Mercurial > repos > galaxyp > peptideshaker

changeset 45:a13e9d712194 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 9dc7c9c3ebd64f14c0ce95a0dc190361a90fa4fb
author galaxyp
date Wed, 16 Jan 2019 08:17:54 -0500
parents 053506071d70
children bfda5aacff85
files macros.xml macros_modifications.xml peptide_shaker.xml searchgui.xml searchgui_mods.loc.sample
diffstat 5 files changed, 180 insertions(+), 181 deletions(-) [+]
line wrap: on
line diff
--- 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>
+    <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>
 
--- /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 @@
+<macros>
+    <xml name="modifications">
+      <option value="18O(1) of peptide C-term">18O(1) of peptide C-term</option>
+      <option value="18O(2) of peptide C-term">18O(2) of peptide C-term</option>
+      <option value="4-Hydroxyproline">4-Hydroxyproline</option>
+      <option value="Acetaldehyde +26">Acetaldehyde +26</option>
+      <option value="Acetylation of K">Acetylation of K</option>
+      <option value="Acetylation of peptide N-term">Acetylation of peptide N-term</option>
+      <option value="Acetylation of protein N-term">Acetylation of protein N-term</option>
+      <option value="Amidation of the peptide C-term">Amidation of the peptide C-term</option>
+      <option value="Amidation of the protein C-term">Amidation of the protein C-term</option>
+      <option value="Arginine 13C(6)">Arginine 13C(6)</option>
+      <option value="Arginine 13C(6) 15N(4)">Arginine 13C(6) 15N(4)</option>
+      <option value="Carbamidomethylation of C">Carbamidomethylation of C</option>
+      <option value="Carbamidomethylation of E">Carbamidomethylation of E</option>
+      <option value="Carbamidomethylation of K">Carbamidomethylation of K</option>
+      <option value="Carbamilation of K">Carbamilation of K</option>
+      <option value="Carbamilation of protein N-term">Carbamilation of protein N-term</option>
+      <option value="Carboxymethylation of C">Carboxymethylation of C</option>
+      <option value="Citrullination of R">Citrullination of R</option>
+      <option value="Deamidation of N">Deamidation of N</option>
+      <option value="Deamidation of N 18O">Deamidation of N 18O</option>
+      <option value="Deamidation of Q">Deamidation of Q</option>
+      <option value="Dehydration of S">Dehydration of S</option>
+      <option value="Dehydration of T">Dehydration of T</option>
+      <option value="Didehydro of T">Didehydro of T</option>
+      <option value="Diiodination of Y">Diiodination of Y</option>
+      <option value="Dimethylation of K">Dimethylation of K</option>
+      <option value="Dimethylation of K 2H(4)">Dimethylation of K 2H(4)</option>
+      <option value="Dimethylation of K 2H(6)">Dimethylation of K 2H(6)</option>
+      <option value="Dimethylation of K 2H(6) 13C(2)">Dimethylation of K 2H(6) 13C(2)</option>
+      <option value="Dimethylation of R">Dimethylation of R</option>
+      <option value="Dimethylation of peptide N-term">Dimethylation of peptide N-term</option>
+      <option value="Dimethylation of peptide N-term 2H(4)">Dimethylation of peptide N-term 2H(4)</option>
+      <option value="Dimethylation of peptide N-term 2H(6)">Dimethylation of peptide N-term 2H(6)</option>
+      <option value="Dimethylation of peptide N-term 2H(6) 13C(2)">Dimethylation of peptide N-term 2H(6) 13C(2)</option>
+      <option value="Dioxidation of M">Dioxidation of M</option>
+      <option value="Dioxidation of W">Dioxidation of W</option>
+      <option value="Farnesylation of C">Farnesylation of C</option>
+      <option value="FormylMet of protein N-term">FormylMet of protein N-term</option>
+      <option value="Formylation of K">Formylation of K</option>
+      <option value="Formylation of S">Formylation of S</option>
+      <option value="Formylation of T">Formylation of T</option>
+      <option value="Formylation of peptide N-term">Formylation of peptide N-term</option>
+      <option value="Formylation of protein N-term">Formylation of protein N-term</option>
+      <option value="Geranyl-geranyl of C">Geranyl-geranyl of C</option>
+      <option value="Glutathione of C">Glutathione of C</option>
+      <option value="Guanidination of K">Guanidination of K</option>
+      <option value="Guanidination of peptide N-term">Guanidination of peptide N-term</option>
+      <option value="Heme B of C">Heme B of C</option>
+      <option value="Heme B of H">Heme B of H</option>
+      <option value="Hex(1)NAc(1) of S">Hex(1)NAc(1) of S</option>
+      <option value="Hex(1)NAc(1) of T">Hex(1)NAc(1) of T</option>
+      <option value="Hex(5) HexNAc(4) NeuAc(2) Na of N">Hex(5) HexNAc(4) NeuAc(2) Na of N</option>
+      <option value="Hex(5) HexNAc(4) NeuAc(2) of N">Hex(5) HexNAc(4) NeuAc(2) of N</option>
+      <option value="HexNAc of S">HexNAc of S</option>
+      <option value="HexNAc of T">HexNAc of T</option>
+      <option value="Hexose of K">Hexose of K</option>
+      <option value="Homoserine lactone of peptide C-term M">Homoserine lactone of peptide C-term M</option>
+      <option value="Homoserine of peptide C-term M">Homoserine of peptide C-term M</option>
+      <option value="ICAT-9">ICAT-9</option>
+      <option value="ICAT-O">ICAT-O</option>
+      <option value="ICPL0 of K">ICPL0 of K</option>
+      <option value="ICPL0 of peptide N-term">ICPL0 of peptide N-term</option>
+      <option value="ICPL10 of K">ICPL10 of K</option>
+      <option value="ICPL10 of peptide N-term">ICPL10 of peptide N-term</option>
+      <option value="ICPL4 of K">ICPL4 of K</option>
+      <option value="ICPL4 of peptide N-term">ICPL4 of peptide N-term</option>
+      <option value="ICPL6 of K">ICPL6 of K</option>
+      <option value="ICPL6 of peptide N-term">ICPL6 of peptide N-term</option>
+      <option value="Isoleucine 13C(6) 15N(1)">Isoleucine 13C(6) 15N(1)</option>
+      <option value="iodoTMT zero of C">iodoTMT zero of C</option>
+      <option value="iodoTMT 6-plex of C">iodoTMT 6-plex of C</option>
+      <option value="Label of K 2H(4)">Label of K 2H(4)</option>
+      <option value="Leucine 13C(6) 15N(1)">Leucine 13C(6) 15N(1)</option>
+      <option value="Lipoyl of K">Lipoyl of K</option>
+      <option value="Lysine 13C(6)">Lysine 13C(6)</option>
+      <option value="Lysine 13C(6) 15N(2)">Lysine 13C(6) 15N(2)</option>
+      <option value="Lysine 2H(4)">Lysine 2H(4)</option>
+      <option value="Methylation of C">Methylation of C</option>
+      <option value="Methylation of D">Methylation of D</option>
+      <option value="Methylation of E">Methylation of E</option>
+      <option value="Methylation of K">Methylation of K</option>
+      <option value="Methylation of R">Methylation of R</option>
+      <option value="Methylation of S">Methylation of S</option>
+      <option value="Methylthio of C">Methylthio of C</option>
+      <option value="Methylthio of D">Methylthio of D</option>
+      <option value="Methylthio of N">Methylthio of N</option>
+      <option value="NIPCAM of C">NIPCAM of C</option>
+      <option value="Nethylmaleimide of C">Nethylmaleimide of C</option>
+      <option value="Oxidation of C">Oxidation of C</option>
+      <option value="Oxidation of K">Oxidation of K</option>
+      <option value="Oxidation of M">Oxidation of M</option>
+      <option value="Oxidation of P">Oxidation of P</option>
+      <option value="Palmitoylation of C">Palmitoylation of C</option>
+      <option value="Palmitoylation of K">Palmitoylation of K</option>
+      <option value="Palmitoylation of S">Palmitoylation of S</option>
+      <option value="Palmitoylation of T">Palmitoylation of T</option>
+      <option value="Palmitoylation of protein N-term">Palmitoylation of protein N-term</option>
+      <option value="Phosphorylation of S">Phosphorylation of S</option>
+      <option value="Phosphorylation of T">Phosphorylation of T</option>
+      <option value="Phosphorylation of Y">Phosphorylation of Y</option>
+      <option value="Proline 13C(5)">Proline 13C(5)</option>
+      <option value="Propionamide of C">Propionamide of C</option>
+      <option value="Propionamide of K">Propionamide of K</option>
+      <option value="Propionamide of peptide N-term">Propionamide of peptide N-term</option>
+      <option value="Propionyl of K heavy">Propionyl of K heavy</option>
+      <option value="Propionyl of K light">Propionyl of K light</option>
+      <option value="Propionyl of peptide N-term heavy">Propionyl of peptide N-term heavy</option>
+      <option value="Propionyl of peptide N-term light">Propionyl of peptide N-term light</option>
+      <option value="Pyridylethyl of C">Pyridylethyl of C</option>
+      <option value="Pyrolidone from E">Pyrolidone from E</option>
+      <option value="Pyrolidone from Q">Pyrolidone from Q</option>
+      <option value="Pyrolidone from carbamidomethylated C">Pyrolidone from carbamidomethylated C</option>
+      <option value="SUMO-2/3 Q87R">SUMO-2/3 Q87R</option>
+      <option value="Sodium adduct to D">Sodium adduct to D</option>
+      <option value="Sodium adduct to E">Sodium adduct to E</option>
+      <option value="Sulfation of S">Sulfation of S</option>
+      <option value="Sulfation of T">Sulfation of T</option>
+      <option value="Sulfation of Y">Sulfation of Y</option>
+      <option value="S-nitrosylation">S-nitrosylation</option>
+      <option value="TMT 10-plex of K">TMT 10-plex of K</option>
+      <option value="TMT 10-plex of peptide N-term">TMT 10-plex of peptide N-term</option>
+      <option value="TMT 2-plex of K">TMT 2-plex of K</option>
+      <option value="TMT 2-plex of peptide N-term">TMT 2-plex of peptide N-term</option>
+      <option value="TMT 6-plex of K">TMT 6-plex of K</option>
+      <option value="TMT 6-plex of K+4">TMT 6-plex of K+4</option>
+      <option value="TMT 6-plex of K+6">TMT 6-plex of K+6</option>
+      <option value="TMT 6-plex of K+8">TMT 6-plex of K+8</option>
+      <option value="TMT 6-plex of peptide N-term">TMT 6-plex of peptide N-term</option>
+      <option value="TMT 10-plex of K+4">TMT 10-plex of K+4</option>
+      <option value="TMT 10-plex of K+6">TMT 10-plex of K+6</option>
+      <option value="TMT 10-plex of K+8">TMT 10-plex of K+8</option>
+      <option value="TMT 10-plex of peptide N-term">TMT 10-plex of peptide N-term</option>
+      <option value="TMT 11-plex of K+4">TMT 11-plex of K+4</option>
+      <option value="TMT 11-plex of K+6">TMT 11-plex of K+6</option>
+      <option value="TMT 11-plex of K+8">TMT 11-plex of K+8</option>
+      <option value="TMT 11-plex of peptide N-term">TMT 11-plex of peptide N-term</option>
+      <option value="Thioacyl of peptide N-term">Thioacyl of peptide N-term</option>
+      <option value="Trideuterated Methyl Ester of D">Trideuterated Methyl Ester of D</option>
+      <option value="Trideuterated Methyl Ester of E">Trideuterated Methyl Ester of E</option>
+      <option value="Trideuterated Methyl Ester of K">Trideuterated Methyl Ester of K</option>
+      <option value="Trideuterated Methyl Ester of R">Trideuterated Methyl Ester of R</option>
+      <option value="Trideuterated Methyl Ester of peptide C-term">Trideuterated Methyl Ester of peptide C-term</option>
+      <option value="Trimethylation of K">Trimethylation of K</option>
+      <option value="Trimethylation of R">Trimethylation of R</option>
+      <option value="Trimethylation of protein N-term A">Trimethylation of protein N-term A</option>
+      <option value="Trioxidation of C">Trioxidation of C</option>
+      <option value="Ubiquitination of K">Ubiquitination of K</option>
+      <option value="iTRAQ 4-plex of K">iTRAQ 4-plex of K</option>
+      <option value="iTRAQ 4-plex of Y">iTRAQ 4-plex of Y</option>
+      <option value="iTRAQ 4-plex of peptide N-term">iTRAQ 4-plex of peptide N-term</option>
+      <option value="iTRAQ 8-plex of K">iTRAQ 8-plex of K</option>
+      <option value="iTRAQ 8-plex of Y">iTRAQ 8-plex of Y</option>
+      <option value="iTRAQ 8-plex of peptide N-term">iTRAQ 8-plex of peptide N-term</option>
+      <option value="mTRAQ of 13C(6) 15N(2)">mTRAQ of 13C(6) 15N(2)</option>
+      <option value="mTRAQ of K 13C(3) 15N">mTRAQ of K 13C(3) 15N</option>
+      <option value="mTRAQ of K light">mTRAQ of K light</option>
+      <option value="mTRAQ of peptide N-term 13C(3) 15N">mTRAQ of peptide N-term 13C(3) 15N</option>
+      <option value="mTRAQ of peptide N-term 13C(6) 15N(2)">mTRAQ of peptide N-term 13C(6) 15N(2)</option>
+      <option value="mTRAQ of peptide N-term light">mTRAQ of peptide N-term light</option>
+    </xml>
+</macros>
--- 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 @@
-<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" />
--- 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 @@
-<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"/>
--- 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