316.16696	108	
-326.16601	145	
-328.21268	874	1+
-335.13393	406	1+
-338.20704	186	
-339.16449	110	
-342.17857	106	
-344.13585	148	
-346.17426	809	1+
-356.21762	685	1+
-358.15839	265	
-359.26213	106	
-362.14671	528	1+
-366.16564	103	
-370.14930	136	
-374.17893	18824	1+
-380.20460	141	
-384.22488	193	
-387.21562	161	
-388.26191	188	
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-BEGIN IONS
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-END IONS
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-BEGIN IONS
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-END IONS
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-BEGIN IONS
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-END IONS
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-BEGIN IONS
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-END IONS
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-BEGIN IONS
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-BEGIN IONS
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-END IONS
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-END IONS
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-BEGIN IONS
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-END IONS
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-BEGIN IONS
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-END IONS
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-BEGIN IONS
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-END IONS
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-BEGIN IONS
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-END IONS
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-BEGIN IONS
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-1117.55479	637	
-1118.57910	362	
-END IONS
-

--- a/tool_dependencies.xml	Fri May 09 04:11:23 2014 -0400
+++ b/tool_dependencies.xml	Mon Jun 09 06:32:28 2014 -0400
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="searchgui" version="1.18.0">
-        <repository changeset_revision="0df4db0edb9d" name="package_searchgui_1_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="searchgui" version="1.19.1">
+        <repository changeset_revision="3b9a00dd3518" name="package_searchgui_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="peptide_shaker" version="0.28.0">
-        <repository changeset_revision="dc40b31c1d5b" name="package_peptideshaker_0_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="peptide_shaker" version="0.30.1">
+        <repository changeset_revision="a0574a1dc512" name="package_peptideshaker_0_30" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <!--<package name="blast+" version="2.2.29">
         <repository name="package_blast_plus_2_2_29" owner="iuc" />