# HG changeset patch
# User iracooke
# Date 1445385707 14400
# Node ID 66a149ef79f7f5e644d5836e5ab796639c753a0c
# Parent  6c751c59ce1868df8ebc3019d22d4cc044f4d617
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty

diff -r 6c751c59ce18 -r 66a149ef79f7 msgfplus_search.xml
--- a/msgfplus_search.xml	Thu Mar 26 20:04:30 2015 -0400
+++ b/msgfplus_search.xml	Tue Oct 20 20:01:47 2015 -0400
@@ -1,8 +1,8 @@
 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.1.0">
     <description>Run an MSGF+ Search</description>
     <requirements>
-        <container type="docker">iracooke/protk-1.4.1</container>
-        <requirement type="package" version="1.4">protk</requirement>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
         <requirement type="package" version="20140210">msgfplus</requirement>
         <requirement type="package" version="3_0_4388">proteowizard</requirement>
     </requirements>
@@ -47,8 +47,7 @@
         --num-reported-matches=$num_reported_matches
         --java-mem=$java_mem
 
-        --threads $threads
-
+        --threads "\${GALAXY_SLOTS:-12}"
         #if $pepxml_output_use:
         --pepxml
         #end if
@@ -75,7 +74,7 @@
         </conditional>
         <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
         <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed">
-            <options from_file="msgfplus_mods.loc">
+            <options from_file="msgfplus_mods_var.loc">
                 <column name="name" index="0" />
                 <column name="value" index="2" />
             </options>
@@ -85,7 +84,7 @@
             <param name="custom_mod" type="text" />
         </repeat>
         <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed">
-            <options from_file="msgfplus_mods.loc">
+            <options from_file="msgfplus_mods_fix.loc">
                 <column name="name" index="0" />
                 <column name="value" index="2" />
             </options>
@@ -155,7 +154,6 @@
         <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/>
         <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/>
         <param name="java_mem" help="Increase this value if you get out of memory errors" type="text" size="80" value="3500M" label="Java Memory Limit"/>
-        <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search."/>        
         <param name="pepxml_output_use" checked="true" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" />
     </inputs>
     <outputs>
diff -r 6c751c59ce18 -r 66a149ef79f7 repository_dependencies.xml
--- a/repository_dependencies.xml	Thu Mar 26 20:04:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Proteomics datatypes">
-    <repository changeset_revision="ac51d9dbfb4d" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
- </repositories>
diff -r 6c751c59ce18 -r 66a149ef79f7 tool-data/msgfplus_mods.loc.sample
--- a/tool-data/msgfplus_mods.loc.sample	Thu Mar 26 20:04:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-#This file lists the names of inbuilt chemical modifications accepted by msgfplus
-#Each entry consists of 4 tab separated fields like this
-#<Displayed Name>	<DBKey>	<Modification String>	<DBKey>
-#
-#Modification strings should conform to the standard MSGFPlus syntax with the following exception
-#The ModType field is overridden by the msgfplus_search.rb tool. In other words any of these mods
-#May be passed to the tool as a variable or fixed mod and the tool will substitute the appropriate ModType
-#value
-#
-#Standard MSGFPlus syntax is
-#
-# To input a modification, use the following command:
-# Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required).
-# CompositionStr (C[Num]H[Num]N[Num]O[Num]S[Num]P[Num])
-# 	- C (Carbon), H (Hydrogen), N (Nitrogen), O (Oxygen), S (Sulfer) and P (Phosphorus) are allowed.
-# 	- Atom can be omitted. The sequence of atoms must be followed. 
-# 	- Negative numbers are allowed.
-# 	- E.g. C2H2O1 (valid), H2C1O1 (invalid) 
-# Mass can be used instead of CompositionStr. It is important to specify accurate masses (integer masses are insufficient).
-# 	- E.g. 15.994915 
-# Residues: affected amino acids (must be upper letters)
-# 	- Must be uppor letters or *
-# 	- Use * if this modification is applicable to any residue. 
-# 	- * should not be "anywhere" modification (e.g. "15.994915, *, opt, any, Oxidation" is not allowed.) 
-# 	- E.g. NQ, *
-# ModType: "fix" for fixed modifications, "opt" for variable modifications (case insensitive)
-# Position: position in the peptide where the modification can be attached. 
-# 	- One of the following five values should be used:
-# 	- any (anywhere), N-term (peptide N-term), C-term (peptide C-term), Prot-N-term (protein N-term), Prot-C-term (protein C-term) 
-# 	- Case insensitive
-# 	- "-" can be omitted
-# 	- E.g. any, Any, Prot-n-Term, ProtNTerm => all valid
-# Name: name of the modification (Unimod PSI-MS name)
-# 	- For proper mzIdentML output, this name should be the same as the Unimod PSI-MS name
-# 	- E.g. Phospho, Acetyl
-#C2H3N1O1,C,fix,any,Carbamidomethyl 		# Fixed Carbamidomethyl C
-# Variable Modifications (default: none)
-#O1,M,opt,any,Oxidation				# Oxidation M
-#15.994915,M,opt,any,Oxidation			# Oxidation M (mass is used instead of CompositionStr)
-#H-1N-1O1,NQ,opt,any,Deamidated			# Negative numbers are allowed.
-#C2H3NO,*,opt,N-term,Carbamidomethyl		# Variable Carbamidomethyl N-term
-#H-2O-1,E,opt,N-term,Pyro_glu			# Pyro-glu from E
-#H-3N-1,Q,opt,N-term,Pyro-glu			# Pyro-glu from Q
-#C2H2O,*,opt,Prot-N-term,Acetyl			# Acetylation Protein N-term
-#C2H2O1,K,opt,any,Acetyl			# Acetylation K
-#CH2,K,opt,any,Methy				# Methylation K
-#HO3P,STY,opt,any,Phospho			# Phosphorylation STY
-
-Carbamidomethyl C	carbamidomethyl_c_	C2H3N1O1,C,opt,any,Carbamidomethyl	carbamidomethyl_c_
-Oxidation M	oxidation_m_	O1,M,opt,any,Oxidation	oxidation_m_
\ No newline at end of file
diff -r 6c751c59ce18 -r 66a149ef79f7 tool-data/msgfplus_mods_fix.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/msgfplus_mods_fix.loc.sample	Tue Oct 20 20:01:47 2015 -0400
@@ -0,0 +1,50 @@
+#This file lists the names of inbuilt chemical modifications accepted by msgfplus
+#Each entry consists of 4 tab separated fields like this
+#<Displayed Name>	<DBKey>	<Modification String>	<DBKey>
+#
+#Modification strings should conform to the standard MSGFPlus syntax with the following exception
+#The ModType field is overridden by the msgfplus_search.rb tool. In other words any of these mods
+#May be passed to the tool as a variable or fixed mod and the tool will substitute the appropriate ModType
+#value
+#
+#Standard MSGFPlus syntax is
+#
+# To input a modification, use the following command:
+# Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required).
+# CompositionStr (C[Num]H[Num]N[Num]O[Num]S[Num]P[Num])
+# 	- C (Carbon), H (Hydrogen), N (Nitrogen), O (Oxygen), S (Sulfer) and P (Phosphorus) are allowed.
+# 	- Atom can be omitted. The sequence of atoms must be followed. 
+# 	- Negative numbers are allowed.
+# 	- E.g. C2H2O1 (valid), H2C1O1 (invalid) 
+# Mass can be used instead of CompositionStr. It is important to specify accurate masses (integer masses are insufficient).
+# 	- E.g. 15.994915 
+# Residues: affected amino acids (must be upper letters)
+# 	- Must be uppor letters or *
+# 	- Use * if this modification is applicable to any residue. 
+# 	- * should not be "anywhere" modification (e.g. "15.994915, *, opt, any, Oxidation" is not allowed.) 
+# 	- E.g. NQ, *
+# ModType: "fix" for fixed modifications, "opt" for variable modifications (case insensitive)
+# Position: position in the peptide where the modification can be attached. 
+# 	- One of the following five values should be used:
+# 	- any (anywhere), N-term (peptide N-term), C-term (peptide C-term), Prot-N-term (protein N-term), Prot-C-term (protein C-term) 
+# 	- Case insensitive
+# 	- "-" can be omitted
+# 	- E.g. any, Any, Prot-n-Term, ProtNTerm => all valid
+# Name: name of the modification (Unimod PSI-MS name)
+# 	- For proper mzIdentML output, this name should be the same as the Unimod PSI-MS name
+# 	- E.g. Phospho, Acetyl
+#C2H3N1O1,C,fix,any,Carbamidomethyl 		# Fixed Carbamidomethyl C
+# Variable Modifications (default: none)
+#O1,M,opt,any,Oxidation				# Oxidation M
+#15.994915,M,opt,any,Oxidation			# Oxidation M (mass is used instead of CompositionStr)
+#H-1N-1O1,NQ,opt,any,Deamidated			# Negative numbers are allowed.
+#C2H3NO,*,opt,N-term,Carbamidomethyl		# Variable Carbamidomethyl N-term
+#H-2O-1,E,opt,N-term,Pyro_glu			# Pyro-glu from E
+#H-3N-1,Q,opt,N-term,Pyro-glu			# Pyro-glu from Q
+#C2H2O,*,opt,Prot-N-term,Acetyl			# Acetylation Protein N-term
+#C2H2O1,K,opt,any,Acetyl			# Acetylation K
+#CH2,K,opt,any,Methy				# Methylation K
+#HO3P,STY,opt,any,Phospho			# Phosphorylation STY
+
+Carbamidomethyl C	carbamidomethyl_c_	C2H3N1O1,C,fix,any,Carbamidomethyl	carbamidomethyl_c_
+
diff -r 6c751c59ce18 -r 66a149ef79f7 tool-data/msgfplus_mods_var.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/msgfplus_mods_var.loc.sample	Tue Oct 20 20:01:47 2015 -0400
@@ -0,0 +1,55 @@
+#This file lists the names of inbuilt chemical modifications accepted by msgfplus
+#Each entry consists of 4 tab separated fields like this
+#<Displayed Name>	<DBKey>	<Modification String>	<DBKey>
+#
+#Modification strings should conform to the standard MSGFPlus syntax with the following exception
+#The ModType field is overridden by the msgfplus_search.rb tool. In other words any of these mods
+#May be passed to the tool as a variable or fixed mod and the tool will substitute the appropriate ModType
+#value
+#
+#Standard MSGFPlus syntax is
+#
+# To input a modification, use the following command:
+# Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required).
+# CompositionStr (C[Num]H[Num]N[Num]O[Num]S[Num]P[Num])
+# 	- C (Carbon), H (Hydrogen), N (Nitrogen), O (Oxygen), S (Sulfer) and P (Phosphorus) are allowed.
+# 	- Atom can be omitted. The sequence of atoms must be followed. 
+# 	- Negative numbers are allowed.
+# 	- E.g. C2H2O1 (valid), H2C1O1 (invalid) 
+# Mass can be used instead of CompositionStr. It is important to specify accurate masses (integer masses are insufficient).
+# 	- E.g. 15.994915 
+# Residues: affected amino acids (must be upper letters)
+# 	- Must be uppor letters or *
+# 	- Use * if this modification is applicable to any residue. 
+# 	- * should not be "anywhere" modification (e.g. "15.994915, *, opt, any, Oxidation" is not allowed.) 
+# 	- E.g. NQ, *
+# ModType: "fix" for fixed modifications, "opt" for variable modifications (case insensitive)
+# Position: position in the peptide where the modification can be attached. 
+# 	- One of the following five values should be used:
+# 	- any (anywhere), N-term (peptide N-term), C-term (peptide C-term), Prot-N-term (protein N-term), Prot-C-term (protein C-term) 
+# 	- Case insensitive
+# 	- "-" can be omitted
+# 	- E.g. any, Any, Prot-n-Term, ProtNTerm => all valid
+# Name: name of the modification (Unimod PSI-MS name)
+# 	- For proper mzIdentML output, this name should be the same as the Unimod PSI-MS name
+# 	- E.g. Phospho, Acetyl
+#C2H3N1O1,C,fix,any,Carbamidomethyl 		# Fixed Carbamidomethyl C
+# Variable Modifications (default: none)
+#O1,M,opt,any,Oxidation				# Oxidation M
+#15.994915,M,opt,any,Oxidation			# Oxidation M (mass is used instead of CompositionStr)
+#H-1N-1O1,NQ,opt,any,Deamidated			# Negative numbers are allowed.
+#C2H3NO,*,opt,N-term,Carbamidomethyl		# Variable Carbamidomethyl N-term
+#H-2O-1,E,opt,N-term,Pyro_glu			# Pyro-glu from E
+#H-3N-1,Q,opt,N-term,Pyro-glu			# Pyro-glu from Q
+#C2H2O,*,opt,Prot-N-term,Acetyl			# Acetylation Protein N-term
+#C2H2O1,K,opt,any,Acetyl			# Acetylation K
+#CH2,K,opt,any,Methy				# Methylation K
+#HO3P,STY,opt,any,Phospho			# Phosphorylation STY
+
+Oxidation M	oxidation_m_	O1,M,opt,any,Oxidation	oxidation_m_
+Acetylation Protein N-term	acetyl_nterm_	C2H2O,*,opt,Prot-N-term,Acetyl	acetyl_nterm_
+Deamidation NQ	deamidation_nq_	H-1N-1O1,NQ,opt,any,Deamidated	deamidation_nq_
+Acetylation K	acetyl_k_	C2H2O1,K,opt,any,Acetyl	acetyl_k_
+Methylation K	methyl_k_	CH2,K,opt,any,Methy	methyl_k_
+Phosphorylation STY	phospho_sty_	HO3P,STY,opt,any,Phospho	phospho_sty_
+Carbamidomethyl N-term	carbamidomethyl_nterm_	C2H3NO,*,opt,N-term,Carbamidomethyl	carbamidomethyl_nterm_
diff -r 6c751c59ce18 -r 66a149ef79f7 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 20 20:01:47 2015 -0400
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="protk" version="1.4.3">
+        <repository changeset_revision="74bf855be117" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="msgfplus" version="20140210">
+        <repository changeset_revision="4e9e5c400a97" name="package_msgfplus_20140210" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="proteowizard" version="3_0_4388">
+        <repository changeset_revision="cc1d68e03362" name="package_proteowizard_3_0_4388" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>