Mercurial > repos > iracooke > msgfplus
changeset 16:66a149ef79f7 draft
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
| author | iracooke |
|---|---|
| date | Tue, 20 Oct 2015 20:01:47 -0400 |
| parents | 6c751c59ce18 |
| children | 7990ee72821b |
| files | msgfplus_search.xml repository_dependencies.xml tool-data/msgfplus_mods.loc.sample tool-data/msgfplus_mods_fix.loc.sample tool-data/msgfplus_mods_var.loc.sample tool_dependencies.xml |
| diffstat | 6 files changed, 122 insertions(+), 61 deletions(-) [+] |
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--- 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>
--- 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>
--- 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
--- /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_ +
--- /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_
--- /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>