# HG changeset patch # User iracooke # Date 1445385046 14400 # Node ID b3427b77073ef27f53f98eb2b8476a7ebbcbd9c6 # Parent 54c7e3593aac1347ffc5f19d6971f61bf4ca0d75 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty diff -r 54c7e3593aac -r b3427b77073e mascot.xml --- a/mascot.xml Sun Mar 29 18:17:54 2015 -0400 +++ b/mascot.xml Tue Oct 20 19:50:46 2015 -0400 @@ -1,249 +1,230 @@ - + + Mascot MS/MS Search + + iracooke/protk-1.4.3 + 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 + + + + + + + + + + - - iracooke/protk-1.4.1 - 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 54c7e3593aac -r b3427b77073e mascot_to_pepxml.xml --- a/mascot_to_pepxml.xml Sun Mar 29 18:17:54 2015 -0400 +++ b/mascot_to_pepxml.xml Tue Oct 20 19:50:46 2015 -0400 @@ -1,83 +1,72 @@ - - - iracooke/protk-1.4.1 - protk - trans_proteomic_pipeline - + + Converts a mascot results file to pepXML + + iracooke/protk-1.4.3 + 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 54c7e3593aac -r b3427b77073e repository_dependencies.xml --- a/repository_dependencies.xml Sun Mar 29 18:17:54 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - - - - diff -r 54c7e3593aac -r b3427b77073e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 20 19:50:46 2015 -0400 @@ -0,0 +1,9 @@ + + + + + + + + +