# HG changeset patch # User iracooke # Date 1445385682 14400 # Node ID 827f19088303fdbb93de88ce81a42b02f89a1568 # Parent dfb2b78b3aff03baad6cbdcd477a992d3680fff3 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty diff -r dfb2b78b3aff -r 827f19088303 README --- a/README Mon Jan 05 17:17:45 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -This package is a galaxy wrapper for the MSGF+ search tool. - -Requirements: -This package uses protk, msgfplus and proteowizard, which must be installed separately. - -For instructions please see: https://github.com/iracooke/protk/#galaxy-integration \ No newline at end of file diff -r dfb2b78b3aff -r 827f19088303 README.md --- a/README.md Mon Jan 05 17:17:45 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -## What is it? -Galaxy tool definition file and wrapper scripts for the [MSGF+ Search Engine](http://proteomics.ucsd.edu/Software/MSGFPlus.html). - -## Installation -Install from the main galaxy toolshed at http://toolshed.g2.bx.psu.edu/ - -Depends on command-line scripts and databases available in the [protk ruby gem](https://bitbucket.org/iracooke/protk). - diff -r dfb2b78b3aff -r 827f19088303 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Oct 20 20:01:22 2015 -0400 @@ -0,0 +1,43 @@ +MS-GF+ +====== + +Galaxy wrapper for the `MS-GF+`__ tandem ms search tool + +.. _msgfplus: http://proteomics.ucsd.edu/software-tools/ms-gf/ +__ msgfplus_ + +Requirements +------------ + +This package uses protk_, msgfplus_ and the `idconvert` tool from Proteowizard_ which need to be present in order for the tool to work. + +.. _protk: https://github.com/iracooke/protk +.. _Proteowizard: http://proteowizard.sourceforge.net/ + + +There are two ways you can satify these dependencies (choose one): + +1. **Manual Install:** Details on how to install protk_, msgfplus_ and Proteowizard_ manually are available here_. + +2. **Use Docker:** These tools are designed to run inside a docker_ container. If your galaxy supports `running tools within a docker container`__ you don't need to worry about dependencies. Simply install and things should just work. The docker container itself is versioned and new versions of this tool will automatically download an update to the container if needed. + +.. _docker: https://www.docker.com/ +.. _here: https://github.com/iracooke/protk/#galaxy-integration +.. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker +__ container_ + + +Further Info +------------ + +The source code for this tool and other protk galaxy tools is on github_. Please visit the github page to contribute to the project or to `report an issue`__ + +.. _github: https://github.com/iracooke/protk-galaxytools +.. _issue: https://github.com/iracooke/protk-galaxytools/issues +__ issue_ + + +Information on the MS-GF+ search tool itself can be found here_ + +.. _here: http://proteowizard.sourceforge.net/ + diff -r dfb2b78b3aff -r 827f19088303 msgfplus_search.xml --- a/msgfplus_search.xml Mon Jan 05 17:17:45 2015 -0500 +++ b/msgfplus_search.xml Tue Oct 20 20:01:22 2015 -0400 @@ -1,8 +1,8 @@ - + Run an MSGF+ Search - simonalpha/protk:1.4.0 - protk + iracooke/protk-1.4.3 + protk msgfplus proteowizard @@ -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 @@ - + @@ -85,7 +84,7 @@ - + @@ -155,7 +154,6 @@ - @@ -165,14 +163,23 @@ + + - - - + + + + + + + + + + **What it does** diff -r dfb2b78b3aff -r 827f19088303 repository_dependencies.xml --- a/repository_dependencies.xml Mon Jan 05 17:17:45 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - - - - diff -r dfb2b78b3aff -r 827f19088303 test-data/testdb.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testdb.fasta Tue Oct 20 20:01:22 2015 -0400 @@ -0,0 +1,38 @@ +>sp|ALBU_BOVIN| +MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIA +FSQYLQQCPFDEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCK +VASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEF +KADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGAC +LLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVARLSQKFPKAE +FVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKE +CCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFL +GSFLYEYSRRHPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKL +KHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVS +RSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCC +TESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQT +ALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVV +STQTALA 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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 dfb2b78b3aff -r 827f19088303 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 20:01:22 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 +# +# +#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 dfb2b78b3aff -r 827f19088303 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 20:01:22 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 +# +# +#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 dfb2b78b3aff -r 827f19088303 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 20 20:01:22 2015 -0400 @@ -0,0 +1,12 @@ + + + + + + + + + + + +