# HG changeset patch # User iracooke # Date 1445380474 14400 # Node ID 487533fa6990d08292a8c38095de20e37043737e # Parent 0ae7738e33e98b9d8f64fa970b210d2b844353bb planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302 diff -r 0ae7738e33e9 -r 487533fa6990 README --- a/README Mon Jan 05 17:01:18 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +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 uses protk which must be installed separately. - -For instructions please see: https://github.com/iracooke/protk/#galaxy-integration diff -r 0ae7738e33e9 -r 487533fa6990 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Oct 20 18:34:34 2015 -0400 @@ -0,0 +1,36 @@ +Mascot +====== + +Galaxy wrapper for the Mascot_ tandem ms search tool and a tool to convert results to `pepXML` + +.. _Mascot: http://www.matrixscience.com/ + +Requirements +------------ + +This package uses protk_, and the trans_proteomic_pipeline_ which need to be present in order for the tool to work. In addition, you will need a working installation of Mascot_ which is commercial software. + +.. _protk: https://github.com/iracooke/protk +.. _trans_proteomic_pipeline: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP + + +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_ diff -r 0ae7738e33e9 -r 487533fa6990 mascot.xml --- a/mascot.xml Mon Jan 05 17:01:18 2015 -0500 +++ b/mascot.xml Tue Oct 20 18:34:34 2015 -0400 @@ -1,249 +1,230 @@ - + + Mascot MS/MS Search + + iracooke/protk-1.4.1 + protk + + 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' + -p $precursor_ion_tol + --precursor-ion-tol-units=$precursor_tolu + + #if $email + --email=$email + #end if + + -v $missed_cleavages + + #if str ( $quant_method ) != 'No Quant' + --quantitation='$quant_method' + #end if + + #if $security.security_use + --use-security + --username $security.username + --password $security.password + #end if + + #if $proxy + --proxy $proxy + #end if + + --timeout=600 + + + + + + + + + + + + + Database + + + + + + + + + + - - simonalpha/protk:1.4.0 - protk - + + + + + + + + + + + + + + + + Missed Cleavages Allowed + + + + - Mascot MS/MS Search + + Enzyme + + + + + + + + + + + + + + + + + + + + + + + + + Peptide Charge + + + + + + + + + + + + + + + + + + + + + + + + + + + Instrument + + + + + + + + + + + + + + - 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' - - -p $precursor_ion_tol - - --precursor-ion-tol-units=$precursor_tolu - - #if $email - --email=$email - #end if - - -v $missed_cleavages - - --quantitation='$quant_method' - - #if $security.security_use - --use-security - --username $security.username - --password $security.password - #end if - - #if $proxy - --proxy $proxy - #end if - - --timeout=600 - - - - - - - - - - - - - - - Database - - - - - - - - - - - - - - - - - + + Quantitation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - Missed Cleavages Allowed - - - - - - - Enzyme - - - - - - - - - - - - - - - - - - - - - - - - - Peptide Charge - - - - - - - - - - - - - - - - - - - - - - - - - - - Instrument - - - - - - - - - - - - - - + + + Precursor Ion Tolerance Units + + + + + + - - - Quantitation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Precursor Ion Tolerance Units - - - - - - - - - - - - - - - - - - - - - - - - - - Run a Mascot MS/MS Ion Search - - + + + + + + + + + + + + + + + Run a Mascot MS/MS Ion Search + diff -r 0ae7738e33e9 -r 487533fa6990 mascot_to_pepxml.xml --- a/mascot_to_pepxml.xml Mon Jan 05 17:01:18 2015 -0500 +++ b/mascot_to_pepxml.xml Tue Oct 20 18:34:34 2015 -0400 @@ -1,83 +1,72 @@ - - - simonalpha/protk:1.4.0 - protk - trans_proteomic_pipeline - + + Converts a mascot results file to pepXML + + iracooke/protk-1.4.1 + protk + trans_proteomic_pipeline + + mascot_to_pepxml.rb + $input_file - Converts a mascot results file to pepXML - -mascot_to_pepxml.rb - $input_file - - -o $output + -o $output - #if $database.source_select=="built_in": - -d $database.dbkey - #else - -d $database.fasta_file - #end if + #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 + #if $explicit_enzyme.explicit_enzyme_use + --enzyme $explicit_enzyme.enzyme + #end if - - - - - + $shortid + + + - - - - - - - - Database - - - - - - - - - - + + + + + + + + Database + + + + + + + + + + - + - - - - - - - - - - - - - - + + + + + + + - - - - - - - - - - - - Convert mascot results from mascotdat to pepXML - - + + + + + + + + + + + + + + Convert mascot results from mascotdat to pepXML + diff -r 0ae7738e33e9 -r 487533fa6990 repository_dependencies.xml --- a/repository_dependencies.xml Mon Jan 05 17:01:18 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - - - - diff -r 0ae7738e33e9 -r 487533fa6990 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 20 18:34:34 2015 -0400 @@ -0,0 +1,6 @@ + + + + + +