| Previous changeset 51:66690eb50a32 (2018-12-31) Next changeset 53:d67a3c1bfd09 (2019-05-08) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 9dc7c9c3ebd64f14c0ce95a0dc190361a90fa4fb |
|
modified:
macros.xml peptide_shaker.xml searchgui.xml |
|
added:
macros_modifications.xml |
|
removed:
searchgui_mods.loc.sample |
| b |
| diff -r 66690eb50a32 -r 864bd76db767 macros.xml --- a/macros.xml Mon Dec 31 02:20:36 2018 -0500 +++ b/macros.xml Wed Jan 16 08:18:39 2019 -0500 |
| b |
| @@ -1,4 +1,5 @@ <macros> + <import>macros_modifications.xml</import> <xml name="stdio"> <stdio> <exit_code range="1:" level="fatal" description="Job Failed" /> @@ -140,17 +141,11 @@ <section name="protein_modification_options" expanded="false" title="Protein Modification Options"> <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> - <options from_file="searchgui_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="0" /> - </options> + <expand macro="modifications"/> </param> <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" - help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> - <options from_file="searchgui_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="0" /> - </options> + help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> + <expand macro="modifications"/> </param> </section> |
| b |
| diff -r 66690eb50a32 -r 864bd76db767 macros_modifications.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_modifications.xml Wed Jan 16 08:18:39 2019 -0500 |
| b |
| b'@@ -0,0 +1,163 @@\n+<macros>\n+ <xml name="modifications">\n+ <option value="18O(1) of peptide C-term">18O(1) of peptide C-term</option>\n+ <option value="18O(2) of peptide C-term">18O(2) of peptide C-term</option>\n+ <option value="4-Hydroxyproline">4-Hydroxyproline</option>\n+ <option value="Acetaldehyde +26">Acetaldehyde +26</option>\n+ <option value="Acetylation of K">Acetylation of K</option>\n+ <option value="Acetylation of peptide N-term">Acetylation of peptide N-term</option>\n+ <option value="Acetylation of protein N-term">Acetylation of protein N-term</option>\n+ <option value="Amidation of the peptide C-term">Amidation of the peptide C-term</option>\n+ <option value="Amidation of the protein C-term">Amidation of the protein C-term</option>\n+ <option value="Arginine 13C(6)">Arginine 13C(6)</option>\n+ <option value="Arginine 13C(6) 15N(4)">Arginine 13C(6) 15N(4)</option>\n+ <option value="Carbamidomethylation of C">Carbamidomethylation of C</option>\n+ <option value="Carbamidomethylation of E">Carbamidomethylation of E</option>\n+ <option value="Carbamidomethylation of K">Carbamidomethylation of K</option>\n+ <option value="Carbamilation of K">Carbamilation of K</option>\n+ <option value="Carbamilation of protein N-term">Carbamilation of protein N-term</option>\n+ <option value="Carboxymethylation of C">Carboxymethylation of C</option>\n+ <option value="Citrullination of R">Citrullination of R</option>\n+ <option value="Deamidation of N">Deamidation of N</option>\n+ <option value="Deamidation of N 18O">Deamidation of N 18O</option>\n+ <option value="Deamidation of Q">Deamidation of Q</option>\n+ <option value="Dehydration of S">Dehydration of S</option>\n+ <option value="Dehydration of T">Dehydration of T</option>\n+ <option value="Didehydro of T">Didehydro of T</option>\n+ <option value="Diiodination of Y">Diiodination of Y</option>\n+ <option value="Dimethylation of K">Dimethylation of K</option>\n+ <option value="Dimethylation of K 2H(4)">Dimethylation of K 2H(4)</option>\n+ <option value="Dimethylation of K 2H(6)">Dimethylation of K 2H(6)</option>\n+ <option value="Dimethylation of K 2H(6) 13C(2)">Dimethylation of K 2H(6) 13C(2)</option>\n+ <option value="Dimethylation of R">Dimethylation of R</option>\n+ <option value="Dimethylation of peptide N-term">Dimethylation of peptide N-term</option>\n+ <option value="Dimethylation of peptide N-term 2H(4)">Dimethylation of peptide N-term 2H(4)</option>\n+ <option value="Dimethylation of peptide N-term 2H(6)">Dimethylation of peptide N-term 2H(6)</option>\n+ <option value="Dimethylation of peptide N-term 2H(6) 13C(2)">Dimethylation of peptide N-term 2H(6) 13C(2)</option>\n+ <option value="Dioxidation of M">Dioxidation of M</option>\n+ <option value="Dioxidation of W">Dioxidation of W</option>\n+ <option value="Farnesylation of C">Farnesylation of C</option>\n+ <option value="FormylMet of protein N-term">FormylMet of protein N-term</option>\n+ <option value="Formylation of K">Formylation of K</option>\n+ <option value="Formylation of S">Formylation of S</option>\n+ <option value="Formylation of T">Formylation of T</option>\n+ <option value="Formylation of peptide N-term">Formylation of peptide N-term</option>\n+ <option value="Formylation of protein N-term">Formylation of protein N-term</option>\n+ <option value="Geranyl-geranyl of C">Geranyl-geranyl of C</option>\n+ <option value="Glutathione of C">Glutathione of C</option>\n+ <option value="Guanidination of K">Guanidination of K</option>\n+ <option value="Guanidination of peptide N-term">Guanidination of peptide N-term</option>\n+ <option value="Heme B of C">Heme B of C</option>\n+ <option value="Heme B of H">Heme B of H</option>\n+ <option value="Hex(1)NAc(1) of S">Hex(1)NAc(1) of S</option>\n+ <option value="Hex(1)N'..b'="Pyridylethyl of C">Pyridylethyl of C</option>\n+ <option value="Pyrolidone from E">Pyrolidone from E</option>\n+ <option value="Pyrolidone from Q">Pyrolidone from Q</option>\n+ <option value="Pyrolidone from carbamidomethylated C">Pyrolidone from carbamidomethylated C</option>\n+ <option value="SUMO-2/3 Q87R">SUMO-2/3 Q87R</option>\n+ <option value="Sodium adduct to D">Sodium adduct to D</option>\n+ <option value="Sodium adduct to E">Sodium adduct to E</option>\n+ <option value="Sulfation of S">Sulfation of S</option>\n+ <option value="Sulfation of T">Sulfation of T</option>\n+ <option value="Sulfation of Y">Sulfation of Y</option>\n+ <option value="S-nitrosylation">S-nitrosylation</option>\n+ <option value="TMT 10-plex of K">TMT 10-plex of K</option>\n+ <option value="TMT 10-plex of peptide N-term">TMT 10-plex of peptide N-term</option>\n+ <option value="TMT 2-plex of K">TMT 2-plex of K</option>\n+ <option value="TMT 2-plex of peptide N-term">TMT 2-plex of peptide N-term</option>\n+ <option value="TMT 6-plex of K">TMT 6-plex of K</option>\n+ <option value="TMT 6-plex of K+4">TMT 6-plex of K+4</option>\n+ <option value="TMT 6-plex of K+6">TMT 6-plex of K+6</option>\n+ <option value="TMT 6-plex of K+8">TMT 6-plex of K+8</option>\n+ <option value="TMT 6-plex of peptide N-term">TMT 6-plex of peptide N-term</option>\n+ <option value="TMT 10-plex of K+4">TMT 10-plex of K+4</option>\n+ <option value="TMT 10-plex of K+6">TMT 10-plex of K+6</option>\n+ <option value="TMT 10-plex of K+8">TMT 10-plex of K+8</option>\n+ <option value="TMT 10-plex of peptide N-term">TMT 10-plex of peptide N-term</option>\n+ <option value="TMT 11-plex of K+4">TMT 11-plex of K+4</option>\n+ <option value="TMT 11-plex of K+6">TMT 11-plex of K+6</option>\n+ <option value="TMT 11-plex of K+8">TMT 11-plex of K+8</option>\n+ <option value="TMT 11-plex of peptide N-term">TMT 11-plex of peptide N-term</option>\n+ <option value="Thioacyl of peptide N-term">Thioacyl of peptide N-term</option>\n+ <option value="Trideuterated Methyl Ester of D">Trideuterated Methyl Ester of D</option>\n+ <option value="Trideuterated Methyl Ester of E">Trideuterated Methyl Ester of E</option>\n+ <option value="Trideuterated Methyl Ester of K">Trideuterated Methyl Ester of K</option>\n+ <option value="Trideuterated Methyl Ester of R">Trideuterated Methyl Ester of R</option>\n+ <option value="Trideuterated Methyl Ester of peptide C-term">Trideuterated Methyl Ester of peptide C-term</option>\n+ <option value="Trimethylation of K">Trimethylation of K</option>\n+ <option value="Trimethylation of R">Trimethylation of R</option>\n+ <option value="Trimethylation of protein N-term A">Trimethylation of protein N-term A</option>\n+ <option value="Trioxidation of C">Trioxidation of C</option>\n+ <option value="Ubiquitination of K">Ubiquitination of K</option>\n+ <option value="iTRAQ 4-plex of K">iTRAQ 4-plex of K</option>\n+ <option value="iTRAQ 4-plex of Y">iTRAQ 4-plex of Y</option>\n+ <option value="iTRAQ 4-plex of peptide N-term">iTRAQ 4-plex of peptide N-term</option>\n+ <option value="iTRAQ 8-plex of K">iTRAQ 8-plex of K</option>\n+ <option value="iTRAQ 8-plex of Y">iTRAQ 8-plex of Y</option>\n+ <option value="iTRAQ 8-plex of peptide N-term">iTRAQ 8-plex of peptide N-term</option>\n+ <option value="mTRAQ of 13C(6) 15N(2)">mTRAQ of 13C(6) 15N(2)</option>\n+ <option value="mTRAQ of K 13C(3) 15N">mTRAQ of K 13C(3) 15N</option>\n+ <option value="mTRAQ of K light">mTRAQ of K light</option>\n+ <option value="mTRAQ of peptide N-term 13C(3) 15N">mTRAQ of peptide N-term 13C(3) 15N</option>\n+ <option value="mTRAQ of peptide N-term 13C(6) 15N(2)">mTRAQ of peptide N-term 13C(6) 15N(2)</option>\n+ <option value="mTRAQ of peptide N-term light">mTRAQ of peptide N-term light</option>\n+ </xml>\n+</macros>\n' |
| b |
| diff -r 66690eb50a32 -r 864bd76db767 peptide_shaker.xml --- a/peptide_shaker.xml Mon Dec 31 02:20:36 2018 -0500 +++ b/peptide_shaker.xml Wed Jan 16 08:18:39 2019 -0500 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@"> +<tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@.2"> <description> Perform protein identification using various search engines based on results from SearchGUI </description> @@ -193,8 +193,8 @@ help="default 95%: '95.0'" /> <conditional name="ptm_score"> <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization"> - <option value="0" selected="True">A-score</option> - <option value="1">PhosphoRS</option> + <option value="0">A-score</option> + <option value="1" selected="True">PhosphoRS</option> <option value="2">None</option> </param> <when value="0" /> |
| b |
| diff -r 66690eb50a32 -r 864bd76db767 searchgui.xml --- a/searchgui.xml Mon Dec 31 02:20:36 2018 -0500 +++ b/searchgui.xml Wed Jan 16 08:18:39 2019 -0500 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@"> +<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1"> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> @@ -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 @@ <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> <param name="precursor_ion_tol" value="100"/> - <param name="fixed_modifications" value="carbamidomethyl c"/> - <param name="variable_modifications" value="oxidation of m"/> + <param name="fixed_modifications" value="Carbamidomethylation of C"/> + <param name="variable_modifications" value="Oxidation of M"/> <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> @@ -1142,8 +1142,8 @@ <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> <param name="precursor_ion_tol" value="100"/> - <param name="fixed_modifications" value="carbamidomethyl c"/> - <param name="variable_modifications" value="oxidation of m"/> + <param name="fixed_modifications" value="Carbamidomethylation of C"/> + <param name="variable_modifications" value="Oxidation of M"/> <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="engines" value="MS_Amanda"/> |
| b |
| diff -r 66690eb50a32 -r 864bd76db767 searchgui_mods.loc.sample --- a/searchgui_mods.loc.sample Mon Dec 31 02:20:36 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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 |