# HG changeset patch
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# Date 1383349381 14400
# Node ID 47b67a4d0de57162db0fc18aab33647a397afb32
# Parent f6e879c9ce8575895faa75e6345a4da8c822a4ba
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diff -r f6e879c9ce85 -r 47b67a4d0de5 MassComb.jar
Binary file MassComb.jar has changed
diff -r f6e879c9ce85 -r 47b67a4d0de5 README.txt
--- a/README.txt Fri Nov 01 19:42:27 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,187 +0,0 @@
-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 f6e879c9ce85 -r 47b67a4d0de5 Xtandem.txt
--- a/Xtandem.txt Fri Nov 01 19:42:27 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,121 +0,0 @@
-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 f6e879c9ce85 -r 47b67a4d0de5 masscomb_dbsearch_converter.xml
--- a/masscomb_dbsearch_converter.xml Fri Nov 01 19:42:27 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-
- 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 f6e879c9ce85 -r 47b67a4d0de5 masscomb_dbsearch_mascot.xml
--- a/masscomb_dbsearch_mascot.xml Fri Nov 01 19:42:27 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-
- 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 f6e879c9ce85 -r 47b67a4d0de5 masscomb_dbsearch_xtandem.xml
--- a/masscomb_dbsearch_xtandem.xml Fri Nov 01 19:42:27 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,296 +0,0 @@
-
- MS/MS DB search
-
-
- xtandem
-
-
- 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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-.. 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
-
-
-
diff -r f6e879c9ce85 -r 47b67a4d0de5 masscomb_fasta_validator.xml
--- a/masscomb_fasta_validator.xml Fri Nov 01 19:42:27 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,42 +0,0 @@
-
- Basic FASTA file validation
-
-
- MassComb.jar
- -action FASTAVALIDATOR
- -fastaFile $inputFile
- -outputFile $outputFile
- -expressions "$expressions"
- -maxLengthSequenceLine $maxLengthSequenceLine
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diff -r f6e879c9ce85 -r 47b67a4d0de5 masscomb_visual_mspicture.xml
--- a/masscomb_visual_mspicture.xml Fri Nov 01 19:42:27 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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-
- 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="${data_type}" type="Unknown" description=""/>
- </Parameters>
-</tns:Program>
-
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-.. class:: infomark
-
-This tool displays the MS data using ProteoWizard's msPicture tool
-
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\ No newline at end of file
diff -r f6e879c9ce85 -r 47b67a4d0de5 static/images/xtandem_results_viewer.png
Binary file static/images/xtandem_results_viewer.png has changed
diff -r f6e879c9ce85 -r 47b67a4d0de5 tool_dependencies.xml
--- a/tool_dependencies.xml Fri Nov 01 19:42:27 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-
-
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-
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- https://downloads.sourceforge.net/project/sashimi/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.6%20%28occupy%29%20rev%203/TPP-4.6.3.tgz
-
-
-
-
-
-
- ./trans_proteomic_pipeline/src/
- echo 'TPP_ROOT=$INSTALL_DIR' > Makefile.config.incl
-
-
- $INSTALL_DIR/bin
- $INSTALL_DIR
-
-
-
-
- Installs and complils the trans proteomic pipeline in version 4.6.3.
- The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
-
- http://tools.proteomecenter.org/
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- PATH will be set.
- TPP_ROOT_PATH will point to the root path of the installation.
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