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Changeset 24:815f93bb3e1b (2015-11-06)

Previous changeset 23:913dbf2b83e0 (2015-08-10) Next changeset 25:0986f68fb410 (2016-02-21)

Commit message:
Uploaded

modified:
README.rst
macros.xml
peptide_shaker.xml
searchgui.xml
searchgui_mods.loc.sample
tool_dependencies.xml

removed:
repository_dependencies.xml

diff -r 913dbf2b83e0 -r 815f93bb3e1b README.rst
--- a/README.rst Mon Aug 10 18:25:37 2015 -0400
+++ b/README.rst Fri Nov 06 15:33:34 2015 -0500

@@ -42,6 +42,8 @@
Note
----

+- Requires Galaxy release v15.10 or later, which fixes the installation of package_peptideshaker_1_1 and provides a searchgui_archive datatype that includes a version
+
- PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server.

See:
@@ -50,6 +52,14 @@
* <https://code.google.com/p/searchgui/>

+Search GUI - Fixed and Variable Modifications
+-------------------------------------------
+
+ - Options for modifications are read from local data file: searchgui_mods.loc
+ This is copied from searchgui_mods.loc.sample on the first installation.
+
+The modifications are from: https://github.com/compomics/compomics-utilities/blob/master/src/main/java/com/compomics/util/experiment/identification/search_parameters_cli/IdentificationParametersInputBean.java
+
GalaxyP Community
-----------------

diff -r 913dbf2b83e0 -r 815f93bb3e1b macros.xml
--- a/macros.xml Mon Aug 10 18:25:37 2015 -0400
+++ b/macros.xml Fri Nov 06 15:33:34 2015 -0500

@@ -25,7 +25,8 @@
             -fi $forward_ion
             -ri $reverse_ion
     </token>
-
+    <token name="@SEARCHGUI_MAJOR_VERSION@">2</token>
+    <token name="@SEARCHGUI_VERSION@">2.1</token>
     <xml name="general_options">
         <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
             help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">

diff -r 913dbf2b83e0 -r 815f93bb3e1b peptide_shaker.xml
--- a/peptide_shaker.xml Mon Aug 10 18:25:37 2015 -0400
+++ b/peptide_shaker.xml Fri Nov 06 15:33:34 2015 -0500

@@ -1,4 +1,4 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="0.40.0">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.1.1">
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.40">peptide_shaker</requirement>
+        <requirement type="package" version="1.1">peptide_shaker</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -33,7 +33,7 @@
             -sample '$samp_str'
             -replicate 1
             -identification_files \$cwd/searchgui_input.zip
-            -out \$cwd/peptideshaker_output.cps
+            -out \$cwd/peptideshaker_output.cpsx
             -zip \$cwd/peptideshaker_output.zip

             -threads "\${GALAXY_SLOTS:-12}"
@@ -166,7 +166,12 @@
     </command>
     <inputs>
         <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
-            help="SearchGUI Results from History"/>
+            help="SearchGUI Results from History">
+            <options options_filter_attribute="metadata.searchgui_major_version" >
+                <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
+            </options>
+            <validator type="expression" message="This version of PeptideShaker will only work with SearchGUI version: @SEARCHGUI_MAJOR_VERSION@ .">value is not None and value.metadata.searchgui_major_version == "@SEARCHGUI_MAJOR_VERSION@"</validator>
+        </param>

         <conditional name="species_type">
             <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
@@ -178,6 +183,7 @@
                 <option value="Protists">Protists</option>
                 <option value="no_species_type" selected="true">No species restriction</option>
             </param>
+            <when value="no_species_type"/>
             <when value="Protists">
                 <param name="species" type="select" label="The species to use for the gene annotation"
                     help="">

diff -r 913dbf2b83e0 -r 815f93bb3e1b repository_dependencies.xml
--- a/repository_dependencies.xml Mon Aug 10 18:25:37 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Required proteomics dependencies.">
- <repository changeset_revision="300fc3aa6954" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
-</repositories>

diff -r 913dbf2b83e0 -r 815f93bb3e1b searchgui.xml
--- a/searchgui.xml Mon Aug 10 18:25:37 2015 -0400
+++ b/searchgui.xml Fri Nov 06 15:33:34 2015 -0500

@@ -1,4 +1,4 @@
-<tool id="search_gui" name="Search GUI" version="1.28.0">
+<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>
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="1.28">searchgui</requirement>
+        <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
         <environment_variable name="LC_ALL" action="set_to">C</environment_variable>
     </requirements>
     <expand macro="stdio" />
@@ -22,6 +22,9 @@
         cwd=`pwd`;
         export HOME=\$cwd;

+        ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
+        echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;
+
         cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin;
         tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`;

@@ -48,7 +51,7 @@
         #####################################################

         (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI
-            -out SEARCHGUI_IdentificationParameters.parameters
+            -out SEARCHGUI_IdentificationParameters.par

             @GENERAL_PARAMETERS@

@@ -168,6 +171,27 @@
                 -myrimatch_max_peak ${myrimatch.myrimatch_max_peak}
             #end if

+            #*
+            #if $andromeda.andromeda_advanced == "yes"
+                -andromeda_max_pep_mass ${andromeda.andromeda_max_pep_mass}
+                -andromeda_max_comb ${andromeda.andromeda_max_comb}
+                -andromeda_top_peaks ${andromeda.andromeda_top_peaks}
+                -andromeda_top_peaks_window ${andromeda.andromeda_top_peaks_window}
+                -andromeda_incl_water ${andromeda.andromeda_incl_water}
+                -andromeda_incl_ammonia ${andromeda.andromeda_incl_ammonia}
+                -andromeda_neutral_losses ${andromeda.andromeda_neutral_losses}
+                -andromeda_fragment_all ${andromeda.andromeda_fragment_all}
+                -andromeda_emp_correction ${andromeda.andromeda_emp_correction}
+                -andromeda_higher_charge ${andromeda.andromeda_higher_charge}
+                -andromeda_equal_il ${andromeda.andromeda_equal_il}
+                -andromeda_frag_method ${andromeda.andromeda_frag_method}
+                -andromeda_max_mods ${andromeda.andromeda_max_mods}
+                -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length}
+                -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length}
+                -andromeda_max_psms ${andromeda.andromeda_max_psms}
+            #end if
+            *#
+
             #if $tide.tide_advanced == "yes"
                 -tide_num_ptms ${tide.tide_num_ptms}
                 -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type}
@@ -256,7 +280,7 @@
             -temp_folder `pwd`
             -spectrum_files \$cwd
             -output_folder \$cwd/output
-            -id_params SEARCHGUI_IdentificationParameters.parameters
+            -id_params SEARCHGUI_IdentificationParameters.par

             -threads "\${GALAXY_SLOTS:-12}"

@@ -316,6 +340,12 @@
                 -ms_amanda 0
             #end if

+            #if 'Andromeda' in $engines_list:
+                -andromeda 1
+            #else
+                -andromeda 0
+            #end if
+
             ## single zip file
             -output_option 0

@@ -330,6 +360,10 @@

         &&

+        (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr)
+
+        &&
+
         exit_code_for_galaxy=\$?;
         cat $temp_stderr 2>&1;
         (exit \$exit_code_for_galaxy)
@@ -357,6 +391,9 @@
             <option value="OMSSA" selected="True">OMSSA</option>
             <option value="Comet">Comet</option>
             <option value="Tide">Tide</option>
+            
             <validator type="no_options" message="Please select at least one output file" />
         </param>

@@ -780,6 +817,39 @@
             </when>
         </conditional>

+        
+        
+
         
         <conditional name="comet">
             <param name="comet_advanced" type="select" label="Comet Options">

diff -r 913dbf2b83e0 -r 815f93bb3e1b searchgui_mods.loc.sample
--- a/searchgui_mods.loc.sample Mon Aug 10 18:25:37 2015 -0400
+++ b/searchgui_mods.loc.sample Fri Nov 06 15:33:34 2015 -0500

b'@@ -1,210 +1,140 @@\n-methylation of k\n-oxidation of m\n-carboxymethyl c\n-carbamidomethyl c\n-deamidation of n and q\n-propionamide c\n-phosphorylation of s\n-phosphorylation of t\n-phosphorylation of y\n-m cleavage from protein n-term\n-acetylation of protein n-term\n-methylation of protein n-term\n-tri-methylation of protein n-term\n-beta methythiolation of d\n-methylation of q\n-tri-methylation of k\n-methylation of d\n-methylation of e\n-methylation of peptide c-term\n-tri-deuteromethylation of d\n-tri-deuteromethylation of e\n-tri-deuteromethylation of peptide c-term\n-n-formyl met addition\n-2-amino-3-oxo-butanoic acid t\n-acetylation of k\n-amidation of peptide c-term\n-beta-methylthiolation of d (duplicate of 13)\n-carboxyamidomethylation of k\n-carboxyamidomethylation of h\n-carboxyamidomethylation of d\n-carboxyamidomethylation of e\n-carbamylation of k\n-carbamylation of n-term peptide\n-citrullination of r\n-oxidation of c to cysteic acid\n-di-iodination of y\n-di-methylation of k\n-di-methylation of r\n-di-methylation of peptide n-term\n-oxidation of f to dihydroxyphenylalanine\n-gammathiopropionylation of k\n-gammathiopropionylation of peptide n-term\n-farnesylation of c\n-formylation of k\n-formylation of peptide n-term\n-oxidation of w to formylkynurenin\n-fluorophenylalanine\n-beta-carboxylation of d\n-gamma-carboxylation of e\n-geranyl-geranyl\n-glucuronylation of protein n-term\n-glutathione disulfide\n-ubiquitinylation residue\n-guanidination of k\n-oxidation of h to n\n-oxidation of h to d\n-homoserine\n-homoserine lactone\n-oxidation of w to hydroxykynurenin\n-hydroxylation of d\n-hydroxylation of k\n-hydroxylation of n\n-hydroxylation of p\n-hydroxylation of f\n-hydroxylation of y\n-iodination of y\n-oxidation of w to kynurenin\n-lipoyl k\n-methyl ester of peptide c-term (duplicate of 18)\n-methyl ester of d\n-methyl ester of e (duplicate of 17)\n-methyl ester of s\n-methyl ester of y\n-methyl c\n-methyl h\n-methyl n\n-methylation of peptide n-term\n-methyl r\n-myristoleylation of g\n-myristoyl-4h of g\n-myristoylation of peptide n-term g\n-myristoylation of k\n-formylation of protein n-term\n-nem c\n-nipcam\n-oxidation of w to nitro\n-oxidation of y to nitro\n-o18 on peptide n-term\n-di-o18 on peptide n-term\n-oxidation of h\n-oxidation of w\n-phosphopantetheine s\n-palmitoylation of c\n-palmitoylation of k\n-palmitoylation of s\n-palmitoylation of t\n-phosphorylation of s with prompt loss\n-phosphorylation of t with prompt loss\n-phosphorylation with prompt loss on y\n-phosphorylation with neutral loss on c\n-phosphorylation with neutral loss on d\n-phosphorylation with neutral loss on h\n-propionyl light k\n-propionyl light on peptide n-term\n-propionyl heavy k\n-propionyl heavy peptide n-term\n-pyridyl k\n-pyridyl peptide n-term\n-pyro-cmc\n-pyro-glu from n-term e\n-pyro-glu from n-term q\n-oxidation of p to pyroglutamic acid\n-s-pyridylethylation of c\n-semet\n-sulfation of y\n-sulphone of m\n-tri-iodination of y\n-tri-methylation of r\n-n-acyl diglyceride cysteine\n-icat light\n-icat heavy\n-camthiopropanoyl k\n-phosphorylation with neutral loss on s\n-phosphorylation with neutral loss on t\n-phosphorylation of s with etd loss\n-phosphorylation of t with etd loss\n-heavy arginine-13c6\n-heavy arginine-13c6-15n4\n-heavy lysine-13c6\n-pngasf in o18 water\n-beta elimination of s\n-beta elimination of t\n-oxidation of c to sulfinic acid\n-arginine to ornithine\n-dehydro of s and t\n-carboxykynurenin of w\n-sumoylation of k\n-itraq114 on nterm\n-itraq114 on k\n-itraq114 on y\n-itraq115 on nterm\n-itraq115 on k\n-itraq115 on y\n-itraq116 on nterm\n-itraq116 on k\n-itraq116 on y\n-itraq117 on nterm\n-itraq117 on k\n-itraq117 on y\n-mmts on c\n-heavy lysine - 2h4\n-heavy lysine - 13c6 15n2\n-asparagine hexnac\n-asparagine dhexhexnac\n-serine hexnac\n-threonine hexnac\n-palmitoleyl of s\n-palmitoleyl of c\n-palmitoleyl of t\n-chd2-di-methylation of k\n-chd2-di-methylation of peptide n-term\n-maleimide-peo2-biotin of c\n-phosphorylation of h\n-oxidation of c\n-oxidation of y (duplicate of 64)\n-uniblue a on k\n-deamidation of n\n-trideuteration of l (silac)\n-tmt duplex '..b'on nterm\n-itraq8plex:13c(6)15n(2) on k\n-itraq8plex:13c(6)15n(2) on y\n-selenocysteine\n-carboxymethylated selenocysteine\n-dimethyl 2d n-terminus\n-dimethyl 2d k\n-gtp desthiobiotinc12\n-gtp desthiobiotinc13\n-user modification 5\n-user modification 6\n-user modification 7\n-user modification 8\n-user modification 9\n-user modification 10\n-user modification 11\n-user modification 12\n-user modification 13\n-user modification 14\n-user modification 15\n-user modification 16\n-user modification 17\n-user modification 18\n-user modification 19\n-user modification 20\n-user modification 21\n-user modification 22\n-user modification 23\n-user modification 24\n-user modification 25\n-user modification 26\n-user modification 27\n-user modification 28\n-user modification 29\n-user modification 30\n+18O(1) of peptide C-term\n+18O(2) of peptide C-term\n+4-Hydroxyproline\n+Acetaldehyde +26\n+Acetylation of K\n+Acetylation of peptide N-term\n+Acetylation of protein N-term\n+Amidation of the peptide C-term\n+Amidation of the protein C-term\n+Arginine 13C(6)\n+Arginine 13C(6) 15N(4)\n+Carbamidomethylation of C\n+Carbamidomethylation of E\n+Carbamidomethylation of K\n+Carbamilation of K\n+Carbamilation of protein N-term\n+Carboxymethylation of C\n+Deamidation of N\n+Deamidation of N 18O\n+Deamidation of Q\n+Dehydration of S\n+Dehydration of T\n+Didehydro of T\n+Diiodination of Y\n+Dimethylation of K\n+Dimethylation of K 2H(4)\n+Dimethylation of K 2H(6)\n+Dimethylation of R\n+Dimethylation of peptide N-term 2H(6)\n+Dimethylation of peptide N-term 2H(6) 13C(2)\n+Dimethylation of peptide N-term K\n+Dimethylation of peptide N-term K 2H(4)\n+Dioxidation of M\n+Dioxidation of W\n+Farnesylation of C\n+FormylMet of protein N-term\n+Formylation of K\n+Formylation of S\n+Formylation of T\n+Formylation of peptide N-term\n+Formylation of protein N-term\n+Geranyl-geranyl of C\n+Glutathione of C\n+Guanidination of K\n+Guanidination of peptide N-term\n+Hex(1)NAc(1) of S\n+Hex(1)NAc(1) of T\n+Hex(5) HexNAc(4) NeuAc(2) Na of N\n+Hex(5) HexNAc(4) NeuAc(2) of N\n+HexNAc of S\n+HexNAc of T\n+Hexose of K\n+Homoserine lactone of peptide C-term M\n+Homoserine of peptide C-term M\n+ICAT-9\n+ICAT-O\n+ICPL0 of K\n+ICPL0 of peptide N-term\n+ICPL10 of K\n+ICPL10 of peptide N-term\n+ICPL4 of K\n+ICPL4 of peptide N-term\n+ICPL6 of K\n+ICPL6 of peptide N-term\n+Isoleucine 13C(6) 15N(1)\n+Leucine 13C(6) 15N(1)\n+Lipoyl of K\n+Lysine 13C(6)\n+Lysine 13C(6) 15N(2)\n+Lysine 2H(4)\n+Methylation of C\n+Methylation of D\n+Methylation of E\n+Methylation of K\n+Methylation of R\n+Methylation of S\n+Methylthio of C\n+Methylthio of D\n+Methylthio of N\n+NIPCAM of C\n+Nethylmaleimide of C\n+Oxidation of C\n+Oxidation of K\n+Oxidation of M\n+Oxidation of P\n+Palmitoylation of C\n+Palmitoylation of K\n+Palmitoylation of S\n+Palmitoylation of T\n+Palmitoylation of protein N-term\n+Phosphorylation of S\n+Phosphorylation of T\n+Phosphorylation of Y\n+Proline 13C(5)\n+Propionamide of C\n+Propionamide of K\n+Propionamide of peptide N-term\n+Propionyl of K heavy\n+Propionyl of K light\n+Propionyl of peptide N-term heavy\n+Propionyl of peptide N-term light\n+Pyridylethyl of C\n+Pyrolidone from E\n+Pyrolidone from Q\n+Pyrolidone from carbamidomethylated C\n+SUMO-2/3 Q87R\n+Sodium adduct to D\n+Sodium adduct to E\n+Sulfonation of S\n+Sulfonation of T\n+Sulfonation of Y\n+TMT 10-plex of K\n+TMT 10-plex of peptide N-term\n+TMT 2-plex of K\n+TMT 2-plex of peptide N-term\n+TMT 6-plex of K\n+TMT 6-plex of peptide N-term\n+Thioacyl of peptide N-term\n+Trideuterated Methyl Ester of D\n+Trideuterated Methyl Ester of E\n+Trideuterated Methyl Ester of K\n+Trideuterated Methyl Ester of R\n+Trideuterated Methyl Ester of peptide C-term\n+Trimethylation of K\n+Trimethylation of R\n+Trimethylation of protein N-term A\n+Trioxidation of C\n+Ubiquitination of K\n+iTRAQ 4-plex of K\n+iTRAQ 4-plex of Y\n+iTRAQ 4-plex of peptide N-term\n+iTRAQ 8-plex of K\n+iTRAQ 8-plex of Y\n+iTRAQ 8-plex of peptide N-term\n+mTRAQ of 13C(6) 15N(2)\n+mTRAQ of K 13C(3) 15N\n+mTRAQ of K light\n+mTRAQ of peptide N-term 13C(3) 15N\n+mTRAQ of peptide N-term 13C(6) 15N(2)\n+mTRAQ of peptide N-term light\n'

diff -r 913dbf2b83e0 -r 815f93bb3e1b tool_dependencies.xml
--- a/tool_dependencies.xml Mon Aug 10 18:25:37 2015 -0400
+++ b/tool_dependencies.xml Fri Nov 06 15:33:34 2015 -0500

@@ -1,9 +1,9 @@
<?xml version="1.0"?>
<tool_dependency>
-    <package name="searchgui" version="1.28">
-        <repository changeset_revision="0d8bbd52ae42" name="package_searchgui_1_28" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="searchgui" version="2.1">
+        <repository changeset_revision="42249a2266ba" name="package_searchgui_2_1" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="peptide_shaker" version="0.40">
-        <repository changeset_revision="9a4d33da1cce" name="package_peptideshaker_0_40" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="peptide_shaker" version="1.1">
+        <repository changeset_revision="d96500b8f698" name="package_peptideshaker_1_1" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
</tool_dependency>