# HG changeset patch # User galaxyp # Date 1547644674 18000 # Node ID a13e9d71219470665e8c5a2f45e76d54624b804c # Parent 053506071d70242baa1adaa782c059188ba3ddd5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 9dc7c9c3ebd64f14c0ce95a0dc190361a90fa4fb diff -r 053506071d70 -r a13e9d712194 macros.xml --- a/macros.xml Mon Dec 31 02:20:00 2018 -0500 +++ b/macros.xml Wed Jan 16 08:17:54 2019 -0500 @@ -1,4 +1,5 @@ + macros_modifications.xml @@ -140,17 +141,11 @@

- - - - + - - - - + help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> +

diff -r 053506071d70 -r a13e9d712194 macros_modifications.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_modifications.xml Wed Jan 16 08:17:54 2019 -0500 @@ -0,0 +1,163 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 053506071d70 -r a13e9d712194 peptide_shaker.xml --- a/peptide_shaker.xml Mon Dec 31 02:20:00 2018 -0500 +++ b/peptide_shaker.xml Wed Jan 16 08:17:54 2019 -0500 @@ -1,4 +1,4 @@ - + Perform protein identification using various search engines based on results from SearchGUI @@ -193,8 +193,8 @@ help="default 95%: '95.0'" /> - - + + diff -r 053506071d70 -r a13e9d712194 searchgui.xml --- a/searchgui.xml Mon Dec 31 02:20:00 2018 -0500 +++ b/searchgui.xml Wed Jan 16 08:17:54 2019 -0500 @@ -1,4 +1,4 @@ - + Perform protein identification using various search engines and prepare results for input to Peptide Shaker @@ -23,7 +23,7 @@ cwd=`pwd`; export HOME=\$cwd; - echo "" > $temp_stderr && + echo "" > $temp_stderr && ## echo the search engines to run (single quotes important because X!Tandem) echo '$search_engines_options.engines'; @@ -46,8 +46,8 @@ ########################################### echo 'Setting paths' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI - --exec_dir="\$cwd/${bin_dir}" - -temp_folder \$cwd + --exec_dir="\$cwd/${bin_dir}" + -temp_folder \$cwd -log \$cwd/searchgui.log 2>> $temp_stderr && ########################################### @@ -55,8 +55,8 @@ ########################################### #if $protein_database_options.create_decoy: echo 'Creating decoy database.' && - searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI - --exec_dir="\$cwd/${bin_dir}" + searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI + --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy 2>> $temp_stderr && rm input_database.fasta && @@ -1128,8 +1128,8 @@ - - + + @@ -1142,8 +1142,8 @@ - - + + diff -r 053506071d70 -r a13e9d712194 searchgui_mods.loc.sample --- a/searchgui_mods.loc.sample Mon Dec 31 02:20:00 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,159 +0,0 @@ -18O(1) of peptide C-term -18O(2) of peptide C-term -4-Hydroxyproline -Acetaldehyde +26 -Acetylation of K -Acetylation of peptide N-term -Acetylation of protein N-term -Amidation of the peptide C-term -Amidation of the protein C-term -Arginine 13C(6) -Arginine 13C(6) 15N(4) -Carbamidomethylation of C -Carbamidomethylation of E -Carbamidomethylation of K -Carbamilation of K -Carbamilation of protein N-term -Carboxymethylation of C -Citrullination of R -Deamidation of N -Deamidation of N 18O -Deamidation of Q -Dehydration of S -Dehydration of T -Didehydro of T -Diiodination of Y -Dimethylation of K -Dimethylation of K 2H(4) -Dimethylation of K 2H(6) -Dimethylation of K 2H(6) 13C(2) -Dimethylation of R -Dimethylation of peptide N-term -Dimethylation of peptide N-term 2H(4) -Dimethylation of peptide N-term 2H(6) -Dimethylation of peptide N-term 2H(6) 13C(2) -Dioxidation of M -Dioxidation of W -Farnesylation of C -FormylMet of protein N-term -Formylation of K -Formylation of S -Formylation of T -Formylation of peptide N-term -Formylation of protein N-term -Geranyl-geranyl of C -Glutathione of C -Guanidination of K -Guanidination of peptide N-term -Heme B of C -Heme B of H -Hex(1)NAc(1) of S -Hex(1)NAc(1) of T -Hex(5) HexNAc(4) NeuAc(2) Na of N -Hex(5) HexNAc(4) NeuAc(2) of N -HexNAc of S -HexNAc of T -Hexose of K -Homoserine lactone of peptide C-term M -Homoserine of peptide C-term M -ICAT-9 -ICAT-O -ICPL0 of K -ICPL0 of peptide N-term -ICPL10 of K -ICPL10 of peptide N-term -ICPL4 of K -ICPL4 of peptide N-term -ICPL6 of K -ICPL6 of peptide N-term -Isoleucine 13C(6) 15N(1) -iodoTMT zero of C -iodoTMT 6-plex of C -Label of K 2H(4) -Leucine 13C(6) 15N(1) -Lipoyl of K -Lysine 13C(6) -Lysine 13C(6) 15N(2) -Lysine 2H(4) -Methylation of C -Methylation of D -Methylation of E -Methylation of K -Methylation of R -Methylation of S -Methylthio of C -Methylthio of D -Methylthio of N -NIPCAM of C -Nethylmaleimide of C -Oxidation of C -Oxidation of K -Oxidation of M -Oxidation of P -Palmitoylation of C -Palmitoylation of K -Palmitoylation of S -Palmitoylation of T -Palmitoylation of protein N-term -Phosphorylation of S -Phosphorylation of T -Phosphorylation of Y -Proline 13C(5) -Propionamide of C -Propionamide of K -Propionamide of peptide N-term -Propionyl of K heavy -Propionyl of K light -Propionyl of peptide N-term heavy -Propionyl of peptide N-term light -Pyridylethyl of C -Pyrolidone from E -Pyrolidone from Q -Pyrolidone from carbamidomethylated C -SUMO-2/3 Q87R -Sodium adduct to D -Sodium adduct to E -Sulfation of S -Sulfation of T -Sulfation of Y -S-nitrosylation -TMT 10-plex of K -TMT 10-plex of peptide N-term -TMT 2-plex of K -TMT 2-plex of peptide N-term -TMT 6-plex of K -TMT 6-plex of K+4 -TMT 6-plex of K+6 -TMT 6-plex of K+8 -TMT 6-plex of peptide N-term -TMT 10-plex of K+4 -TMT 10-plex of K+6 -TMT 10-plex of K+8 -TMT 10-plex of peptide N-term -TMT 11-plex of K+4 -TMT 11-plex of K+6 -TMT 11-plex of K+8 -TMT 11-plex of peptide N-term -Thioacyl of peptide N-term -Trideuterated Methyl Ester of D -Trideuterated Methyl Ester of E -Trideuterated Methyl Ester of K -Trideuterated Methyl Ester of R -Trideuterated Methyl Ester of peptide C-term -Trimethylation of K -Trimethylation of R -Trimethylation of protein N-term A -Trioxidation of C -Ubiquitination of K -iTRAQ 4-plex of K -iTRAQ 4-plex of Y -iTRAQ 4-plex of peptide N-term -iTRAQ 8-plex of K -iTRAQ 8-plex of Y -iTRAQ 8-plex of peptide N-term -mTRAQ of 13C(6) 15N(2) -mTRAQ of K 13C(3) 15N -mTRAQ of K light -mTRAQ of peptide N-term 13C(3) 15N -mTRAQ of peptide N-term 13C(6) 15N(2) -mTRAQ of peptide N-term light