# HG changeset patch
# User bgruening
# Date 1383141871 14400
# Node ID 035f1902741ab354cace89d28ba7c543359a8256
# Parent 0f06bf18433cf2301fe33db2529fba5fc3079dcb
Uploaded
diff -r 0f06bf18433c -r 035f1902741a MassComb.jar
Binary file MassComb.jar has changed
diff -r 0f06bf18433c -r 035f1902741a README.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt Wed Oct 30 10:04:31 2013 -0400
@@ -0,0 +1,187 @@
+Suite of tools that enable combining popular external mass spectrometry
+data processing tools (like X!Tandem and ProteoWizard's MsPicture)
+into your own Galaxy workflows.
+
+
+TODO - add license info, including info on X!Tandem and ProteoWizard
+
+
+
+
+
+X!TANDEM LICENSE AND README ===========================================
+
+
+ X! tandem protein sequence modeler
+
+ What is it?
+ -----------
+ X! tandem open source software that can model tandem
+ mass spectra with protein sequences. This software
+ has a very simple, unsophistocated application programming
+ interface (API): it simply takes an XML file of instructions
+ on its command line, and output the results into an XML file,
+ which has been specified in the input XML file.
+
+ The Latest Version
+ ------------------
+
+ Details of the latest version can be found on the X! tandem
+ project page under http://www.thegpm.org.
+ This version is the first release the CYCLONE edition (version 2012.10.01.1).
+
+
+ Documentation
+ -------------
+
+ This version of X! tandem is a full release, only including source
+ level documentation. As more releases occur, better documentation
+ will be included.
+
+ Installation
+ ------------
+
+ (IN this case installation is automatically done by Galaxy's Toolshed).
+
+ Licensing
+ ---------
+
+ The Artistic License for all X! software, binaries and documentation
+
+ Preamble
+ The intent of this document is to state the conditions under which a
+ Package may be copied, such that the Copyright Holder maintains some
+ semblance of artistic control over the development of the package,
+ while giving the users of the package the right to use and distribute
+ the Package in a more-or-less customary fashion, plus the right to
+ make reasonable modifications.
+
+ Definitions
+ "Package" refers to the collection of files distributed by the Copyright
+ Holder, and derivatives of that collection of files created through
+ textual modification.
+
+ "Standard Version" refers to such a Package if it has not been modified,
+ or has been modified in accordance with the wishes of the Copyright
+ Holder as specified below.
+
+ "Copyright Holder" is whoever is named in the copyright or copyrights
+ for the package.
+
+ "You" is you, if you're thinking about copying or distributing this Package.
+
+ "Reasonable copying fee" is whatever you can justify on the basis of
+ media cost, duplication charges, time of people involved, and so on.
+ (You will not be required to justify it to the Copyright Holder, but
+ only to the computing community at large as a market that must bear
+ the fee.)
+
+ "Freely Available" means that no fee is charged for the item itself,
+ though there may be fees involved in handling the item. It also means
+ that recipients of the item may redistribute it under the same
+ conditions they received it.
+
+ 1. You may make and give away verbatim copies of the source form of the
+ Standard Version of this Package without restriction, provided that
+ you duplicate all of the original copyright notices and associated
+ disclaimers.
+
+ 2. You may apply bug fixes, portability fixes and other modifications
+ derived from the Public Domain or from the Copyright Holder. A
+ Package modified in such a way shall still be considered the Standard
+ Version.
+
+ 3. You may otherwise modify your copy of this Package in any way, provided
+ that you insert a prominent notice in each changed file stating how and
+ when you changed that file, and provided that you do at least ONE of the
+ following:
+
+ a. place your modifications in the Public Domain or otherwise make them
+ Freely Available, such as by posting said modifications to Usenet
+ or an equivalent medium, or placing the modifications on a major
+ archive site such as uunet.uu.net, or by allowing the Copyright Holder
+ to include your modifications in the Standard Version of the Package.
+ b. use the modified Package only within your corporation or organization.
+ c. rename any non-standard executables so the names do not conflict
+ with standard executables, which must also be provided, and provide
+ a separate manual page for each non-standard executable that clearly
+ documents how it differs from the Standard Version.
+ d. make other distribution arrangements with the Copyright Holder.
+
+ 4. You may distribute the programs of this Package in object code or
+ executable form, provided that you do at least ONE of the following:
+
+ a. distribute a Standard Version of the executables and library files,
+ together with instructions (in the manual page or equivalent) on
+ where to get the Standard Version.
+ b. accompany the distribution with the machine-readable source of the
+ Package with your modifications.
+ c. give non-standard executables non-standard names, and clearly
+ document the differences in manual pages (or equivalent), together
+ with instructions on where to get the Standard Version.
+ d. make other distribution arrangements with the Copyright Holder.
+
+ 5. You may charge a reasonable copying fee for any distribution of
+ this Package. You may charge any fee you choose for support of
+ this Package. You may not charge a fee for this Package itself.
+ However, you may distribute this Package in aggregate with other
+ (possibly commercial) programs as part of a larger (possibly
+ commercial) software distribution provided that you do not a
+ dvertise this Package as a product of your own. You may embed this
+ Package's interpreter within an executable of yours (by linking);
+ this shall be construed as a mere form of aggregation, provided that
+ the complete Standard Version of the interpreter is so embedded.
+
+ 6. The scripts and library files supplied as input to or produced as
+ output from the programs of this Package do not automatically fall
+ under the copyright of this Package, but belong to whomever generated
+ them, and may be sold commercially, and may be aggregated with this
+ Package. If such scripts or library files are aggregated with this
+ Package via the so-called "undump" or "unexec" methods of producing
+ a binary executable image, then distribution of such an image shall
+ neither be construed as a distribution of this Package nor shall it
+ fall under the restrictions of Paragraphs 3 and 4, provided that you
+ do not represent such an executable image as a Standard Version of
+ this Package.
+
+ 7. C subroutines (or comparably compiled subroutines in other languages)
+ supplied by you and linked into this Package in order to emulate
+ subroutines and variables of the language defined by this Package
+ shall not be considered part of this Package, but are the equivalent
+ of input as in Paragraph 6, provided these subroutines do not change
+ the language in any way that would cause it to fail the regression
+ tests for the language.
+
+ 8. Aggregation of this Package with a commercial distribution is always
+ permitted provided that the use of this Package is embedded; that is,
+ when no overt attempt is made to make this Package's interfaces visible
+ to the end user of the commercial distribution. Such use shall not be
+ construed as a distribution of this Package.
+
+ 9. The name of the Copyright Holder may not be used to endorse or promote
+ products derived from this software without specific prior written permission.
+
+ 10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+ WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
+ MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+
+ The End
+
+
+ Contacts
+ --------
+
+ For any questions involving X! tandem, please contact
+ contact@thegpm.org
+
+ Acknowledgments
+ ----------------
+
+ Ron Beavis - system design and implementation
+ Rob Craig - debugging and LINUX implementation
+ Jayson Falkner - code for GeeToo LINUX implementation
+ Patrick Lacasse - initial additions for mzxml and mzdata functionality
+ Brendan McLean - optimized changes for mzxml and mzdata functionality using expat library
+
+
+
diff -r 0f06bf18433c -r 035f1902741a Xtandem.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Xtandem.txt Wed Oct 30 10:04:31 2013 -0400
@@ -0,0 +1,121 @@
+The Artistic License for all X! software, binaries and documentation
+
+Preamble
+The intent of this document is to state the conditions under which a
+Package may be copied, such that the Copyright Holder maintains some
+semblance of artistic control over the development of the package,
+while giving the users of the package the right to use and distribute
+the Package in a more-or-less customary fashion, plus the right to
+make reasonable modifications.
+
+Definitions
+"Package" refers to the collection of files distributed by the Copyright
+ Holder, and derivatives of that collection of files created through
+ textual modification.
+
+"Standard Version" refers to such a Package if it has not been modified,
+ or has been modified in accordance with the wishes of the Copyright
+ Holder as specified below.
+
+"Copyright Holder" is whoever is named in the copyright or copyrights
+ for the package.
+
+"You" is you, if you're thinking about copying or distributing this Package.
+
+"Reasonable copying fee" is whatever you can justify on the basis of
+ media cost, duplication charges, time of people involved, and so on.
+ (You will not be required to justify it to the Copyright Holder, but
+ only to the computing community at large as a market that must bear
+ the fee.)
+
+"Freely Available" means that no fee is charged for the item itself,
+ though there may be fees involved in handling the item. It also means
+ that recipients of the item may redistribute it under the same
+ conditions they received it.
+
+1. You may make and give away verbatim copies of the source form of the
+Standard Version of this Package without restriction, provided that
+you duplicate all of the original copyright notices and associated
+disclaimers.
+
+2. You may apply bug fixes, portability fixes and other modifications
+derived from the Public Domain or from the Copyright Holder. A
+Package modified in such a way shall still be considered the Standard
+Version.
+
+3. You may otherwise modify your copy of this Package in any way, provided
+that you insert a prominent notice in each changed file stating how and
+when you changed that file, and provided that you do at least ONE of the
+following:
+
+ a. place your modifications in the Public Domain or otherwise make them
+ Freely Available, such as by posting said modifications to Usenet
+ or an equivalent medium, or placing the modifications on a major
+ archive site such as uunet.uu.net, or by allowing the Copyright Holder
+ to include your modifications in the Standard Version of the Package.
+ b. use the modified Package only within your corporation or organization.
+ c. rename any non-standard executables so the names do not conflict
+ with standard executables, which must also be provided, and provide
+ a separate manual page for each non-standard executable that clearly
+ documents how it differs from the Standard Version.
+ d. make other distribution arrangements with the Copyright Holder.
+
+4. You may distribute the programs of this Package in object code or
+executable form, provided that you do at least ONE of the following:
+
+ a. distribute a Standard Version of the executables and library files,
+ together with instructions (in the manual page or equivalent) on
+ where to get the Standard Version.
+ b. accompany the distribution with the machine-readable source of the
+ Package with your modifications.
+ c. give non-standard executables non-standard names, and clearly
+ document the differences in manual pages (or equivalent), together
+ with instructions on where to get the Standard Version.
+ d. make other distribution arrangements with the Copyright Holder.
+
+5. You may charge a reasonable copying fee for any distribution of
+this Package. You may charge any fee you choose for support of
+this Package. You may not charge a fee for this Package itself.
+However, you may distribute this Package in aggregate with other
+(possibly commercial) programs as part of a larger (possibly
+commercial) software distribution provided that you do not a
+dvertise this Package as a product of your own. You may embed this
+Package's interpreter within an executable of yours (by linking);
+this shall be construed as a mere form of aggregation, provided that
+the complete Standard Version of the interpreter is so embedded.
+
+6. The scripts and library files supplied as input to or produced as
+output from the programs of this Package do not automatically fall
+under the copyright of this Package, but belong to whomever generated
+them, and may be sold commercially, and may be aggregated with this
+Package. If such scripts or library files are aggregated with this
+Package via the so-called "undump" or "unexec" methods of producing
+a binary executable image, then distribution of such an image shall
+neither be construed as a distribution of this Package nor shall it
+fall under the restrictions of Paragraphs 3 and 4, provided that you
+do not represent such an executable image as a Standard Version of
+this Package.
+
+7. C subroutines (or comparably compiled subroutines in other languages)
+supplied by you and linked into this Package in order to emulate
+subroutines and variables of the language defined by this Package
+shall not be considered part of this Package, but are the equivalent
+of input as in Paragraph 6, provided these subroutines do not change
+the language in any way that would cause it to fail the regression
+tests for the language.
+
+8. Aggregation of this Package with a commercial distribution is always
+permitted provided that the use of this Package is embedded; that is,
+when no overt attempt is made to make this Package's interfaces visible
+to the end user of the commercial distribution. Such use shall not be
+construed as a distribution of this Package.
+
+9. The name of the Copyright Holder may not be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
+MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+
+The End
+
diff -r 0f06bf18433c -r 035f1902741a masscomb_dbsearch_converter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/masscomb_dbsearch_converter.xml Wed Oct 30 10:04:31 2013 -0400
@@ -0,0 +1,82 @@
+
+ Convert X!tandem output to mzIdentML standard format
+
+
+ MassComb.jar
+ -action DBSEARCHCONVERT
+ -fileGrouping $fileType.type
+ -searchResultsFormat $fileType.inputFormatType.inputFormat
+ #if $fileType.inputFormatType.inputFormat == "xtandem"
+ -isMs2SpectrumIdStartingAtZero $fileType.inputFormatType.isMs2SpectrumIdStartingAtZero
+ #end if
+ -inputFile $fileType.inputFormatType.inputFile
+ -outputFile $outputFile
+
+
+
+
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+
+
+.. class:: infomark
+
+This tool translates X!Tandem and OMSSA results to mzIdentML format.
+It uses the library at http://code.google.com/p/mzidentml-parsers/
+-----
+
+
+
+
diff -r 0f06bf18433c -r 035f1902741a masscomb_dbsearch_mascot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/masscomb_dbsearch_mascot.xml Wed Oct 30 10:04:31 2013 -0400
@@ -0,0 +1,49 @@
+
+ MS/MS DB search
+
+
+ SedMat_cli.jar -pl $inputMS -ppids $inputPedtipeList -out $outputData -mtol $mtol -rttol $rttol -dataset $outputData.dataset.id
+
+
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+.. class:: infomark
+
+This tool matches MS and MS/MS results.
+It can match peaks found in the MS spectra with the peptides found using the MS/MS spectra.
+The result is the list of MS peaks annotated with peptides and proteins.
+
+-----
+
+**Output example**
+
+This tools returns APML output, a Cytoscape network (.xgmml) of the matches and Retention Time plots (.pdf).
+
+
+
diff -r 0f06bf18433c -r 035f1902741a masscomb_dbsearch_xtandem.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/masscomb_dbsearch_xtandem.xml Wed Oct 30 10:04:31 2013 -0400
@@ -0,0 +1,293 @@
+
+ MS/MS DB search
+
+
+ MassComb.jar
+ -action XTANDEMSEARCH
+ -outputFile $outputFile
+ -fileGrouping $fileType.type
+ -inputFile $fileType.inputFile
+ -parametersFile $parametersFile
+ -outputTsv $outTsv
+ -outReport $htmlReportFile
+ -outReportPicturesPath $htmlReportFile.files_path
+
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+<?xml version="1.0" encoding="UTF-8"?>
+<tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="XTandemWrapper" program="XTandemWrapper">
+ <Files/>
+ <Parameters>
+ <Attribute attributeName="xtandemLocation" value="" type="Unknown" description=""/>
+ <Attribute attributeName="database" value="${database}" type="Unknown" description=""/>
+ <Attribute attributeName="precursor_mass_tolerance_lower" toolSpecificName="spectrum, parent monoisotopic mass error minus" value="${precursor_mass_tolerance_lower}" type="Unknown" description=""/>
+ <Attribute attributeName="precursor_mass_tolerance_upper" toolSpecificName="spectrum, parent monoisotopic mass error plus" value="${precursor_mass_tolerance_upper}" type="Unknown" description=""/>
+ <Attribute attributeName="precursor_error_units" toolSpecificName="spectrum, parent monoisotopic mass error units" value="${precursor_error_units}" type="Unknown" description=""/>
+ <Attribute attributeName="fragment_mass_tolerance" toolSpecificName="spectrum, fragment monoisotopic mass error" value="${fragment_mass_tolerance}" type="Unknown" description=""/>
+ <Attribute attributeName="fragment_error_units" toolSpecificName="spectrum, fragment monoisotopic mass error units" value="${fragment_error_units}" type="Unknown" description=""/>
+ <Attribute attributeName="fixed_modifications" toolSpecificName="residue, modification mass" value="${fixed_modifications}" type="Unknown" description=""/>
+ <Attribute attributeName="potential_modifications" toolSpecificName="residue, potential modification mass" value="${potential_modifications}" type="Unknown" description=""/>
+ <Attribute attributeName="minimum_fragment_mz" toolSpecificName="spectrum, minimum fragment mz" value="${minimum_fragment_mz}" type="Unknown" description=""/>
+ <Attribute attributeName="cleavage_site" toolSpecificName="protein, cleavage site" value="${cleavage_site}" type="Unknown" description=""/>
+ <Attribute attributeName="maximum_missed_cleavage_sites" toolSpecificName="scoring, maximum missed cleavage sites" value="${maximum_missed_cleavage_sites}" type="Unknown" description=""/>
+ <Attribute attributeName="max_valid_expect" toolSpecificName="output, maximum valid expectation value" value="${max_valid_expect}" type="Unknown" description=""/>
+ <Attribute attributeName="refinement" toolSpecificName="refine" value="${refinementOpt.refinement}" type="Unknown" description=""/>
+ #if $refinementOpt.refinement == "yes"
+ <Attribute attributeName="refine_point_mutation" toolSpecificName="refine, point mutations" value="${refinementOpt.refine_point_mutation}" type="Unknown" description=""/>
+ <Attribute attributeName="refine_potential_modifications" toolSpecificName="refine, potential modification mass" value="${refinementOpt.refine_potential_modifications}" type="Unknown" description=""/>
+ <Attribute attributeName="refine_max_valid_expect" toolSpecificName="refine, maximum valid expectation value" value="${refinementOpt.refine_max_valid_expect}" type="Unknown" description=""/>
+ #end if
+ <Attribute attributeName="reverse_scoring" toolSpecificName="scoring, include reverse" value="${reverse_scoring}" type="Unknown" description=""/>
+ </Parameters>
+</tns:Program>
+
+
+
+
+
+
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+
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+
+
+
+
+
+
+.. class:: infomark
+
+This tool searches MS/MS spectra against a database using X!Tandem.
+
+For a complete set of parameters and their default values see `the X!Tandem parameters documentation page`_ .
+Parameters that are not
+made available in the UI above but are listed in the given link are submitted with their
+default values.
+
+For more information on the refine step see: `Why should I use "refinement" to find modifications?`_ .
+
+For more information on the expectation value calculation see:
+`A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes`_
+, David Fenyö and Ronald C. Beavis, Anal. Chem., 2003, 75, 768-774.
+This reference describes how peptides are scored by X!Tandem.
+The expectation values on the individual peptides are calculated using this method.
+
+
+.. _the X!Tandem parameters documentation page: http://www.thegpm.org/tandem/api/index.html
+
+.. _Why should I use "refinement" to find modifications?: http://www.thegpm.org/GPM/refine.html
+
+.. _A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes: http://www.ncbi.nlm.nih.gov/pubmed/12622365
+
+-----
+
+**Output**
+
+This tools returns the X!Tandem XML output which can be converted to MzIdentML using the DBSearch converter tool.
+
+It also returns an HTML file with the list of peptides and the option to visualize the peptide to spectrum match
+using an embedded spectrum viewer.
+
+.. image:: $PATH_TO_IMAGES/xtandem_results_viewer.png
+
+Last but not least, it returns the list of identifications in TSV (tab separated values) format for users that are satisfied with this
+and do not need further processing steps like protein inference.
+
+For the GPM web UI of X!Tandem see:
+http://ppp.thegpm.org/tandem/thegpm_ppp.html
+
+
+
\ No newline at end of file
diff -r 0f06bf18433c -r 035f1902741a masscomb_fasta_validator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/masscomb_fasta_validator.xml Wed Oct 30 10:04:31 2013 -0400
@@ -0,0 +1,42 @@
+
+ Basic FASTA file validation
+
+
+ MassComb.jar
+ -action FASTAVALIDATOR
+ -fastaFile $inputFile
+ -outputFile $outputFile
+ -expressions "$expressions"
+ -maxLengthSequenceLine $maxLengthSequenceLine
+
+
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diff -r 0f06bf18433c -r 035f1902741a masscomb_visual_mspicture.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/masscomb_visual_mspicture.xml Wed Oct 30 10:04:31 2013 -0400
@@ -0,0 +1,87 @@
+
+ MS data view
+
+
+ MassComb.jar -action MSPICTURE
+ -outputFile $html_file
+ -picturesPath $html_file.files_path
+ -fileGrouping $fileType.type
+ #if $fileType.type == "single"
+ -inputFile $fileType.inputFormatType.inputFile
+ -inputFormat $fileType.inputFormatType.inputFormat
+ #elif $fileType.type == "fileSet"
+ -inputFile $fileType.inputFile
+ #end if
+ -parametersFile $parametersFile
+
+
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+<?xml version="1.0" encoding="UTF-8"?>
+<tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="MsPictureWrapper" program="MsPictureWrapper">
+ <Files/>
+ <Parameters>
+ <Attribute attributeName="toolLocation" value="/home/lukas007/bin/" type="Unknown" description=""/>
+ <Attribute attributeName="gray_scale" toolSpecificName="--grey" value="${gray_scale}" type="Unknown" description=""/>
+ <Attribute attributeName="data_type" value="${data_type}" type="Unknown" description=""/>
+ </Parameters>
+</tns:Program>
+
+
+
+
+
+
+
+
+
+
+
+.. class:: infomark
+
+This tool displays the MS data using ProteoWizard's msPicture tool
+
+
+
+
\ No newline at end of file
diff -r 0f06bf18433c -r 035f1902741a static/images/xtandem_results_viewer.png
Binary file static/images/xtandem_results_viewer.png has changed
diff -r 0f06bf18433c -r 035f1902741a tool_dependencies.xml
--- a/tool_dependencies.xml Mon Oct 21 02:29:17 2013 -0400
+++ b/tool_dependencies.xml Wed Oct 30 10:04:31 2013 -0400
@@ -1,40 +1,23 @@
-
-
-
-
-
-
-
-
-
-
-
- http://downloads.sourceforge.net/project/open-ms/OpenMS/OpenMS-1.10/OpenMS-1.10.0.tar.gz
-
-
-
-
-
-
-
-
-
-
-
- contrib
- cmake .
- ..
- cmake . -DINSTALL_PREFIX=$INSTALL_DIR
-
-
- $INSTALL_DIR/bin
- $INSTALL_DIR/lib
-
-
-
-
- This package downloads and installs OpenMS.
- http://open-ms.sourceforge.net/
-
-
-
+
+
+
+
+
+
+ ftp://ftp.thegpm.org/projects/tandem/source/2011-12-01/tandem-linux-12-10-01-1.zip
+
+
+ tandem-linux-12-10-01-1
+ $INSTALL_DIR/tandem-linux-12-10-01-1
+
+
+ $INSTALL_DIR/tandem-linux-12-10-01-1
+
+
+
+
+Ensures XTandem is installed.
+
+
+
\ No newline at end of file