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LICENSE MassComb.jar NOTICE README.rst XTANDEM_README.txt datatypes_conf.xml masscomb_dbsearch_converter.xml masscomb_dbsearch_xtandem.xml masscomb_fasta_validator.xml masscomb_visual_mspicture.xml prims_masscomb_datatypes.py static/images/xtandem_results_viewer.png tool_dependencies.xml |
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diff -r 000000000000 -r d6001e8d7441 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Wed Jan 08 11:34:51 2014 +0100 |
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b'@@ -0,0 +1,202 @@\n+\n+ Apache License\n+ Version 2.0, January 2004\n+ http://www.apache.org/licenses/\n+\n+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION\n+\n+ 1. Definitions.\n+\n+ "License" shall mean the terms and conditions for use, reproduction,\n+ and distribution as defined by Sections 1 through 9 of this document.\n+\n+ "Licensor" shall mean the copyright owner or entity authorized by\n+ the copyright owner that is granting the License.\n+\n+ "Legal Entity" shall mean the union of the acting entity and all\n+ other entities that control, are controlled by, or are under common\n+ control with that entity. 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We also recommend that a\n+ file or class name and description of purpose be included on the\n+ same "printed page" as the copyright notice for easier\n+ identification within third-party archives.\n+\n+ Copyright [yyyy] [name of copyright owner]\n+\n+ Licensed under the Apache License, Version 2.0 (the "License");\n+ you may not use this file except in compliance with the License.\n+ You may obtain a copy of the License at\n+\n+ http://www.apache.org/licenses/LICENSE-2.0\n+\n+ Unless required by applicable law or agreed to in writing, software\n+ distributed under the License is distributed on an "AS IS" BASIS,\n+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n+ See the License for the specific language governing permissions and\n+ limitations under the License.\n' |
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diff -r 000000000000 -r d6001e8d7441 MassComb.jar |
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Binary file MassComb.jar has changed |
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diff -r 000000000000 -r d6001e8d7441 NOTICE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NOTICE Wed Jan 08 11:34:51 2014 +0100 |
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@@ -0,0 +1,17 @@ +PRIMS-masscomb toolset & Galaxy wrappers +========================================== + +Tools and wrappers for the PRIMS-masscomb toolset. +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.. + +Can be used a.o. in combination with PRIMV-visualization (primv_visualization package) and +PRIMS-proteomics (prims_proteomics package). + +Copyright 2010-2013 by Pieter Lukasse, Plant Research International (PRI), +Wageningen, The Netherlands. All rights reserved. See the license text in LICENSE file. + +Galaxy wrappers and installation are available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_masscomb + |
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diff -r 000000000000 -r d6001e8d7441 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed Jan 08 11:34:51 2014 +0100 |
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@@ -0,0 +1,70 @@ +PRIMS-masscomb toolset & Galaxy wrappers +======================================== + +MASSCOMB module of Plant Research International's Mass Spectrometry (PRIMS) toolsuite. + +This toolset consists of tools that enable combining popular external mass spectrometry +data processing tools (like X!Tandem and ProteoWizard's MsPicture) +into your own Galaxy workflows. + +Can be used a.o. in combination with PRIMV-visualization (primv_visualization package) and +PRIMS-proteomics (prims_proteomics package). + +Copyright 2010-2013 by Pieter Lukasse, Plant Research International (PRI), +Wageningen, The Netherlands. All rights reserved. See the license text in LICENSE file. + +Galaxy wrappers and installation are available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/pieterlukasse/prims_masscomb + + +History +======= + +============== ======================================================================== +Date Changes +-------------- ------------------------------------------------------------------------ +January 2014 * first release via Tool Shed +November 2013 * tools used internally at PRI +... ... +December 2011 * added wrapper for X!Tandem and tool for converting output to MzIdentML +============== ======================================================================== + +Tool Versioning +=============== + +Tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta. + + +Bug Reports & other questions +============================= + +For the time being issues can be reported via the contact form at +http://www.wageningenur.nl/en/Persons/PNJ-Pieter-Lukasse.htm + +Developers, Contributions & Collaborations +========================================== + +If you wish to join forces and collaborate on some of the +tools do not hesitate to contact Pieter Lukasse via the contact form above. + +License (Apache, Version 2.0) +============================= + +Copyright 2013 Pieter Lukasse, Plant Research International (PRI). + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this software except in compliance with the License. +You may obtain a copy of the License at + +http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + \ No newline at end of file |
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diff -r 000000000000 -r d6001e8d7441 XTANDEM_README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/XTANDEM_README.txt Wed Jan 08 11:34:51 2014 +0100 |
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b'@@ -0,0 +1,177 @@\n+\r\n+X!TANDEM LICENSE AND README ===========================================\r\n+\r\n+\r\n+ X! tandem protein sequence modeler\r\n+\r\n+ What is it?\r\n+ -----------\r\n+ X! tandem open source software that can model tandem\r\n+ mass spectra with protein sequences. This software\r\n+ has a very simple, unsophistocated application programming\r\n+ interface (API): it simply takes an XML file of instructions\r\n+ on its command line, and output the results into an XML file,\r\n+ which has been specified in the input XML file. \r\n+ \r\n+ The Latest Version\r\n+ ------------------\r\n+\r\n+ Details of the latest version can be found on the X! tandem\r\n+ project page under http://www.thegpm.org. \r\n+ This version is the first release the CYCLONE edition (version 2012.10.01.1).\r\n+\r\n+\r\n+ Documentation\r\n+ -------------\r\n+\r\n+ This version of X! tandem is a full release, only including source\r\n+ level documentation. As more releases occur, better documentation\r\n+ will be included.\r\n+\r\n+ Installation\r\n+ ------------\r\n+\r\n+ (IN this case installation is automatically done by Galaxy\'s Toolshed).\r\n+\r\n+ Licensing\r\n+ ---------\r\n+\r\n+\tThe Artistic License for all X! software, binaries and documentation\r\n+\r\n+\tPreamble\r\n+\tThe intent of this document is to state the conditions under which a\r\n+\tPackage may be copied, such that the Copyright Holder maintains some \r\n+\tsemblance of artistic control over the development of the package, \r\n+\twhile giving the users of the package the right to use and distribute \r\n+\tthe Package in a more-or-less customary fashion, plus the right to \r\n+\tmake reasonable modifications. \r\n+\r\n+\tDefinitions\r\n+\t"Package" refers to the collection of files distributed by the Copyright \r\n+\t Holder, and derivatives of that collection of files created through \r\n+\t textual modification. \r\n+\r\n+\t"Standard Version" refers to such a Package if it has not been modified, \r\n+\t or has been modified in accordance with the wishes of the Copyright \r\n+\t Holder as specified below. \r\n+\r\n+\t"Copyright Holder" is whoever is named in the copyright or copyrights \r\n+\t for the package. \r\n+\r\n+\t"You" is you, if you\'re thinking about copying or distributing this Package. \r\n+\r\n+\t"Reasonable copying fee" is whatever you can justify on the basis of \r\n+\t media cost, duplication charges, time of people involved, and so on. \r\n+\t (You will not be required to justify it to the Copyright Holder, but \r\n+\t only to the computing community at large as a market that must bear \r\n+\t the fee.) \r\n+\r\n+\t"Freely Available" means that no fee is charged for the item itself, \r\n+\t though there may be fees involved in handling the item. It also means \r\n+\t that recipients of the item may redistribute it under the same\r\n+\t conditions they received it. \r\n+\r\n+\t1. You may make and give away verbatim copies of the source form of the \r\n+\tStandard Version of this Package without restriction, provided that \r\n+\tyou duplicate all of the original copyright notices and associated \r\n+\tdisclaimers. \r\n+\r\n+\t2. You may apply bug fixes, portability fixes and other modifications \r\n+\tderived from the Public Domain or from the Copyright Holder. A \r\n+\tPackage modified in such a way shall still be considered the Standard \r\n+\tVersion. \r\n+\r\n+\t3. You may otherwise modify your copy of this Package in any way, provided \r\n+\tthat you insert a prominent notice in each changed file stating how and \r\n+\twhen you changed that file, and provided that you do at least ONE of the \r\n+\tfollowing: \r\n+\r\n+\t a. place your modifications in the Public Domain or otherwise make them \r\n+\t\t Freely Available, such as by posting said modifications to Usenet \r\n+\t\t or an equivalent medium, or placing the modifications on a major \r\n+\t\t archive site such as uunet.uu.net, or by allowing the Copyright Holder \r\n+\t\t to include your modifications in the Standard Version of the Package. \r\n+\t b. use the modified Package only within your corporation or organization. \r\n+\t c. rename any non-standard executables so the names do not'..b'ocuments how it differs from the Standard Version. \r\n+\t d. make other distribution arrangements with the Copyright Holder. \r\n+\r\n+\t4. You may distribute the programs of this Package in object code or \r\n+\texecutable form, provided that you do at least ONE of the following: \r\n+\r\n+\t a. distribute a Standard Version of the executables and library files, \r\n+\t\t together with instructions (in the manual page or equivalent) on \r\n+\t\t where to get the Standard Version. \r\n+\t b. accompany the distribution with the machine-readable source of the \r\n+\t\t Package with your modifications. \r\n+\t c. give non-standard executables non-standard names, and clearly \r\n+\t\t document the differences in manual pages (or equivalent), together \r\n+\t\t with instructions on where to get the Standard Version. \r\n+\t d. make other distribution arrangements with the Copyright Holder. \r\n+\r\n+\t5. You may charge a reasonable copying fee for any distribution of \r\n+\tthis Package. You may charge any fee you choose for support of \r\n+\tthis Package. You may not charge a fee for this Package itself. \r\n+\tHowever, you may distribute this Package in aggregate with other \r\n+\t(possibly commercial) programs as part of a larger (possibly \r\n+\tcommercial) software distribution provided that you do not a\r\n+\tdvertise this Package as a product of your own. You may embed this \r\n+\tPackage\'s interpreter within an executable of yours (by linking); \r\n+\tthis shall be construed as a mere form of aggregation, provided that \r\n+\tthe complete Standard Version of the interpreter is so embedded. \r\n+\r\n+\t6. The scripts and library files supplied as input to or produced as \r\n+\toutput from the programs of this Package do not automatically fall \r\n+\tunder the copyright of this Package, but belong to whomever generated \r\n+\tthem, and may be sold commercially, and may be aggregated with this \r\n+\tPackage. If such scripts or library files are aggregated with this \r\n+\tPackage via the so-called "undump" or "unexec" methods of producing \r\n+\ta binary executable image, then distribution of such an image shall \r\n+\tneither be construed as a distribution of this Package nor shall it \r\n+\tfall under the restrictions of Paragraphs 3 and 4, provided that you \r\n+\tdo not represent such an executable image as a Standard Version of \r\n+\tthis Package. \r\n+\r\n+\t7. C subroutines (or comparably compiled subroutines in other languages) \r\n+\tsupplied by you and linked into this Package in order to emulate \r\n+\tsubroutines and variables of the language defined by this Package \r\n+\tshall not be considered part of this Package, but are the equivalent \r\n+\tof input as in Paragraph 6, provided these subroutines do not change \r\n+\tthe language in any way that would cause it to fail the regression \r\n+\ttests for the language. \r\n+\r\n+\t8. Aggregation of this Package with a commercial distribution is always \r\n+\tpermitted provided that the use of this Package is embedded; that is, \r\n+\twhen no overt attempt is made to make this Package\'s interfaces visible \r\n+\tto the end user of the commercial distribution. Such use shall not be \r\n+\tconstrued as a distribution of this Package. \r\n+\r\n+\t9. The name of the Copyright Holder may not be used to endorse or promote \r\n+\tproducts derived from this software without specific prior written permission. \r\n+\r\n+\t10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED \r\n+\tWARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF \r\n+\tMERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. \r\n+\r\n+\tThe End \r\n+\r\n+\r\n+ Contacts\r\n+ --------\r\n+\r\n+ For any questions involving X! tandem, please contact \r\n+ contact@thegpm.org\r\n+\r\n+ Acknowledgments\r\n+ ----------------\r\n+\r\n+ Ron Beavis - system design and implementation\r\n+ Rob Craig - debugging and LINUX implementation\r\n+ Jayson Falkner - code for GeeToo LINUX implementation\r\n+ Patrick Lacasse - initial additions for mzxml and mzdata functionality\r\n+ Brendan McLean - optimized changes for mzxml and mzdata functionality using expat library\r\n+\r\n+\r\n+\r\n' |
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diff -r 000000000000 -r d6001e8d7441 datatypes_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Wed Jan 08 11:34:51 2014 +0100 |
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@@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<datatypes> + <datatype_files> + <datatype_file name="prims_masscomb_datatypes.py"/> + </datatype_files> + <registration display_path="display_applications"> + <datatype extension="prims.fileset.zip" type="galaxy.datatypes.prims_masscomb_datatypes:FileSet" display_in_upload="true"/> + </registration> +</datatypes> \ No newline at end of file |
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diff -r 000000000000 -r d6001e8d7441 masscomb_dbsearch_converter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/masscomb_dbsearch_converter.xml Wed Jan 08 11:34:51 2014 +0100 |
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@@ -0,0 +1,82 @@ +<tool name="DB search converter" id="masscomb_dbsearch_converter" version="1.0.1"> + <description> Convert search results to MzIdentML (aka mzid) format</description> + <!-- + For remote debugging start you listener on port 8000 and use the following as command interpreter: + java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 + ////////////////////////// + --> + <command interpreter="java -jar"> + 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 + </command> + <inputs> + <conditional name="fileType"> + <param name="type" type="select" label="select file grouping type"> + <option value="single" selected="true">single-File</option> + <option value="fileSet">fileSet</option> + </param> + <when value="single"> + <conditional name="inputFormatType"> + <param name="inputFormat" type="select" label="inputFormat"> + <option value="xtandem">X!Tandem</option> + <option value="omssa">OMSSA</option> + </param> + <when value="xtandem"> + <param name="inputFile" type="data" format="bioml,xml" label="MS/MS search results" help="Note: the spectra index values in the resulting file will only be reliable for when X!Tandem has executed on MzML data"/> + <param name="isMs2SpectrumIdStartingAtZero" type="select" label="Spectrum numbering starting at zero in original spectra file" help="Some formats, like mzML, start their spectrum numbering from 0, other formats start from 1. "> + <option value="true" selected="true">Yes, starting at 0</option> + <option value="false">No, starting at 1</option> + </param> + </when> + <when value="omssa"> + <param name="inputFile" type="data" format="omx" label="MS/MS search results"/> + </when> + </conditional> + </when> + <when value="fileSet"> + <conditional name="inputFormatType"> + <param name="inputFormat" type="select" label="inputFormat"> + <option value="xtandem">X!Tandem</option> + <option value="omssa">OMSSA</option> + </param> + <when value="xtandem"> + <param name="inputFile" type="data" format="prims.fileset.zip" label="MS/MS search results" /> + <param name="isMs2SpectrumIdStartingAtZero" type="select" label="Spectrum numbering starting at zero in original spectra file" help="Some formats, like mzML, start their spectrum numbering from 0, other formats start from 1. "> + <option value="true" selected="true">Yes, starting at 0</option> + <option value="false">No, starting at 1</option> + </param> + </when> + <when value="omssa"> + <param name="inputFile" type="data" format="prims.fileset.zip" label="MS/MS search results"/> + </when> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <data name="outputFile" format="mzid" label="${tool.name} (to MzIdentML) on ${on_string} "> + <change_format> + <when input="fileType.type" value="fileSet" format="prims.fileset.zip" label="${tool.name} (to MzIdentML) on ${on_string} "/> + </change_format> + </data> + </outputs> + <tests> + </tests> + <help> + +.. 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/ +----- + + + </help> +</tool> |
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diff -r 000000000000 -r d6001e8d7441 masscomb_dbsearch_xtandem.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/masscomb_dbsearch_xtandem.xml Wed Jan 08 11:34:51 2014 +0100 |
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b'@@ -0,0 +1,293 @@\n+<tool name="X!Tandem" id="masscomb_xtandem200" version="2.0.0">\r\n+\t<description>MS/MS DB search</description>\r\n+\t<!-- \r\n+\t For remote debugging start you listener on port 8000 and use the following as command interpreter:\r\n+\t java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 \r\n+\t--> \r\n+\t<command interpreter="java -jar">\r\n+\t MassComb.jar \r\n+\t -action XTANDEMSEARCH \r\n+\t -outputFile $outputFile \r\n+\t -fileGrouping $fileType.type\r\n+ \t-inputFile $fileType.inputFile\r\n+ \t-parametersFile $parametersFile\r\n+\t\t-outputTsv $outTsv\r\n+\t\t-outReport $htmlReportFile\r\n+\t -outReportPicturesPath $htmlReportFile.files_path\r\n+\t </command>\r\n+<inputs>\r\n+ <conditional name="fileType">\r\n+ <param name="type" type="select" label="select MS/MS input type">\r\n+ <option value="single" selected="true">single-File</option>\r\n+ <option value="fileSet">fileSet</option>\r\n+ </param>\r\n+ <when value="single">\r\n+ \t\t<param name="inputFile" type="data" format="mzml" label="MS/MS input file (mzml)"/>\r\n+ </when>\r\n+ <when value="fileSet">\r\n+ <param name="inputFile" type="data" format="prims.fileset.zip" label="input file"/>\r\n+ </when>\r\n+ </conditional>\r\n+\r\n+ <param name="precursor_mass_tolerance_lower" type="text" size="30" label="precursor monoisotopic mass_tolerance_lower" value="100" help=""/>\r\n+ <param name="precursor_mass_tolerance_upper" type="text" size="30" label="precursor monoisotopic mass_tolerance_upper" value="100" help=""/>\r\n+ <param name="precursor_error_units" type="select" label="precursor_error_units" help="">\r\n+ \t<option value="ppm" selected="true">ppm</option>\r\n+ \t<option value="Daltons">Daltons</option>\r\n+ </param>\r\n+ <param name="fragment_mass_tolerance" type="text" size="30" label="fragment_mass_tolerance" value="0.4" help=""/>\r\n+ <param name="fragment_error_units" type="select" label="fragment_error_units" help="">\r\n+ \t<option value="ppm">ppm</option>\r\n+ \t<option value="Daltons" selected="true">Daltons</option>\r\n+ </param>\r\n+ <param name="database" type="data" format="fasta" label="Protein sequences DB (FASTA)"/>\r\n+ <!-- \r\n+ <param name="min_precursor_charge" type="text" size="30" label="min_precursor_charge" value="1" help=""/>\r\n+ <param name="max_precursor_charge" type="text" size="30" label="max_precursor_charge" value="4" help=""/>-->\r\n+ <param name="fixed_modifications" type="select" display="checkboxes" multiple="true" label="Complete modifications" help="">\r\n+\t \t<option value="57.021464@C">Carbamidomethyl (C)</option>\r\n+\t\t<option value="57.021464@C,10.008269@R,8.014199@K">Cam+SILAC (8@K,10@R)</option>\r\n+\t\t<option value="57.021464@C,4.025107@K,6.020129@R">Cam+SILAC (4@K,6@R)</option>\r\n+\t\t<option value="57.021464@C,4.025107@K,6.020129@R,6.020129@L">Cam+SILAC (4@K,6@R,6@L)</option>\r\n+\t\t<option value="58.005479@C">Carboxymethyl (C)</option>\r\n+\t\t<option value="45.987721@C">Methylthio (C)</option>\r\n+\t\t<option value="47.984744@C">Trioxidation (C)</option>\r\n+\t\t<option value="442.224991@C">ICAT-D (C)</option>\r\n+\t\t<option value="450.275205@C">ICAT-D:2H(8) (C)</option>\r\n+\t\t<option value="227.126991@C">ICAT-C (C)</option>\r\n+\t\t<option value="236.157185@C">ICAT-C:13C(9) (C)</option>\r\n+\t\t<option value="58.005479@C">Carboxymethyl (C)</option>\r\n+\t\t<option value="105.057849@C">Pyridylethyl (C)</option>\r\n+\t\t<option value="71.037114@C">Propionamide (C)</option>\r\n+\t\t<option value="125.047679@C">Nethylmaleimide (C)</option>\r\n+\t\t<option value="144.102063@[,144.102063@K">iTRAQ (N-term,K)</option>\r\n+\t\t<option value="57.021464@C,144.102063@[,144.102063@K">Cam + iTRAQ (C,N-term,K)</option>\r\n+\t\t<option value="57.021464@C,224.152478@K,224.152478@[">Cam + TMT (C,K,nt)</option>\r\n+\t\t<option value="57.021464@C,225.155833@K,225.155833@[">Cam + TMT2plex (C,K,nt)</option>\r\n+\t\t<option value="57.021464@C,229.1629328@K,229.1629328@[">Cam + TMT6plex (C,K,nt)</option>\r\n+\t\t<option value="57.021464@C,28.0313@[,28.0313@K">Cam + Dim'..b' missed cleavage sites" value="${maximum_missed_cleavage_sites}" type="Unknown" description=""/>\r\n+\t\t <Attribute attributeName="max_valid_expect" toolSpecificName="output, maximum valid expectation value" value="${max_valid_expect}" type="Unknown" description=""/>\r\n+\t\t <Attribute attributeName="refinement" toolSpecificName="refine" value="${refinementOpt.refinement}" type="Unknown" description=""/>\r\n+\t#if $refinementOpt.refinement == "yes"\r\n+\t\t <Attribute attributeName="refine_point_mutation" toolSpecificName="refine, point mutations" value="${refinementOpt.refine_point_mutation}" type="Unknown" description=""/>\r\n+\t\t <Attribute attributeName="refine_potential_modifications" toolSpecificName="refine, potential modification mass" value="${refinementOpt.refine_potential_modifications}" type="Unknown" description=""/>\r\n+\t\t <Attribute attributeName="refine_max_valid_expect" toolSpecificName="refine, maximum valid expectation value" value="${refinementOpt.refine_max_valid_expect}" type="Unknown" description=""/>\r\n+\t#end if\r\n+\t\t <Attribute attributeName="reverse_scoring" toolSpecificName="scoring, include reverse" value="${reverse_scoring}" type="Unknown" description=""/>\r\n+\t</Parameters>\r\n+</tns:Program> \r\n+</configfile>\r\n+</configfiles>\r\n+<outputs>\r\n+\t<data name="outputFile" format="bioml" label="${tool.name} on ${on_string} - Results XML">\r\n+\t\t<change_format>\r\n+\t\t <when input="fileType.type" value="fileSet" format="prims.fileset.zip" />\r\n+\t\t</change_format>\r\n+\t</data>\r\n+\t<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report"> </data>\r\n+\t<data name="outTsv" format="tabular" label="${tool.name} on ${on_string} - TSV report"> </data>\r\n+</outputs>\r\n+<tests>\r\n+\t<test>\r\n+\t</test>\r\n+</tests>\r\n+<help>\r\n+\r\n+.. class:: infomark\r\n+ \r\n+This tool searches MS/MS spectra against a database using X!Tandem.\r\n+\r\n+For a complete set of parameters and their default values see `the X!Tandem parameters documentation page`_ . \r\n+Parameters that are not\r\n+made available in the UI above but are listed in the given link are submitted with their\r\n+default values.\r\n+\r\n+For more information on the refine step see: `Why should I use "refinement" to find modifications?`_ .\r\n+\r\n+For more information on the expectation value calculation see: \r\n+`A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes`_\r\n+, David Feny\xc3\xb6 and Ronald C. Beavis, Anal. Chem., 2003, 75, 768-774.\r\n+This reference describes how peptides are scored by X!Tandem. \r\n+The expectation values on the individual peptides are calculated using this method. \r\n+<!-- Add this from Ron\'s email ? :\r\n+They are an estimate of the spectrum-to-peptide match E-value associated with the \r\n+null-hypothesis "all spectrum-to-peptide matches are stochasitic".\r\n+-->\r\n+\r\n+.. _the X!Tandem parameters documentation page: http://www.thegpm.org/tandem/api/index.html\r\n+\r\n+.. _Why should I use "refinement" to find modifications?: http://www.thegpm.org/GPM/refine.html\r\n+\r\n+.. _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\r\n+\r\n+-----\r\n+\r\n+**Output**\r\n+\r\n+This tools returns the X!Tandem XML output which can be converted to MzIdentML using the DBSearch converter tool.\r\n+\r\n+It also returns an HTML file with the list of peptides and the option to visualize the peptide to spectrum match\r\n+using an embedded spectrum viewer. \r\n+\r\n+.. image:: $PATH_TO_IMAGES/xtandem_results_viewer.png \r\n+\r\n+Last but not least, it returns the list of identifications in TSV (tab separated values) format for users that are satisfied with this\r\n+and do not need further processing steps like protein inference. \r\n+\r\n+For the GPM web UI of X!Tandem see:\r\n+http://ppp.thegpm.org/tandem/thegpm_ppp.html\r\n+\r\n+</help>\r\n+</tool>\n\\ No newline at end of file\n' |
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diff -r 000000000000 -r d6001e8d7441 masscomb_fasta_validator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/masscomb_fasta_validator.xml Wed Jan 08 11:34:51 2014 +0100 |
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@@ -0,0 +1,42 @@ +<tool name="Fasta Validator" id="masscomb_fastavalidator" version="1.0.1"> + <description>Basic FASTA file validation</description> + <!-- + For remote debugging start you listener on port 8000 and use the following as command interpreter: + java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 + --> + <command interpreter="java -jar"> + MassComb.jar + -action FASTAVALIDATOR + -fastaFile $inputFile + -outputFile $outputFile + -expressions "$expressions" + -maxLengthSequenceLine $maxLengthSequenceLine + </command> +<inputs> + <param name="inputFile" type="data" format="" label="Fasta file to validate"/> + + <param name="expressions" type="select" display="checkboxes" multiple="true" label="Error patterns to search for in each line" help=""> + <option value="description=White space in SEQUENCE;regex=^[a-zA-Z]+SLASHs[a-zA-Z]">White space in SEQUENCE (^[a-zA-Z]+\s[a-zA-Z])</option> + <option value="description=Numbers in SEQUENCE;regex=^[0-9]PIPE^[a-zA-Z]+.*[0-9]">Numbers in SEQUENCE (^[0-9]|^[a-zA-Z]+.*[0-9])</option> + <option value="description=Line starting with white space followed by alpha numeric characters;regex=^SLASHs[a-zA-Z0-9]+">Line starting with white space followed by alpha numeric characters (^\s[a-zA-Z0-9]+)</option> + <option value="description=Line ending with white space;regex=.*SLASHsDOLLAR">Line ending with white space (.*\s$)</option> + <option value="description=Sequence lines with non-Amino Acid characters;regex=(^[SLASHwAMPAMP[^ARNDCEQGHILKMFPSTWYV]])PIPE(^[ARNDCEQGHILKMFPSTWYV]+[SLASHwAMPAMP[^ARNDCEQGHILKMFPSTWYV]]+)">Sequence lines with non-Amino Acid characters ((^[\w&&[^ARNDCEQGHILKMFPSTWYV]])|(^[ARNDCEQGHILKMFPSTWYV]+[\w&&[^ARNDCEQGHILKMFPSTWYV]]+))</option> + <option value="description=Hyphen in accession numbers;regex=^SLASHS*-">Hyphen in accession numbers (^\S*-)</option> + <option value="description=Lines with stretches of X;regex=XX+">Lines with stretches of X (XX+)</option> + </param> + + <param name="maxLengthSequenceLine" type="integer" size="10" value="0" label="Max length sequence line " + help="(Optional) the maximum line width in the protein sequence part. Leave to 0 (zero) for no restrictions "/> + +</inputs> +<outputs> + <data format="txt" name="outputFile" /> +</outputs> +<tests> + <test> + </test> +</tests> +<help> + +</help> +</tool> |
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diff -r 000000000000 -r d6001e8d7441 masscomb_visual_mspicture.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/masscomb_visual_mspicture.xml Wed Jan 08 11:34:51 2014 +0100 |
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@@ -0,0 +1,87 @@ +<tool name="MsPicture" id="masscomb_mspicture" version="1.0.1"> + <description>MS data view</description> + <!-- + For remote debugging start you listener on port 8000 and use the following as command interpreter: + java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 + --> + <command interpreter="java -jar"> + 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 $parametersFile + + </command> +<inputs> + <conditional name="fileType"> + <param name="type" type="select" label="select MS/MS input type"> + <option value="single" selected="true">single-File</option> + <option value="fileSet">fileSet</option> + </param> + <when value="single"> + <conditional name="inputFormatType"> + <param name="inputFormat" type="select" label="inputFormat"> + <option value="mzml" selected="true">mzml</option> + <option value="mzxml">mzxml</option> + <option value="apml">apml</option> + </param> + <when value="mzxml"> + <param name="inputFile" type="data" format="mzxml" label="MS input file (mzXML)"/> + </when> + <when value="mzml"> + <param name="inputFile" type="data" format="mzml" label="MS input file (mzml)"/> + </when> + <when value="apml"> + <param name="inputFile" type="data" format="apml" label="MS or MS/MS input file (APML)"/> + </when> + </conditional> + </when> + <when value="fileSet"> + <param name="inputFile" type="data" format="prims.fileset.zip" label="input file"/> + </when> + </conditional> + + <param name="data_type" type="select" label="Data type" help=""> + <option value="LC-MS">LC-MS</option> + <option value="LC-MS/MS">LC-MS/MS</option> + </param> + + <param name="gray_scale" type="select" display="checkboxes" multiple="True" label="Use gray scale" help=""> + <option value="Yes">Yes</option> + </param> + +</inputs> +<configfiles> +<configfile name="parametersFile"><?xml version="1.0" encoding="UTF-8"?> +<tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="MsPictureWrapper" program="MsPictureWrapper"> + <Files/> + <Parameters> + <Attribute attributeName="toolLocation" value="/home/lukas007/bin/" type="Unknown" description=""/> + <Attribute attributeName="gray_scale" toolSpecificName="--grey" value="${gray_scale}" type="Unknown" description=""/> + <Attribute attributeName="data_type" value="${data_type}" type="Unknown" description=""/> + </Parameters> +</tns:Program> +</configfile> +</configfiles> +<outputs> + <data format="html" name="html_file" /> +</outputs> +<tests> + <test> + </test> +</tests> +<help> + +.. class:: infomark + +This tool displays the MS data using ProteoWizard's msPicture tool + + +</help> +</tool> \ No newline at end of file |
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diff -r 000000000000 -r d6001e8d7441 prims_masscomb_datatypes.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prims_masscomb_datatypes.py Wed Jan 08 11:34:51 2014 +0100 |
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@@ -0,0 +1,29 @@ +""" +PRIMS masscomb classes for types defined in datatypes_conf.xml +""" +import logging +import zipfile +import re +from galaxy.datatypes.data import * +from galaxy.datatypes.xml import * +from galaxy.datatypes.sniff import * +from galaxy.datatypes.binary import * +from galaxy.datatypes.interval import * + +log = logging.getLogger(__name__) + +class FileSet( Binary ): + """FileSet containing N files""" + file_ext = "prims.fileset.zip" + blurb = "(zipped) FileSet containing multiple files" + def sniff( self, filename ): + # If the zip file contains multiple files then return true, false otherwise: + zf = zipfile.ZipFile(filename) + if (len(zf.infolist())>1): + return True + else : + return False + +# the if is just for backwards compatibility...could remove this at some point +if hasattr(Binary, 'register_sniffable_binary_format'): + Binary.register_sniffable_binary_format('FileSet', 'prims.fileset.zip', FileSet) |
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diff -r 000000000000 -r d6001e8d7441 static/images/xtandem_results_viewer.png |
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Binary file static/images/xtandem_results_viewer.png has changed |
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diff -r 000000000000 -r d6001e8d7441 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jan 08 11:34:51 2014 +0100 |
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@@ -0,0 +1,28 @@ +<?xml version="1.0"?> +<tool_dependency> +<!-- see also http://wiki.galaxyproject.org/ToolShedToolFeatures for syntax help --> + <package name="xtandem" version="12.10011"> + <install version="1.0"> + <actions> + <action type="download_by_url">ftp://ftp.thegpm.org/projects/tandem/source/2011-12-01/tandem-linux-12-10-01-1.zip</action> + <!--<action type="shell_command">make clean</action> + <action type="shell_command">make</action>--> + <action type="move_directory_files"> + <source_directory>../tandem-linux-12-10-01-1</source_directory> + <destination_directory>$INSTALL_DIR/tandem-linux-12-10-01-1</destination_directory> + </action> + <action type="shell_command">chmod 755 $INSTALL_DIR/tandem-linux-12-10-01-1/bin/tandem.exe</action> + <!--<action type="chmod"><file mode="755">$INSTALL_DIR/tandem-linux-12-10-01-1/bin/tandem.exe</file><action>--> + <action type="set_environment"> + <environment_variable name="XTANDEM_12_10_01_PATH" action="set_to">$INSTALL_DIR/tandem-linux-12-10-01-1</environment_variable> + </action> + </actions> + </install> + <readme> +Ensures XTandem is installed. + </readme> + </package> + <set_environment version="1.0"> + <environment_variable name="XTANDEM_12_10_01_PATH" action="set_to">$INSTALL_DIR/tandem-linux-12-10-01-1</environment_variable> + </set_environment> +</tool_dependency> \ No newline at end of file |