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Deleted selected files
author bgruening
date Fri, 01 Nov 2013 19:43:01 -0400
parents f6e879c9ce85
children 57e35cd85712
files MassComb.jar README.txt Xtandem.txt masscomb_dbsearch_converter.xml masscomb_dbsearch_mascot.xml masscomb_dbsearch_xtandem.xml masscomb_fasta_validator.xml masscomb_visual_mspicture.xml static/images/xtandem_results_viewer.png tool_dependencies.xml
diffstat 10 files changed, 0 insertions(+), 899 deletions(-) [+]
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Binary file MassComb.jar has changed
--- 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
-
-
-
--- 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 
-
--- 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 @@
-<tool name="DB search converter" id="masscomb_dbsearch_converter" version="1.0.1">
-	<description>Convert X!tandem output to mzIdentML standard 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="mscfileset" 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="mscfileset" label="MS/MS search results"/>
-		      	</when>
-		      </conditional>
-	    </when>
-	  </conditional>
-	</inputs>
-	<outputs>
-	  <data name="outputFile" format="mzid" >
-		<change_format>
-		    <when input="fileType.type" value="fileSet" format="mscfileset" />
-		</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>
--- 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 @@
-<tool name="Mascot" id="masscomb_mascot" version="1.0.1">
-	<description>MS/MS DB search</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 
-	                    //////////////////////////
-	   This part is a WORKAROUND for the Cytoscape X11 dependency problem, even when running 'headless':
-	       export DISPLAY=:995;
-	       ...TODO -> this is linux specific...follow issue fix on Cytoscape...perhaps we can add try/catch in python here (see http://www.unix.com/shell-programming-scripting/107334-how-use-catch-try-final-bash-script.html)
-	       ...check how other tools do this  
-	    -->
-	<command interpreter="export DISPLAY=:995; java -jar">
-	    SedMat_cli.jar -pl $inputMS -ppids $inputPedtipeList -out $outputData -mtol  $mtol -rttol $rttol -dataset $outputData.dataset.id
-	</command>
-	<inputs>
-	 	<param name="inputMS" type="data" format="apml" label="MS data" />
-	 	<param name="inputPedtipeList" type="data" format="apml" label="Peptide ID data from MS/MS" />
-	 	<param name="outputFormat" type="select" label="Output format">
-	    	<option value="apml">APML</option>
-		</param>
-		<param name="mtol" type="integer" size="10" value="50" label="Set m/z tolerance (ppm) " />
-		<param name="rttol" type="integer" size="10" value="60" label="Set rention time tolerance (seconds) " />
-	</inputs>
-	<outputs>
-	  <data name="outputData" format="apml"/>
-	</outputs>
-	<tests>
-	  <!--  find out how to use -->
-	  <test>
-	    <param name="inputMS" value="testfile.pkl" ftype="pkl" />
-	    <output name="outputData" file="testsedmatout.pkl" ftype="tabular" />
-	  </test>
-	</tests>
-  <help>
-  
-.. 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). 
-
-  </help>
-</tool>
--- 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 @@
-<tool name="X Tandem" id="masscomb_xtandem200" version="1.0.1">
-	<description>MS/MS DB search</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 
-	-->
-    <requirements>
-        <requirement type="package" version="12.10011">xtandem</requirement>
-    </requirements>
-	<command interpreter="java -jar">
-	    MassComb.jar 
-	    -action XTANDEMSEARCH 
-	    -outputFile $outputFile 
-	    -fileGrouping $fileType.type
-    	-inputFile $fileType.inputFile
-       	-parametersFile $parametersFile
-		-outputTsv $outTsv
-		-outReport $htmlReportFile
-	    -outReportPicturesPath $htmlReportFile.files_path
-	    </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">
-   		<param name="inputFile" type="data" format="mzml" label="MS/MS input file (mzml)"/>
-    </when>
-    <when value="fileSet">
-      <param name="inputFile" type="data" format="mscfileset" label="input file"/>
-    </when>
-  </conditional>
-
-   <param name="precursor_mass_tolerance_lower" type="text" size="30" label="precursor monoisotopic mass_tolerance_lower" value="100" help=""/>
-   <param name="precursor_mass_tolerance_upper" type="text" size="30" label="precursor monoisotopic mass_tolerance_upper" value="100" help=""/>
-   <param name="precursor_error_units" type="select" label="precursor_error_units" help="">
-   	<option value="ppm" selected="true">ppm</option>
-   	<option value="Daltons">Daltons</option>
-   </param>
-   <param name="fragment_mass_tolerance" type="text" size="30" label="fragment_mass_tolerance" value="0.4" help=""/>
-   <param name="fragment_error_units" type="select" label="fragment_error_units" help="">
-   	<option value="ppm">ppm</option>
-   	<option value="Daltons" selected="true">Daltons</option>
-   </param>
-   <param name="database" type="data" format="fasta" label="Protein sequences DB (FASTA)"/>
-   <!-- 
-   <param name="min_precursor_charge" type="text" size="30" label="min_precursor_charge" value="1" help=""/>
-   <param name="max_precursor_charge" type="text" size="30" label="max_precursor_charge" value="4" help=""/>-->
-   <param name="fixed_modifications" type="select" display="checkboxes" multiple="true" label="Complete modifications" help="">
-	   	<option value="57.021464@C">Carbamidomethyl (C)</option>
-		<option value="57.021464@C,10.008269@R,8.014199@K">Cam+SILAC (8@K,10@R)</option>
-		<option value="57.021464@C,4.025107@K,6.020129@R">Cam+SILAC (4@K,6@R)</option>
-		<option value="57.021464@C,4.025107@K,6.020129@R,6.020129@L">Cam+SILAC (4@K,6@R,6@L)</option>
-		<option value="58.005479@C">Carboxymethyl (C)</option>
-		<option value="45.987721@C">Methylthio (C)</option>
-		<option value="47.984744@C">Trioxidation (C)</option>
-		<option value="442.224991@C">ICAT-D (C)</option>
-		<option value="450.275205@C">ICAT-D:2H(8) (C)</option>
-		<option value="227.126991@C">ICAT-C (C)</option>
-		<option value="236.157185@C">ICAT-C:13C(9) (C)</option>
-		<option value="58.005479@C">Carboxymethyl (C)</option>
-		<option value="105.057849@C">Pyridylethyl (C)</option>
-		<option value="71.037114@C">Propionamide (C)</option>
-		<option value="125.047679@C">Nethylmaleimide (C)</option>
-		<option value="144.102063@[,144.102063@K">iTRAQ (N-term,K)</option>
-		<option value="57.021464@C,144.102063@[,144.102063@K">Cam + iTRAQ (C,N-term,K)</option>
-		<option value="57.021464@C,224.152478@K,224.152478@[">Cam + TMT (C,K,nt)</option>
-		<option value="57.021464@C,225.155833@K,225.155833@[">Cam + TMT2plex (C,K,nt)</option>
-		<option value="57.021464@C,229.1629328@K,229.1629328@[">Cam + TMT6plex (C,K,nt)</option>
-		<option value="57.021464@C,28.0313@[,28.0313@K">Cam + Dimethyl (C,28@N-term,K)</option>
-		<option value="57.021464@C,32.0564@[,32.0564@K">Cam + Dimethyl (C,32@N-term,K)</option>
-		<option value="57.021464@C,36.0757@[,36.0757@K">Cam + Dimethyl (C,36@N-term,K)</option>
-		<option value="45.987721@C,144.102063@[,144.102063@K">Methylthio + iTRAQ (C,N-term,K)</option>
-		<option value="45.987721@C,224.152478@K,224.152478@[">Methylthio + TMT (C,K,nt)</option>
-		<option value="45.987721@C,225.155833@K,225.155833@[">Methylthio + TMT2plex (C,K,nt)</option>
-		<option value="45.987721@C,229.1629328@K,229.1629328@[">Methylthio + TMT6plex (C,K,nt)</option>
-		<option value="14.0156@],14.0156@D,14.0156@E">Methy +14Da (D,E,C-term)</option>
-   </param>
-      <param name="potential_modifications" type="select" display="checkboxes" multiple="true" label="Potential modifications" help="">
-      	<option value="15.994915@M">Oxidation (M)</option>
-		<option value="15.994915@W">Oxidation (W)</option>
-		<option value="0.984016@N">Deamidation (N)</option>
-		<option value="0.984016@Q">Deamidation (Q)</option>
-		<option value="79.966331@S">Phospho (S)</option>
-		<option value="79.966331@T">Phospho (T)</option>
-		<option value="79.966331@Y">Phospho (Y)</option>
-		<option value="79.956815@Y">Sulfo (Y)</option>
-		<option value="42.010565@K">Acetyl (K)</option>
-		<option value="43.005814@[">Carbamyl (nt)</option>
-		<option value="43.005814@K">Carbamyl (K)</option>
-		<option value="72.021129@[">Carboxyethyl (nt)</option>
-		<option value="72.021129@K">Carboxyethyl (K)</option>
-		<option value="57.021464@[">Carbamidomethyl (nt)</option>
-		<option value="57.021464@K">Carbamidomethyl (K)</option>
-		<option value="57.021464@C">Carbamidomethyl (C)</option>
-		<option value="58.005479@C">Carboxymethyl (C)</option>
-		<option value="45.987721@C">Methylthio (C)</option>
-		<option value="125.047679@C">Nethylmaleimide (C)</option>
-		<option value="31.989829@C">Dioxidation (C)</option>
-		<option value="47.984744@C">Trioxidation (C)</option>
-		<option value="27.994915@K">formyl (K)</option>
-		<option value="27.994915@[">formyl (nt)</option>
-		<option value="114.042927@K">GlyGly (K)</option>
-		<option value="8.0502@C">ICAT-D:2H(8) (C)</option>
-		<option value="9.0302@C">ICAT-C:13C(9) (C)</option>
-		<option value="144.102063@[">iTRAQ (N-term)</option>
-		<option value="144.102063@K">iTRAQ (K)</option>
-		<option value="6.020129@L">Label:13C(6) (L)</option>
-		<option value="6.020129@K">Label:13C(6) (K)</option>
-		<option value="8.014199@K">Label:13C(6)15N(2) (K)</option>
-		<option value="6.020129@R">Label:13C(6) (R)</option>
-		<option value="4.025107@K">Label:2H(4) (K)</option>
-		<option value="125.047679@C">Nethylmaleimide (C)</option>
-		<option value="31.005814@C">Sulfinamide (C)</option>
-		<option value="224.152478@K,224.152478@[">TMT (K,nt)</option>
-		<option value="225.155833@K,225.155833@[">TMT2plex (K,nt)</option>
-		<option value="229.1629328@K,229.1629328@[">TMT6plex (K,nt)</option>      	
-      </param>
-      <!-- 
-      <param name="missed_cleavages" type="text" size="30" label="missed_cleavages" value="1" help="Nr. of possible cleavage sites missed by the enzyme"/>-->
-      <param name="minimum_fragment_mz" type="text" size="30" label="minimum_fragment_mz" value="150" help=""/>
-      <param name="cleavage_site" type="select" label="cleavage_site" help="">
-      	<option selected="true" value="[RK]|{P}">trypsin, [RK]|{P}</option>
-		<option value="[R]|[X]">endo-arg-C, [R]|[X]</option>
-		<option value="[K]|[X]">endo-lys-C, [K]|[X]</option>
-		<option value="[E]|[X]">endo-glu-C, [E]|[X]</option>
-		<option value="[X]|[D]">endo-asp-N, [X]|[D]</option>
-		<option value="[ED]|[X]">V8, [ED]|[X]</option>
-		<option value="[FYWL]|{P}">chymotrypsin, [FYWL]|{P}</option>
-      </param>
-      <param name="maximum_missed_cleavage_sites" type="integer" size="10" value="1" 
-      label="maximum missed cleavage sites" 
-      help="maximum number of missed cleavage sites allowed within a peptide. For a specific, 
-      aggressive enzyme such as trypsin, the number of missed sites will be low: a value of 1 or 2 is appropriate. 
-      For a non-specific enzyme, such as pepsin, then a value of 50 is more appropriate."/>
-      <param name="max_valid_expect" type="text" size="30" label="maximum valid expectation value" value="0.1" 
-      help="Max E-Value of a hit to be reported. All results with expectation values less than this value 
-      are considered to be statisitically significant and are recorded. "/>
-      <conditional name="refinementOpt">
-	      <param name="refinement" type="select" label="Refine search" help="Select this to enable a second round of more 
-	      detailed searching, using only the set of proteins found by the contraints above. E.g. 
-	      Rather than entering the 'potential modifications' in the options above, try entering them here only. This is 
-	      faster and limits this more thorough searching to a set of proteins for which there is already some evidence.">
-	      	<option value="yes">Yes</option>
-	      	<option value="no" selected="true">No</option>
-	      </param>
-	      <when value="yes">
-            <param name="refine_point_mutation" type="select" label="Allow for point mutations (substitutions)" 
-            help="Test the selected sequences for the possibility of a point mutation in each one of the 
-            peptides generated with the initial cleavage chemistry.">
-		      	<option value="yes" selected="true">Yes</option>
-		      	<option value="no">No</option>
-			</param>
-			<param name="refine_potential_modifications" type="select" display="checkboxes" multiple="true" label="Potential modifications to look for in refined search" help="">
-		      	<option value="15.994915@M">Oxidation (M)</option>
-				<option value="15.994915@W">Oxidation (W)</option>
-				<option value="0.984016@N">Deamidation (N)</option>
-				<option value="0.984016@Q">Deamidation (Q)</option>
-				<option value="79.966331@S">Phospho (S)</option>
-				<option value="79.966331@T">Phospho (T)</option>
-				<option value="79.966331@Y">Phospho (Y)</option>
-				<option value="79.956815@Y">Sulfo (Y)</option>
-				<option value="42.010565@K">Acetyl (K)</option>
-				<option value="43.005814@[">Carbamyl (nt)</option>
-				<option value="43.005814@K">Carbamyl (K)</option>
-				<option value="72.021129@[">Carboxyethyl (nt)</option>
-				<option value="72.021129@K">Carboxyethyl (K)</option>
-				<option value="57.021464@[">Carbamidomethyl (nt)</option>
-				<option value="57.021464@K">Carbamidomethyl (K)</option>
-				<option value="57.021464@C">Carbamidomethyl (C)</option>
-				<option value="58.005479@C">Carboxymethyl (C)</option>
-				<option value="45.987721@C">Methylthio (C)</option>
-				<option value="125.047679@C">Nethylmaleimide (C)</option>
-				<option value="31.989829@C">Dioxidation (C)</option>
-				<option value="47.984744@C">Trioxidation (C)</option>
-				<option value="27.994915@K">formyl (K)</option>
-				<option value="27.994915@[">formyl (nt)</option>
-				<option value="114.042927@K">GlyGly (K)</option>
-				<option value="8.0502@C">ICAT-D:2H(8) (C)</option>
-				<option value="9.0302@C">ICAT-C:13C(9) (C)</option>
-				<option value="144.102063@[">iTRAQ (N-term)</option>
-				<option value="144.102063@K">iTRAQ (K)</option>
-				<option value="6.020129@L">Label:13C(6) (L)</option>
-				<option value="6.020129@K">Label:13C(6) (K)</option>
-				<option value="8.014199@K">Label:13C(6)15N(2) (K)</option>
-				<option value="6.020129@R">Label:13C(6) (R)</option>
-				<option value="4.025107@K">Label:2H(4) (K)</option>
-				<option value="125.047679@C">Nethylmaleimide (C)</option>
-				<option value="31.005814@C">Sulfinamide (C)</option>
-				<option value="224.152478@K,224.152478@[">TMT (K,nt)</option>
-				<option value="225.155833@K,225.155833@[">TMT2plex (K,nt)</option>
-				<option value="229.1629328@K,229.1629328@[">TMT6plex (K,nt)</option>      	
-      		</param>
-      		<param name="refine_max_valid_expect" type="text" size="30" label="maximum valid expectation value for identifications coming from refine step" value="0.01" 
-      		help="Max E-Value of a 'refine based' hit to be reported. Notice that the default value here is stricter than
-      		the same parameter for 'non-refine based' identifications above. "/>
-	      </when>
-	  </conditional>
-      <param name="reverse_scoring" type="select" label="Scoring, include reverse" help=" Use the X! Tandem protein sequence reverse method (sequences are reversed in memory and searched again, the tag ':reversed' is added to the protein description).">
-      	<option value="yes">Yes</option>
-      	<option value="no" selected="true">No</option>
-      	<option value="only">Only</option>
-      </param>
-
-</inputs>
-<configfiles>
-<configfile name="parametersFile">&lt;?xml version="1.0" encoding="UTF-8"?&gt;
-&lt;tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="XTandemWrapper" program="XTandemWrapper"&gt;
-	&lt;Files/&gt;
-	&lt;Parameters&gt;  
-		  &lt;Attribute attributeName="xtandemLocation" value="" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="database" value="${database}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="precursor_mass_tolerance_lower" toolSpecificName="spectrum, parent monoisotopic mass error minus" value="${precursor_mass_tolerance_lower}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="precursor_mass_tolerance_upper" toolSpecificName="spectrum, parent monoisotopic mass error plus" value="${precursor_mass_tolerance_upper}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="precursor_error_units" toolSpecificName="spectrum, parent monoisotopic mass error units" value="${precursor_error_units}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="fragment_mass_tolerance" toolSpecificName="spectrum, fragment monoisotopic mass error" value="${fragment_mass_tolerance}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="fragment_error_units" toolSpecificName="spectrum, fragment monoisotopic mass error units" value="${fragment_error_units}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="fixed_modifications" toolSpecificName="residue, modification mass" value="${fixed_modifications}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="potential_modifications" toolSpecificName="residue, potential modification mass" value="${potential_modifications}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="minimum_fragment_mz" toolSpecificName="spectrum, minimum fragment mz" value="${minimum_fragment_mz}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="cleavage_site" toolSpecificName="protein, cleavage site" value="${cleavage_site}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="maximum_missed_cleavage_sites" toolSpecificName="scoring, maximum missed cleavage sites" value="${maximum_missed_cleavage_sites}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="max_valid_expect" toolSpecificName="output, maximum valid expectation value" value="${max_valid_expect}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="refinement" toolSpecificName="refine" value="${refinementOpt.refinement}" type="Unknown" description=""/&gt;
-	#if $refinementOpt.refinement == "yes"
-		  &lt;Attribute attributeName="refine_point_mutation" toolSpecificName="refine, point mutations" value="${refinementOpt.refine_point_mutation}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="refine_potential_modifications" toolSpecificName="refine, potential modification mass" value="${refinementOpt.refine_potential_modifications}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="refine_max_valid_expect" toolSpecificName="refine, maximum valid expectation value" value="${refinementOpt.refine_max_valid_expect}" type="Unknown" description=""/&gt;
-	#end if
-		  &lt;Attribute attributeName="reverse_scoring" toolSpecificName="scoring, include reverse" value="${reverse_scoring}" type="Unknown" description=""/&gt;
-	&lt;/Parameters&gt;
-&lt;/tns:Program&gt;  
-</configfile>
-</configfiles>
-<outputs>
-	<data name="outputFile" format="bioml"  label="${tool.name} on ${on_string} - Results XML">
-		<change_format>
-		    <when input="fileType.type" value="fileSet" format="mscfileset" />
-		</change_format>
-	</data>
-	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report"> </data>
-	<data name="outTsv" format="tabular" label="${tool.name} on ${on_string} - TSV report"> </data>
-</outputs>
-<tests>
-	<test>
-	</test>
-</tests>
-<help>
-
-.. 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. 
-<!-- Add this from Ron's email ? :
-They are an estimate of the spectrum-to-peptide match E-value associated with the 
-null-hypothesis "all spectrum-to-peptide matches are stochasitic".
--->
-
-.. _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
-
-</help>
-</tool>
--- 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 @@
-<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&amp;&amp;[^ARNDCEQGHILKMFPSTWYV]])|(^[ARNDCEQGHILKMFPSTWYV]+[\w&amp;&amp;[^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>
--- a/masscomb_visual_mspicture.xml	Fri Nov 01 19:42:27 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,87 +0,0 @@
-<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 $parametersFile
-		
-	    </command>
-<inputs>
-  <conditional name="fileType">
-    <param name="type" type="select" label="select MS/MS input type">
-      <option value="single" selected="true">single-File</option>
-      <option value="fileSet">fileSet</option>
-    </param>
-    <when value="single">
-      <conditional name="inputFormatType">
-      	<param name="inputFormat" type="select" label="inputFormat">
-	    		<option value="mzml" selected="true">mzml</option>
-				<option value="mzxml">mzxml</option>
-	    		<option value="apml">apml</option>
-		</param>
-		<when value="mzxml">
-      		<param name="inputFile" type="data" format="mzxml" label="MS input file (mzXML)"/>
-      	</when>
-      	<when value="mzml">
-      		<param name="inputFile" type="data" format="mzml" label="MS input file (mzml)"/>
-      	</when>
-      	<when value="apml">
-      		<param name="inputFile" type="data" format="apml" label="MS or MS/MS input file (APML)"/>
-      	</when>
-      </conditional>
-    </when>
-    <when value="fileSet">
-      <param name="inputFile" type="data" format="mscfileset" label="input file"/>
-    </when>
-  </conditional>
-
-  <param name="data_type" type="select" label="Data type" help=""> 
-   	    <option value="LC-MS">LC-MS</option>
-   	    <option value="LC-MS/MS">LC-MS/MS</option>
-  </param>
-
-  <param name="gray_scale" type="select" display="checkboxes" multiple="True" label="Use gray scale" help=""> 
-   	    <option value="Yes">Yes</option>
-  </param>
-
-</inputs>
-<configfiles>
-<configfile name="parametersFile">&lt;?xml version="1.0" encoding="UTF-8"?&gt;
-&lt;tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="MsPictureWrapper" program="MsPictureWrapper"&gt;
-	&lt;Files/&gt;
-	&lt;Parameters&gt;
-		  &lt;Attribute attributeName="toolLocation" value="/home/lukas007/bin/" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="gray_scale" toolSpecificName="--grey" value="${gray_scale}" type="Unknown" description=""/&gt;
-		  &lt;Attribute attributeName="data_type" value="${data_type}" type="Unknown" description=""/&gt;
-	&lt;/Parameters&gt;
-&lt;/tns:Program&gt;  
-</configfile>
-</configfiles>
-<outputs>
-	<data format="html" name="html_file" />
-</outputs>
-<tests>
-	<test>
-	</test>
-</tests>
-<help>
-
-.. class:: infomark
-  
-This tool displays the MS data using ProteoWizard's msPicture tool
-
-
-</help>
-</tool>
\ No newline at end of file
Binary file static/images/xtandem_results_viewer.png has changed
--- a/tool_dependencies.xml	Fri Nov 01 19:42:27 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="libgd" version="2.1.0">
-        <repository changeset_revision="1efb934d4600" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="trans_proteomic_pipeline" version="4.6.3">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://downloads.sourceforge.net/project/sashimi/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.6%20%28occupy%29%20rev%203/TPP-4.6.3.tgz</action>
-                <!-- populate the environment variables from the dependend repos -->
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="1efb934d4600" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="libgd" version="2.1.0" />
-                    </repository>
-                </action>
-                <action type="change_directory">./trans_proteomic_pipeline/src/</action>
-                <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR' &gt; Makefile.config.incl</action>
-                <action type="make_install" />
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            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/
-
-            PATH will be set.
-            TPP_ROOT_PATH will point to the root path of the installation.
-        </readme>
-    </package>
-</tool_dependency>