changeset 6:f36b84d1ac09 draft

Uploaded
author iracooke
date Fri, 13 Jun 2014 18:26:15 -0400
parents 327b2d99d4c5
children 75184e45bf84
files README mascot.xml mascot_to_pepxml.xml repository_dependencies.xml tool-data/mascot_databases.loc.sample tool-data/mascot_mods.loc.sample tool-data/pepxml_databases.loc.sample tool-data/tandem_mods.loc.sample tool_dependencies.xml
diffstat 9 files changed, 0 insertions(+), 405 deletions(-) [+]
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line diff
--- a/README	Sun Jun 09 08:17:38 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-This includes tools for running Mascot MS/MS searches
-
-Running this tool requires a working installation of Mascot (commercial software).
-Mascot is available from http://www.matrixscience.com/
-
-Requirements:
-This package depends on the galaxy_protk and protk_trans_proteomic_pipeline packages
-Please see instructions for those packages before installing. In particular 
-you will need to install system package requirements for galaxy_protk and protk_trans_proteomic_pipeline
-using your package manager
--- a/mascot.xml	Sun Jun 09 08:17:38 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,186 +0,0 @@
-<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.1">
-
-
-	<requirements>
-	    <requirement type="package" version="1.2.2">galaxy_protk</requirement>
-   </requirements>
-
-	<description>Mascot MS/MS Search</description>
-
-
-	<command>rvm 1.9.3@protk-1.2.2 do mascot_search.rb 
-
-		#if $database.source_select=="built_in":
-		-d $database.dbkey
-		#else 
-		-d $database.custom_db
-		#end if
-
-		-f $fragment_ion_tol 
-
-		-S $server $input_file 
-
-		-o $output 
-
-		-r
-		
-		## Variable Mods
-
-		--var-mods='
-		$variable_mods
-		'
-		
-		--fix-mods='
-		$fixed_mods
-		'		
-		--allowed-charges=$allowed_charges	
-
-		--enzyme=$enzyme 
-
-		--instrument=$instrument 
-
-		--precursor-ion-tol-units=$precursor_tolu 
-
-		--email=$email 
-
-		-v $missed_cleavages
-
-		#if $security.security_use
-		--use-security
-		--username $security.username
-		--password $security.password
-		#end if
-
-		#if $proxy
-		--proxy $proxy
-		#end if
-
-	</command>
-
-	<inputs>
-	
-    <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/>
-
-	<conditional name="database">
-		<param name="source_select" type="select" label="Database Type">
-			<option value="built_in">Built-In</option>
-			<option value="custom_defined">Custom</option>
-		</param>
-		<when value="built_in">
-			<param name="dbkey" type="select" format="text" >
-				<label>Database</label>
-				<options from_file="mascot_databases.loc">
-					<column name="name" index="0" />
-					<column name="value" index="2" />
-				</options>
-			</param>
-		</when>
-		<when value="custom_defined">
-			<param name="custom_db" type="text" size="80" value="SwissProt" label="Database Name" help="Exact name of a database defined on the Mascot server (case-sensitive)"/>
-		</when>
-	</conditional>
-
-	<param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed">
-		<options from_file="mascot_mods.loc">
-			<column name="name" index="0" />
-			<column name="value" index="2" />
-		</options>
-	</param>		
-
-	<param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple values allowed">
-		<options from_file="mascot_mods.loc">
-			<column name="name" index="0" />
-			<column name="value" index="2" />
-		</options>
-	</param>
-	
-	<param name="missed_cleavages" type="select" format="text">
-		<label>Missed Cleavages Allowed</label>
-	    <option value="0">0</option>		
-		<option value="1">1</option>
-		<option value="2">2</option>
-	</param>
-	
-	<param name="enzyme" type="select" format="text">
-	    <label>Enzyme</label>
-	    <option value="Trypsin">Trypsin</option>		
-	</param>
-	
-	<param name="allowed_charges" type="select" format="text">
-	    <label>Peptide Charge</label>
-		<option value="8-">8-</option>
-		<option value="7-">7-</option>
-		<option value="6-">6-</option>
-		<option value="5-">5-</option>
-		<option value="4-">4-</option>
-		<option value="3-">3-</option>
-		<option value="2-,3- and 4-">2-,3- and 4-</option>
-		<option value="2- and 3-">2- and 3-</option>
-		<option value="2-">2-</option>
-		<option value="1-,2- and 3-">1-,2- and 3-</option>
-		<option value="1-">1-</option>
-		<option value="Mr">Mr</option>
-		<option value="1+">1+</option>
-	    <option value="1+, 2+ and 3+">1+,2+ and 3+</option>		
-		<option value="2+">2+</option>
-		<option value="2+ and 3+">2+ and 3+</option>
-		<option value="2+,3+ and 4+">2+,3+ and 4+</option>
-		<option value="3+">3+</option>
-		<option value="4+">4+</option>
-		<option value="5+">5+</option>
-		<option value="6+">6+</option>
-		<option value="7+">7+</option>
-		<option value="8+">8+</option>
-	</param>
-	
-	<param name="instrument" type="select" format="text">
-	    <label>Instrument</label>
-		<option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option>
-		<option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option>
-		<option value="ESI-TRAP">ESI-TRAP</option>
-		<option value="ESI-QUAD">ESI-QUAD</option>
-		<option value="ESI-FTICR">ESI-FTICR</option>
-	    <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option>
-		<option value="ESI-4SECTOR">ESI-4SECTOR</option>
-		<option value="FTMS-ECD">FTMS-ECD</option>
-		<option value="ETD-TRAP">ETD-TRAP</option>
-		<option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option>
-		<option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option>
-		<option value="MALDI-ISD">MALDI-ISD</option>
-		<option value="CID+ETD">CID+ETD</option>
-	</param>
-	
-	<param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
-
-	<param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/>
-	<param name="precursor_tolu" type="select" format="text">
-	    <label>Precursor Ion Tolerance Units</label>
-	    <option value="ppm">ppm</option>		
-		<option value="Da">Da</option>
-	</param>
-
-	<param name="server" type="text" label="URL to the cgi directory on the Mascot Server " size="60" value="http://www.exampleserver.com/mascot/cgi/"/>
-	<param name="proxy" type="text" label="Proxy Server URL including proxy port" size="60" value="" help="eg http://proxy.latrobe.edu.au:8080"/>
-
-	<conditional name="security">
-		<param name="security_use" type="boolean" label="Use Mascot Security?" help="Select this if you need to enter a username and password" truevalue="true" falsevalue="false" />
-		<when value="false" />
-		<when value="true">
-			<param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/>
-			<param name="password" type="text" label="Password" size="60" value="" help="Mascot Password. Password is encrypted when over the internet but is stored in clear-text on the Galaxy server"/>
-		</when>
-	</conditional>
-	<param name="email" type="text" label="Email " size="60" value="" help=""/>
-	
-	
-
-  </inputs>
-  <outputs>
-    <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database.dbkey if $database.has_key('dbkey') else $database.custom_db}.${input_file.display_name}.mascotdat"/>
-  </outputs>
-
-  <help>
-	Run a Mascot Search
-  </help>
-
-</tool>
--- a/mascot_to_pepxml.xml	Sun Jun 09 08:17:38 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.1">
-	<requirements>
-	    <requirement type="package" version="1.2.2">galaxy_protk</requirement>
-	    <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
-   </requirements>
-
-  <description>Converts a mascot results file to pepXML</description>
-
-<command>rvm 1.9.3@protk-1.2.2 do mascot_to_pepxml.rb 
-	$input_file 
-
-	-o $output 
-
-	#if $database.source_select=="built_in":
-	-d $database.dbkey
-	#else 
-	-d $database.fasta_file
-	#end if
-
-	#if $explicit_enzyme.explicit_enzyme_use
-	--enzyme $explicit_enzyme.enzyme
-	#end if
-
-	$shortid
-
-</command>
-<inputs>
-
-
-	<param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/>
-
-	<conditional name="database">
-		<param name="source_select" type="select" label="Database source" help="A local copy of the database used in the Mascot search">
-			<option value="built_in">Built-In</option>
-			<option value="input_ref">Uploaded fasta file</option>
-		</param>
-		<when value="built_in">
-			<param name="dbkey" type="select" format="text" >
-				<label>Database</label>
-				<options from_file="pepxml_databases.loc">
-					<column name="name" index="0" />
-					<column name="value" index="2" />
-				</options>
-			</param>
-		</when>
-		<when value="input_ref">
-			<param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
-		</when>
-	</conditional>
-
-	<param name="shortid" type="boolean" label="Short ID" help="Use protein id from the Mascot result file instead reading from the fasta database." truevalue="--shortid" falsevalue="" />
-
-	<conditional name="explicit_enzyme">
-		<param name="explicit_enzyme_use" type="boolean" label="Specify Enzyme" help="If left unchecked the Enzyme will be read from the input file" truevalue="true" falsevalue="false" />
-		<when value="false" />
-		<when value="true">
-			<param name="enzyme" type="text" label="Enzyme" size="80" value="trypsin" help="Semi-cleavage can be specified as semisample_enyzme eg semitrypsin"/>
-		</when>
-	</conditional>
-
-
-
-</inputs>
-<outputs>
-	<data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
-</outputs>
-
-	<tests>
-    	<test>
-    		<param name="source_select" value="input_ref"/>
-	      	<param name="fasta_file" value="bsa.fasta"/>
-   		   	<param name="input_file" value="F002832.dat"/>
-      		<output name="output" file="bsa_mascot2xml.pep.xml" compare="sim_size" delta="600" /> 
-    	</test>
-    	
-  	</tests>
-
-<help>
-	Convert mascot results from mascotdat to pepXML
-</help>
-
-</tool>
--- a/repository_dependencies.xml	Sun Jun 09 08:17:38 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Requires the Proteomics Datatypes package">
-
-     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2"/>
-
-</repositories>
--- a/tool-data/mascot_databases.loc.sample	Sun Jun 09 08:17:38 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-#This file lists the names of protein databases installed on Mascot
-#
-#In order to use interprophet to combine results from different search engines
-#it is important that all searches are performed on the same database
-#you should therefore ensure that each database installed on mascot has an equivalent
-#database installed in the Protk databases directory (databases used by omssa and x!tandem)
-#the mascot_to_pepxml tool will ask for this database when performing the conversion.
-#
-# Entries should follow the be structured as follows
-# Display_name dbkey dbNameOnMascot dbkey
-#
-Swissprot	spall_	SwissProt	spall_
-Swissprot Human	sphuman_	SPHuman	sphuman_
\ No newline at end of file
--- a/tool-data/mascot_mods.loc.sample	Sun Jun 09 08:17:38 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,77 +0,0 @@
-#This file lists the names of chemical modifications acceptable for proteomics search engines
-#
-#
-Acetyl (K)	acetyl_k_	Acetyl (K)	acetyl_k_
-Acetyl (N-term)	acetyl_n-term_	Acetyl (N-term)	acetyl_n-term_
-Acetyl (Protein N-term)	acetyl_proteinn-term_	Acetyl (Protein N-term)	acetyl_proteinn-term_
-Amidated (C-term)	amidated_c-term_	Amidated (C-term)	amidated_c-term_
-Amidated (Protein C-term)	amidated_proteinc-term_	Amidated (Protein C-term)	amidated_proteinc-term_
-Ammonia-loss (N-term C)	ammonia-loss_n-termc_	Ammonia-loss (N-term C)	ammonia-loss_n-termc_
-Biotin (K)	biotin_k_	Biotin (K)	biotin_k_
-Biotin (N-term)	biotin_n-term_	Biotin (N-term)	biotin_n-term_
-Carbamidomethyl (C)	carbamidomethyl_c_	Carbamidomethyl (C)	carbamidomethyl_c_
-Carbamyl (K)	carbamyl_k_	Carbamyl (K)	carbamyl_k_
-Carbamyl (N-term)	carbamyl_n-term_	Carbamyl (N-term)	carbamyl_n-term_
-Carboxymethyl (C)	carboxymethyl_c_	Carboxymethyl (C)	carboxymethyl_c_
-Cation:Na (C-term)	cation_na_c-term_	Cation:Na (C-term)	cation_na_c-term_
-Cation:Na (DE)	cation_na_de_	Cation:Na (DE)	cation_na_de_
-Deamidated (NQ)	deamidated_nq_	Deamidated (NQ)	deamidated_nq_
-Deamidated-N (N)	deamidated-n_n_	Deamidated-N (N)	deamidated-n_n_
-Dehydrated (N-term C)	dehydrated_n-termc_	Dehydrated (N-term C)	dehydrated_n-termc_
-Dehydro (C)	dehydro_c_	Dehydro (C)	dehydro_c_
-Dioxidation (M)	dioxidation_m_	Dioxidation (M)	dioxidation_m_
-Ethanolyl (C)	ethanolyl_c_	Ethanolyl (C)	ethanolyl_c_
-ExacTagAmine (K)	exactagamine_k_	ExacTagAmine (K)	exactagamine_k_
-ExacTagThiol (C)	exactagthiol_c_	ExacTagThiol (C)	exactagthiol_c_
-Formyl (N-term)	formyl_n-term_	Formyl (N-term)	formyl_n-term_
-Formyl (Protein N-term)	formyl_proteinn-term_	Formyl (Protein N-term)	formyl_proteinn-term_
-Gln->pyro-Glu (N-term Q)	gln_pyro-glu_n-termq_	Gln->pyro-Glu (N-term Q)	gln_pyro-glu_n-termq_
-Glu->pyro-Glu (N-term E)	glu_pyro-glu_n-terme_	Glu->pyro-Glu (N-term E)	glu_pyro-glu_n-terme_
-Guanidinyl (K)	guanidinyl_k_	Guanidinyl (K)	guanidinyl_k_
-ICAT-C (C)	icat-c_c_	ICAT-C (C)	icat-c_c_
-ICAT-C:13C(9) (C)	icat-c_13c_9__c_	ICAT-C:13C(9) (C)	icat-c_13c_9__c_
-ICPL (K)	icpl_k_	ICPL (K)	icpl_k_
-ICPL (Protein N-term)	icpl_proteinn-term_	ICPL (Protein N-term)	icpl_proteinn-term_
-ICPL:13C(6) (K)	icpl_13c_6__k_	ICPL:13C(6) (K)	icpl_13c_6__k_
-ICPL:13C(6) (Protein N-term)	icpl_13c_6__proteinn-term_	ICPL:13C(6) (Protein N-term)	icpl_13c_6__proteinn-term_
-ICPL:13C(6)2H(4) (K)	icpl_13c_6_2h_4__k_	ICPL:13C(6)2H(4) (K)	icpl_13c_6_2h_4__k_
-ICPL:13C(6)2H(4) (N-term)	icpl_13c_6_2h_4__n-term_	ICPL:13C(6)2H(4) (N-term)	icpl_13c_6_2h_4__n-term_
-ICPL:13C(6)2H(4) (Protein N-term)	icpl_13c_6_2h_4__proteinn-term_	ICPL:13C(6)2H(4) (Protein N-term)	icpl_13c_6_2h_4__proteinn-term_
-ICPL:2H(4) (K)	icpl_2h_4__k_	ICPL:2H(4) (K)	icpl_2h_4__k_
-ICPL:2H(4) (Protein N-term)	icpl_2h_4__proteinn-term_	ICPL:2H(4) (Protein N-term)	icpl_2h_4__proteinn-term_
-iTRAQ4plex (K)	itraq4plex_k_	iTRAQ4plex (K)	itraq4plex_k_
-iTRAQ4plex (N-term)	itraq4plex_n-term_	iTRAQ4plex (N-term)	itraq4plex_n-term_
-iTRAQ4plex (Y)	itraq4plex_y_	iTRAQ4plex (Y)	itraq4plex_y_
-iTRAQ8plex (K)	itraq8plex_k_	iTRAQ8plex (K)	itraq8plex_k_
-iTRAQ8plex (N-term)	itraq8plex_n-term_	iTRAQ8plex (N-term)	itraq8plex_n-term_
-iTRAQ8plex (Y)	itraq8plex_y_	iTRAQ8plex (Y)	itraq8plex_y_
-Label:18O(1) (C-term)	label_18o_1__c-term_	Label:18O(1) (C-term)	label_18o_1__c-term_
-Label:18O(2) (C-term)	label_18o_2__c-term_	Label:18O(2) (C-term)	label_18o_2__c-term_
-Met->Hse (C-term M)	met_hse_c-termm_	Met->Hse (C-term M)	met_hse_c-termm_
-Met->Hsl (C-term M)	met_hsl_c-termm_	Met->Hsl (C-term M)	met_hsl_c-termm_
-Methyl (C-term)	methyl_c-term_	Methyl (C-term)	methyl_c-term_
-Methyl (DE)	methyl_de_	Methyl (DE)	methyl_de_
-Methylthio (C)	methylthio_c_	Methylthio (C)	methylthio_c_
-mTRAQ (K)	mtraq_k_	mTRAQ (K)	mtraq_k_
-mTRAQ (N-term)	mtraq_n-term_	mTRAQ (N-term)	mtraq_n-term_
-mTRAQ (Y)	mtraq_y_	mTRAQ (Y)	mtraq_y_
-mTRAQ:13C(3)15N(1) (K)	mtraq_13c_3_15n_1__k_	mTRAQ:13C(3)15N(1) (K)	mtraq_13c_3_15n_1__k_
-mTRAQ:13C(3)15N(1) (N-term)	mtraq_13c_3_15n_1__n-term_	mTRAQ:13C(3)15N(1) (N-term)	mtraq_13c_3_15n_1__n-term_
-mTRAQ:13C(3)15N(1) (Y)	mtraq_13c_3_15n_1__y_	mTRAQ:13C(3)15N(1) (Y)	mtraq_13c_3_15n_1__y_
-NIPCAM (C)	nipcam_c_	NIPCAM (C)	nipcam_c_
-Oxidation (HW)	oxidation_hw_	Oxidation (HW)	oxidation_hw_
-Oxidation (M)	oxidation_m_	Oxidation (M)	oxidation_m_
-Phospho (ST)	phospho_st_	Phospho (ST)	phospho_st_
-Phospho (Y)	phospho_y_	Phospho (Y)	phospho_y_
-Propionamide (C)	propionamide_c_	Propionamide (C)	propionamide_c_
-Pyridylethyl (C)	pyridylethyl_c_	Pyridylethyl (C)	pyridylethyl_c_
-Pyro-carbamidomethyl (N-term C)	pyro-carbamidomethyl_n-termc_	Pyro-carbamidomethyl (N-term C)	pyro-carbamidomethyl_n-termc_
-Sulfo (S)	sulfo_s_	Sulfo (S)	sulfo_s_
-Sulfo (T)	sulfo_t_	Sulfo (T)	sulfo_t_
-Sulfo (Y)	sulfo_y_	Sulfo (Y)	sulfo_y_
-TMT (K)	tmt_k_	TMT (K)	tmt_k_
-TMT (N-term)	tmt_n-term_	TMT (N-term)	tmt_n-term_
-TMT2plex (K)	tmt2plex_k_	TMT2plex (K)	tmt2plex_k_
-TMT2plex (N-term)	tmt2plex_n-term_	TMT2plex (N-term)	tmt2plex_n-term_
-TMT6plex (K)	tmt6plex_k_	TMT6plex (K)	tmt6plex_k_
-TMT6plex (N-term)	tmt6plex_n-term_	TMT6plex (N-term)	tmt6plex_n-term_
--- a/tool-data/pepxml_databases.loc.sample	Sun Jun 09 08:17:38 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-#This file lists the names of protein databases installed locally in protk. 
-# These are used by omssa and x!tandem as well as the "mascot to pepxml" tool
-# In order to combine search results with Interprophet searches must be run against an identical database
-#
-# Entries should follow the be structured as follows
-# Display_name omssa_tandem_dbname dbkey
-#
-#
-Swissprot	spall_	SwissProt	spall_
-Combined PlasmboDB (falciparum) and Swissprot Human	plasmodb_pfalciparum_sphuman_	plasmodb_pfalciparum_sphuman	plasmodb_pfalciparum_sphuman_
-Swissprot Human	sphuman_	sphuman	sphuman_
-Combined Swissprot/TRembl Human	sptrhuman_	sptrhuman	sptrhuman_
-Swissprot Mouse	spmouse_	spmouse	spmouse_
--- a/tool-data/tandem_mods.loc.sample	Sun Jun 09 08:17:38 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-#This file lists the names of inbuilt chemical modifications accepted by X!Tandem
-#
-#
-Carbamidomethyl C	carbamidomethyl_c_	57.021464@C	carbamidomethyl_c_
-Glycocapture-N	glycocapture_n_	0.998@N!{P}[ST]	glycocapture_n_
-Oxidation M	oxidation_m_	15.994915@M	oxidation_m_
\ No newline at end of file
--- a/tool_dependencies.xml	Sun Jun 09 08:17:38 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-
-    <package name="galaxy_protk" version="1.2.2">
-	     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/>
-    </package>
-
-	<package name="trans_proteomic_pipeline" version="4.6.1">
-        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="e85a18371516"/>
-    </package>
-
-</tool_dependency>