Mercurial > repos > iracooke > msgfplus
changeset 9:827f19088303 draft default tip
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
| author | iracooke |
|---|---|
| date | Tue, 20 Oct 2015 20:01:22 -0400 |
| parents | dfb2b78b3aff |
| children | |
| files | README README.md README.rst msgfplus_search.xml repository_dependencies.xml test-data/testdb.fasta test-data/tiny.mzML tool-data/msgfplus_mods.loc.sample tool-data/msgfplus_mods_fix.loc.sample tool-data/msgfplus_mods_var.loc.sample tool_dependencies.xml |
| diffstat | 11 files changed, 533 insertions(+), 79 deletions(-) [+] |
line wrap: on
line diff
--- a/README Mon Jan 05 17:17:45 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -This package is a galaxy wrapper for the MSGF+ search tool. - -Requirements: -This package uses protk, msgfplus and proteowizard, which must be installed separately. - -For instructions please see: https://github.com/iracooke/protk/#galaxy-integration \ No newline at end of file
--- a/README.md Mon Jan 05 17:17:45 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -## What is it? -Galaxy tool definition file and wrapper scripts for the [MSGF+ Search Engine](http://proteomics.ucsd.edu/Software/MSGFPlus.html). - -## Installation -Install from the main galaxy toolshed at http://toolshed.g2.bx.psu.edu/ - -Depends on command-line scripts and databases available in the [protk ruby gem](https://bitbucket.org/iracooke/protk). -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Oct 20 20:01:22 2015 -0400 @@ -0,0 +1,43 @@ +MS-GF+ +====== + +Galaxy wrapper for the `MS-GF+`__ tandem ms search tool + +.. _msgfplus: http://proteomics.ucsd.edu/software-tools/ms-gf/ +__ msgfplus_ + +Requirements +------------ + +This package uses protk_, msgfplus_ and the `idconvert` tool from Proteowizard_ which need to be present in order for the tool to work. + +.. _protk: https://github.com/iracooke/protk +.. _Proteowizard: http://proteowizard.sourceforge.net/ + + +There are two ways you can satify these dependencies (choose one): + +1. **Manual Install:** Details on how to install protk_, msgfplus_ and Proteowizard_ 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_ + + +Information on the MS-GF+ search tool itself can be found here_ + +.. _here: http://proteowizard.sourceforge.net/ +
--- a/msgfplus_search.xml Mon Jan 05 17:17:45 2015 -0500 +++ b/msgfplus_search.xml Tue Oct 20 20:01:22 2015 -0400 @@ -1,8 +1,8 @@ -<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.3"> +<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.1.0"> <description>Run an MSGF+ Search</description> <requirements> - <container type="docker">simonalpha/protk:1.4.0</container> - <requirement type="package" version="1.3">protk</requirement> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> <requirement type="package" version="20140210">msgfplus</requirement> <requirement type="package" version="3_0_4388">proteowizard</requirement> </requirements> @@ -47,8 +47,7 @@ --num-reported-matches=$num_reported_matches --java-mem=$java_mem - --threads $threads - + --threads "\${GALAXY_SLOTS:-12}" #if $pepxml_output_use: --pepxml #end if @@ -75,7 +74,7 @@ </conditional> <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/> <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed"> - <options from_file="msgfplus_mods.loc"> + <options from_file="msgfplus_mods_var.loc"> <column name="name" index="0" /> <column name="value" index="2" /> </options> @@ -85,7 +84,7 @@ <param name="custom_mod" type="text" /> </repeat> <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed"> - <options from_file="msgfplus_mods.loc"> + <options from_file="msgfplus_mods_fix.loc"> <column name="name" index="0" /> <column name="value" index="2" /> </options> @@ -155,7 +154,6 @@ <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/> <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/> <param name="java_mem" help="Increase this value if you get out of memory errors" type="text" size="80" value="3500M" label="Java Memory Limit"/> - <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search."/> <param name="pepxml_output_use" checked="true" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" /> </inputs> <outputs> @@ -165,14 +163,23 @@ </change_format> </data> </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="bsa.fasta"/> - <param name="input_file" value="bsa.mzML"/> - <output name="output" file="bsa.mzid" compare="sim_size" delta="600" /> + <param name="fasta_file" value="testdb.fasta" format="fasta"/> + <param name="input_file" value="tiny.mzML" format="mzml"/> + <param name="precursor_ion_tol" value="200"/> + <param name="pepxml_output_use" value="true"/> + <output name="output" format="raw_pepxml"> + <assert_contents> + <has_text text="FALPQYLKTVYQHQKAMKPWIQPKTKVIPYVRYL" /> + </assert_contents> + </output> </test> </tests> + <help> **What it does**
--- a/repository_dependencies.xml Mon Jan 05 17:17:45 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Proteomics datatypes"> - <repository changeset_revision="9cfabf0b942d" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testdb.fasta Tue Oct 20 20:01:22 2015 -0400 @@ -0,0 +1,38 @@ +>sp|ALBU_BOVIN| +MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIA +FSQYLQQCPFDEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCK +VASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEF +KADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGAC +LLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVARLSQKFPKAE +FVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKE +CCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFL +GSFLYEYSRRHPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKL +KHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVS +RSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCC +TESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQT +ALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVV +STQTALA +>sp|AMYS_HUMAN| +MKLFWLLFTIGFCWAQYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPK +GFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTR +CNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWD +FNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNH +LIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVI +DLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWG +FMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGF +TRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCE +HRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWT +FSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAED +PFIAIHAESKL +>sp|CAS1_BOVIN| +MKLLILTCLVAVALARPKHPIKHQGLPQEVLNENLLRFFVAPFPEVFGKE +KVNELSKDIGSESTEDQAMEDIKQMEAESISSSEEIVPNSVEQKHIQKED +VPSERYLGYLEQLLRLKKYKVPQLEIVPNSAEERLHSMKEGIHAQQKEPM +IGVNQELAYFYPELFRQFYQLDAYPSGAWYYVPLGTQYTDAPSFSDIPNP +IGSENSEKTTMPLW +>sp|CAS2_BOVIN| +MKFFIFTCLLAVALAKNTMEHVSSSEESIISQETYKQEKNMAINPSKENL +CSTFCKEVVRNANEEEYSIGSSSEESAEVATEEVKITVDDKHYQKALNEI +NQFYQKFPQYLQYLYQGPIVLNPWDQVKRNAVPITPTLNREQLSTSEENS +KKTVDMESTEVFTKKTKLTEEEKNRLNFLKKISQRYQKFALPQYLKTVYQ +HQKAMKPWIQPKTKVIPYVRYL \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tiny.mzML Tue Oct 20 20:01:22 2015 -0400 @@ -0,0 +1,317 @@ +<?xml version="1.0" encoding="ISO-8859-1"?> +<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.1_idx.xsd"> + <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="tiny" version="1.1.0"> + <cvList count="2"> + <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="3.7.3" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/> + <cv id="UO" fullName="Unit Ontology" version="18:03:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/> + </cvList> + <fileDescription> + <fileContent> + <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/> + <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/> + <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/> + </fileContent> + <sourceFileList count="2"> + <sourceFile id="sourceFile" name="ANALYSIS.BAF" location="Q:/Data/MALDI/1110/MT573/Tilo%20Knobs%20S2_BAF.d"> + <cvParam cvRef="MS" accession="MS:1000772" name="Bruker BAF nativeID format" value=""/> + <cvParam cvRef="MS" accession="MS:1000815" name="Bruker BAF file" value=""/> + <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="2107bc8ebc6160293e3c95b1848d4afa96435c39"/> + </sourceFile> + <sourceFile id="tiny.mzML" name="tiny.mzML" location="file://."> + <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="c52beeb6ca5b6865b55e67b919317a96a064854b"/> + </sourceFile> + </sourceFileList> + <contact> + <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value=" pfaou"/> + <cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value=""/> + </contact> + </fileDescription> + <sampleList count="1"> + <sample id="sample" name=""> + </sample> + </sampleList> + <softwareList count="3"> + <software id="exportSoftware" version="3.0.1"> + <cvParam cvRef="MS" accession="MS:1000717" name="CompassXport" value=""/> + </software> + <software id="instrumentSoftware" version="3.3.85.0"> + <cvParam cvRef="MS" accession="MS:1000692" name="Bruker software" value=""/> + <userParam name="AcquisitionProgram" value="flexControl"/> + </software> + <software id="pwiz_2.2.0_x0020__x0028_TPP_x0020_v4.6_x0020_OCCUPY_x0020_rev_x0020_1_x002c__x0020_Build_x0020_201210300824_x0020__x0028_linux_x0029__x0029_" version="2.2.0 (TPP v4.6 OCCUPY rev 1, Build 201210300824 (linux))"> + <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard" value=""/> + </software> + </softwareList> + <instrumentConfigurationList count="1"> + <instrumentConfiguration id="instrument"> + <cvParam cvRef="MS" accession="MS:1000705" name="ultraflex III TOF/TOF" value=""/> + <componentList count="3"> + <source order="1"> + <cvParam cvRef="MS" accession="MS:1000075" name="matrix-assisted laser desorption ionization" value=""/> + </source> + <analyzer order="2"> + <cvParam cvRef="MS" accession="MS:1000084" name="time-of-flight" value=""/> + </analyzer> + <detector order="3"> + <cvParam cvRef="MS" accession="MS:1000026" name="detector type" value=""/> + </detector> + </componentList> + <softwareRef ref="instrumentSoftware"/> + </instrumentConfiguration> + </instrumentConfigurationList> + <dataProcessingList count="2"> + <dataProcessing id="exportation"> + <processingMethod order="1" softwareRef="instrumentSoftware"> + <cvParam cvRef="MS" accession="MS:1000035" name="peak picking" value=""/> + </processingMethod> + <processingMethod order="2" softwareRef="exportSoftware"> + <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/> + <cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="2011-10-11T01:50:11"/> + </processingMethod> + </dataProcessing> + <dataProcessing id="pwiz_Reader_conversion"> + <processingMethod order="0" softwareRef="pwiz_2.2.0_x0020__x0028_TPP_x0020_v4.6_x0020_OCCUPY_x0020_rev_x0020_1_x002c__x0020_Build_x0020_201210300824_x0020__x0028_linux_x0029__x0029_"> + <cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" value=""/> + </processingMethod> + </dataProcessing> + </dataProcessingList> + <run id="tiny" defaultInstrumentConfigurationRef="instrument" startTimeStamp="2011-10-01T12:55:24.000+00:00"> + <spectrumList count="6" defaultDataProcessingRef="pwiz_Reader_conversion"> + <spectrum index="0" id="scan=1" defaultArrayLength="1"> + <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/> + <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/> + <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/> + <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="292.75354107"/> + <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="1251.52908446" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="292.75354107" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/> + <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/> + <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1251.52908446" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="1251.52908446" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan> + <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="24" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/> + </scan> + </scanList> + <binaryDataArrayList count="2"> + <binaryDataArray encodedLength="12"> + <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <binary>AAAAwB2Ok0A=</binary> + </binaryDataArray> + <binaryDataArray encodedLength="8"> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/> + <binary>dGCSQw==</binary> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum index="1" id="scan=2" defaultArrayLength="3"> + <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/> + <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/> + <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/> + <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="635.53870230"/> + <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="977.60470404" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="355.11991292" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/> + <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/> + <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="3376.77756017" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="977.60470404" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan> + <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="24.1667" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/> + </scan> + </scanList> + <binaryDataArrayList count="2"> + <binaryDataArray encodedLength="32"> + <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <binary>AAAAYNaMjkAAAABAVAyPQAAAACCOYapA</binary> + </binaryDataArray> + <binaryDataArray encodedLength="16"> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/> + <binary>WY+xQyRdf0ONcMhB</binary> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum index="2" id="scan=3" defaultArrayLength="1"> + <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/> + <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/> + <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/> + <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="399.45785685"/> + <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="1251.53115856" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="399.45785685" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/> + <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1"/> + <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1251.53115856" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="1251.53115856" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan> + <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="24.3333" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/> + </scan> + </scanList> + <binaryDataArrayList count="2"> + <binaryDataArray encodedLength="12"> + <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <binary>AAAA4B+Ok0A=</binary> + </binaryDataArray> + <binaryDataArray encodedLength="8"> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/> + <binary>m7rHQw==</binary> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum index="3" id="scan=4" defaultArrayLength="100"> + <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/> + <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/> + <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/> + <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="170131.96561892"/> + <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="1370.83346708" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="87545.77844029" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/> + <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/> + <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1370.83346708" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="42.72572498" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan> + <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="46" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/> + </scan> + </scanList> + <precursorList count="1"> + <precursor> + <selectedIonList count="1"> + <selectedIon> + <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1370.72" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + </selectedIon> + </selectedIonList> + <activation> + <cvParam cvRef="MS" accession="MS:1000044" name="dissociation method" value=""/> + </activation> + </precursor> + </precursorList> + <binaryDataArrayList count="2"> + <binaryDataArray encodedLength="1068"> + <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <binary>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</binary> + </binaryDataArray> + <binaryDataArray encodedLength="536"> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/> + <binary>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</binary> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum index="4" id="scan=5" defaultArrayLength="74"> + <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/> + <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/> + <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/> + <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="71858.26664074"/> + <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="1392.93812397" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="32154.98453642" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/> + <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/> + <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1392.93812397" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="41.86566780" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan> + <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="46" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/> + </scan> + </scanList> + <precursorList count="1"> + <precursor> + <selectedIonList count="1"> + <selectedIon> + <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1392.7" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + </selectedIon> + </selectedIonList> + <activation> + <cvParam cvRef="MS" accession="MS:1000044" name="dissociation method" value=""/> + </activation> + </precursor> + </precursorList> + <binaryDataArrayList count="2"> + <binaryDataArray encodedLength="792"> + <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <binary>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</binary> + </binaryDataArray> + <binaryDataArray encodedLength="396"> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/> + <binary>fTeCQvvemELrqctC4FtcQxBcYEOv2wdE+RO/Ql9K2kPIlP5C8b7YQlUhoEKUBRhDJUb1QoxHr0I7iHBDJEZZQ0uh9UJTPURDWj4cRPXrHEM7LfRCeJHFQnepDkM6gvNChXSTQpxAQkMacZhDgXYnQ1AVGkPGsghDnblmQ02IHUMGiQBD7L4EQzifP0M5LEdDBV86Q+IIckOcXF9DA8U+Q3RS5EOwYzRDXg0IQ+rsGENjnPJCxu4HQ7+Nf0NRm2xDTjhxQzs0iEOd4NdDkJ+OQ5hxXUMblIFDk/YBRCES8UMtL6FDp56EQyBFhkOwkutEGWqLRBfjk0P9U7FEMYqLRArhj0MDKORD+dRARHmCNESti51EoEBCRGy8YUQJ1wlGXOXhRfg1+0Y=</binary> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + <spectrum index="5" id="scan=6" defaultArrayLength="48"> + <cvParam cvRef="MS" accession="MS:1000130" name="positive scan" value=""/> + <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" value=""/> + <cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" value=""/> + <cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="31088.32173543"/> + <cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="1488.98220680" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="9322.68373807" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/> + <cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="2"/> + <cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="1491.24548135" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="59.96272840" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <scanList count="1"> + <cvParam cvRef="MS" accession="MS:1000795" name="no combination" value=""/> + <scan> + <cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="87.8333" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/> + </scan> + </scanList> + <precursorList count="1"> + <precursor> + <selectedIonList count="1"> + <selectedIon> + <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="1489.86" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + </selectedIon> + </selectedIonList> + <activation> + <cvParam cvRef="MS" accession="MS:1000044" name="dissociation method" value=""/> + </activation> + </precursor> + </precursorList> + <binaryDataArrayList count="2"> + <binaryDataArray encodedLength="512"> + <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/> + <binary>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</binary> + </binaryDataArray> + <binaryDataArray encodedLength="256"> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/> + <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/> + <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/> + <binary>DykLQ5jS4kJ0ggxDC8pKQ/sT+0JBi/xC6V0RQ+8nhUOldBFD3dHoQm+cI0N9sgxDumcAQ3Zc8UKzwLNDiQUTQ8XNIUONE1lD3Q+gQ9aVJkPvReFD/Q4uQ2eyZkMvRitDeOMTQ8E0cUNzSotDWOkdQ83tfkP1u6xDDTHOQ575v0P4BVlDlp+dQ1Fkq0PCvJVDx2SfQ3ams0PnGgpENKcMRDawDkTCaiJEuCkyRLUbA0WRVBtFWFIdRbyqEUbw0T9F</binary> + </binaryDataArray> + </binaryDataArrayList> + </spectrum> + </spectrumList> + </run> + </mzML> + <indexList count="2"> + <index name="spectrum"> + <offset idRef="scan=1">4983</offset> + <offset idRef="scan=2">7468</offset> + <offset idRef="scan=3">9985</offset> + <offset idRef="scan=4">12475</offset> + <offset idRef="scan=5">17113</offset> + <offset idRef="scan=6">21331</offset> + </index> + </indexList> + <indexListOffset>25171</indexListOffset> + <fileChecksum>0a78dcf8705de44cf7673d1a237899b2eec9bafe</fileChecksum> +</indexedmzML>
--- a/tool-data/msgfplus_mods.loc.sample Mon Jan 05 17:17:45 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ -#This file lists the names of inbuilt chemical modifications accepted by msgfplus -#Each entry consists of 4 tab separated fields like this -#<Displayed Name> <DBKey> <Modification String> <DBKey> -# -#Modification strings should conform to the standard MSGFPlus syntax with the following exception -#The ModType field is overridden by the msgfplus_search.rb tool. In other words any of these mods -#May be passed to the tool as a variable or fixed mod and the tool will substitute the appropriate ModType -#value -# -#Standard MSGFPlus syntax is -# -# To input a modification, use the following command: -# Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required). -# CompositionStr (C[Num]H[Num]N[Num]O[Num]S[Num]P[Num]) -# - C (Carbon), H (Hydrogen), N (Nitrogen), O (Oxygen), S (Sulfer) and P (Phosphorus) are allowed. -# - Atom can be omitted. The sequence of atoms must be followed. -# - Negative numbers are allowed. -# - E.g. C2H2O1 (valid), H2C1O1 (invalid) -# Mass can be used instead of CompositionStr. It is important to specify accurate masses (integer masses are insufficient). -# - E.g. 15.994915 -# Residues: affected amino acids (must be upper letters) -# - Must be uppor letters or * -# - Use * if this modification is applicable to any residue. -# - * should not be "anywhere" modification (e.g. "15.994915, *, opt, any, Oxidation" is not allowed.) -# - E.g. NQ, * -# ModType: "fix" for fixed modifications, "opt" for variable modifications (case insensitive) -# Position: position in the peptide where the modification can be attached. -# - One of the following five values should be used: -# - any (anywhere), N-term (peptide N-term), C-term (peptide C-term), Prot-N-term (protein N-term), Prot-C-term (protein C-term) -# - Case insensitive -# - "-" can be omitted -# - E.g. any, Any, Prot-n-Term, ProtNTerm => all valid -# Name: name of the modification (Unimod PSI-MS name) -# - For proper mzIdentML output, this name should be the same as the Unimod PSI-MS name -# - E.g. Phospho, Acetyl -#C2H3N1O1,C,fix,any,Carbamidomethyl # Fixed Carbamidomethyl C -# Variable Modifications (default: none) -#O1,M,opt,any,Oxidation # Oxidation M -#15.994915,M,opt,any,Oxidation # Oxidation M (mass is used instead of CompositionStr) -#H-1N-1O1,NQ,opt,any,Deamidated # Negative numbers are allowed. -#C2H3NO,*,opt,N-term,Carbamidomethyl # Variable Carbamidomethyl N-term -#H-2O-1,E,opt,N-term,Pyro_glu # Pyro-glu from E -#H-3N-1,Q,opt,N-term,Pyro-glu # Pyro-glu from Q -#C2H2O,*,opt,Prot-N-term,Acetyl # Acetylation Protein N-term -#C2H2O1,K,opt,any,Acetyl # Acetylation K -#CH2,K,opt,any,Methy # Methylation K -#HO3P,STY,opt,any,Phospho # Phosphorylation STY - -Carbamidomethyl C carbamidomethyl_c_ C2H3N1O1,C,opt,any,Carbamidomethyl carbamidomethyl_c_ -Oxidation M oxidation_m_ O1,M,opt,any,Oxidation oxidation_m_ \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/msgfplus_mods_fix.loc.sample Tue Oct 20 20:01:22 2015 -0400 @@ -0,0 +1,50 @@ +#This file lists the names of inbuilt chemical modifications accepted by msgfplus +#Each entry consists of 4 tab separated fields like this +#<Displayed Name> <DBKey> <Modification String> <DBKey> +# +#Modification strings should conform to the standard MSGFPlus syntax with the following exception +#The ModType field is overridden by the msgfplus_search.rb tool. In other words any of these mods +#May be passed to the tool as a variable or fixed mod and the tool will substitute the appropriate ModType +#value +# +#Standard MSGFPlus syntax is +# +# To input a modification, use the following command: +# Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required). +# CompositionStr (C[Num]H[Num]N[Num]O[Num]S[Num]P[Num]) +# - C (Carbon), H (Hydrogen), N (Nitrogen), O (Oxygen), S (Sulfer) and P (Phosphorus) are allowed. +# - Atom can be omitted. The sequence of atoms must be followed. +# - Negative numbers are allowed. +# - E.g. C2H2O1 (valid), H2C1O1 (invalid) +# Mass can be used instead of CompositionStr. It is important to specify accurate masses (integer masses are insufficient). +# - E.g. 15.994915 +# Residues: affected amino acids (must be upper letters) +# - Must be uppor letters or * +# - Use * if this modification is applicable to any residue. +# - * should not be "anywhere" modification (e.g. "15.994915, *, opt, any, Oxidation" is not allowed.) +# - E.g. NQ, * +# ModType: "fix" for fixed modifications, "opt" for variable modifications (case insensitive) +# Position: position in the peptide where the modification can be attached. +# - One of the following five values should be used: +# - any (anywhere), N-term (peptide N-term), C-term (peptide C-term), Prot-N-term (protein N-term), Prot-C-term (protein C-term) +# - Case insensitive +# - "-" can be omitted +# - E.g. any, Any, Prot-n-Term, ProtNTerm => all valid +# Name: name of the modification (Unimod PSI-MS name) +# - For proper mzIdentML output, this name should be the same as the Unimod PSI-MS name +# - E.g. Phospho, Acetyl +#C2H3N1O1,C,fix,any,Carbamidomethyl # Fixed Carbamidomethyl C +# Variable Modifications (default: none) +#O1,M,opt,any,Oxidation # Oxidation M +#15.994915,M,opt,any,Oxidation # Oxidation M (mass is used instead of CompositionStr) +#H-1N-1O1,NQ,opt,any,Deamidated # Negative numbers are allowed. +#C2H3NO,*,opt,N-term,Carbamidomethyl # Variable Carbamidomethyl N-term +#H-2O-1,E,opt,N-term,Pyro_glu # Pyro-glu from E +#H-3N-1,Q,opt,N-term,Pyro-glu # Pyro-glu from Q +#C2H2O,*,opt,Prot-N-term,Acetyl # Acetylation Protein N-term +#C2H2O1,K,opt,any,Acetyl # Acetylation K +#CH2,K,opt,any,Methy # Methylation K +#HO3P,STY,opt,any,Phospho # Phosphorylation STY + +Carbamidomethyl C carbamidomethyl_c_ C2H3N1O1,C,fix,any,Carbamidomethyl carbamidomethyl_c_ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/msgfplus_mods_var.loc.sample Tue Oct 20 20:01:22 2015 -0400 @@ -0,0 +1,55 @@ +#This file lists the names of inbuilt chemical modifications accepted by msgfplus +#Each entry consists of 4 tab separated fields like this +#<Displayed Name> <DBKey> <Modification String> <DBKey> +# +#Modification strings should conform to the standard MSGFPlus syntax with the following exception +#The ModType field is overridden by the msgfplus_search.rb tool. In other words any of these mods +#May be passed to the tool as a variable or fixed mod and the tool will substitute the appropriate ModType +#value +# +#Standard MSGFPlus syntax is +# +# To input a modification, use the following command: +# Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required). +# CompositionStr (C[Num]H[Num]N[Num]O[Num]S[Num]P[Num]) +# - C (Carbon), H (Hydrogen), N (Nitrogen), O (Oxygen), S (Sulfer) and P (Phosphorus) are allowed. +# - Atom can be omitted. The sequence of atoms must be followed. +# - Negative numbers are allowed. +# - E.g. C2H2O1 (valid), H2C1O1 (invalid) +# Mass can be used instead of CompositionStr. It is important to specify accurate masses (integer masses are insufficient). +# - E.g. 15.994915 +# Residues: affected amino acids (must be upper letters) +# - Must be uppor letters or * +# - Use * if this modification is applicable to any residue. +# - * should not be "anywhere" modification (e.g. "15.994915, *, opt, any, Oxidation" is not allowed.) +# - E.g. NQ, * +# ModType: "fix" for fixed modifications, "opt" for variable modifications (case insensitive) +# Position: position in the peptide where the modification can be attached. +# - One of the following five values should be used: +# - any (anywhere), N-term (peptide N-term), C-term (peptide C-term), Prot-N-term (protein N-term), Prot-C-term (protein C-term) +# - Case insensitive +# - "-" can be omitted +# - E.g. any, Any, Prot-n-Term, ProtNTerm => all valid +# Name: name of the modification (Unimod PSI-MS name) +# - For proper mzIdentML output, this name should be the same as the Unimod PSI-MS name +# - E.g. Phospho, Acetyl +#C2H3N1O1,C,fix,any,Carbamidomethyl # Fixed Carbamidomethyl C +# Variable Modifications (default: none) +#O1,M,opt,any,Oxidation # Oxidation M +#15.994915,M,opt,any,Oxidation # Oxidation M (mass is used instead of CompositionStr) +#H-1N-1O1,NQ,opt,any,Deamidated # Negative numbers are allowed. +#C2H3NO,*,opt,N-term,Carbamidomethyl # Variable Carbamidomethyl N-term +#H-2O-1,E,opt,N-term,Pyro_glu # Pyro-glu from E +#H-3N-1,Q,opt,N-term,Pyro-glu # Pyro-glu from Q +#C2H2O,*,opt,Prot-N-term,Acetyl # Acetylation Protein N-term +#C2H2O1,K,opt,any,Acetyl # Acetylation K +#CH2,K,opt,any,Methy # Methylation K +#HO3P,STY,opt,any,Phospho # Phosphorylation STY + +Oxidation M oxidation_m_ O1,M,opt,any,Oxidation oxidation_m_ +Acetylation Protein N-term acetyl_nterm_ C2H2O,*,opt,Prot-N-term,Acetyl acetyl_nterm_ +Deamidation NQ deamidation_nq_ H-1N-1O1,NQ,opt,any,Deamidated deamidation_nq_ +Acetylation K acetyl_k_ C2H2O1,K,opt,any,Acetyl acetyl_k_ +Methylation K methyl_k_ CH2,K,opt,any,Methy methyl_k_ +Phosphorylation STY phospho_sty_ HO3P,STY,opt,any,Phospho phospho_sty_ +Carbamidomethyl N-term carbamidomethyl_nterm_ C2H3NO,*,opt,N-term,Carbamidomethyl carbamidomethyl_nterm_
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 20 20:01:22 2015 -0400 @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="protk" version="1.4.3"> + <repository changeset_revision="2b240f1be1ce" name="package_protk_1_4_3" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="msgfplus" version="20140210"> + <repository changeset_revision="7d4a89b80c17" name="package_msgfplus_20140210" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="proteowizard" version="3_0_4388"> + <repository changeset_revision="d21f91402d1c" name="package_proteowizard_3_0_4388" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>