# HG changeset patch
# User galaxyp
# Date 1628777212 0
# Node ID 3ec27b4cee7c138b4227ede038274b53bcbabc38
# Parent  a6ff76e057fdc9d353f356fa7a748a1aa0112b93
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"

diff -r a6ff76e057fd -r 3ec27b4cee7c fasta_cli.xml
--- a/fasta_cli.xml	Tue Jul 20 08:55:11 2021 +0000
+++ b/fasta_cli.xml	Thu Aug 12 14:06:52 2021 +0000
@@ -46,7 +46,7 @@
 
         <section name="database_processing_options" expanded="true" title="Database Processing Options">
 
-            <param name="decoy_tag" type="text" value="-REVERSED" label="The decoy flag">
+            <param name="decoy_tag" type="text" value="_REVERSED" label="The decoy flag">
             </param>
             <param name="decoy_type" type="select" label="Location of the decoy flag: prefix or suffix">
                 <option value="1">Prefix</option>
@@ -74,7 +74,7 @@
 
 Appends decoy sequences to FASTA files. Default format is adequated to be used by SearchGUI and PeptideShaker tools, ie:
 
-* Decoy flag: -REVERSED
+* Decoy flag: _REVERSED
 
 * Location: suffix
 
diff -r a6ff76e057fd -r 3ec27b4cee7c ident_params.xml
--- a/ident_params.xml	Tue Jul 20 08:55:11 2021 +0000
+++ b/ident_params.xml	Thu Aug 12 14:06:52 2021 +0000
@@ -525,7 +525,13 @@
 
             ## SPECTRUM ANNOTATION
             -annotation_level $advanced_options.spectrum_annotation_options.annotation_level
+
+            ## if the user modifies fragment_tol but he does not modify annotation_mz_tolerance,
+            ## we must overwrite default annotation_mz_tolerance value with fragment_tol value
+
+            #if not ($spectrum_matching_options.fragment_tol != 0.5 and $advanced_options.spectrum_annotation_options.annotation_mz_tolerance == 0.5)
             -annotation_mz_tolerance $advanced_options.spectrum_annotation_options.annotation_mz_tolerance
+            #end if
             -annotation_high_resolution $advanced_options.spectrum_annotation_options.annotation_high_resolution
             ## TODO: There are still many options from the GUI to be incorporated to the CLI
 
@@ -1203,9 +1209,9 @@
                             </param>
                             <param name="comet_isotope_correction" label="Comet: Isotope Correction" type="select" help="Controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement">
                                 <option value="0">off</option>
-                                <option value="1" selected="True">0,+1</option>
+                                <option value="1">0,+1</option>
                                 <option value="2">0,+1,+2</option>
-                                <option value="3">0,+1,+2,+3</option>
+                                <option value="3" selected="True">0,+1,+2,+3</option>
                                 <option value="4">-8,-4,0,+4,+8</option>
                             </param>
                             <param name="comet_min_prec_mass"  type="float" value="600.0"
@@ -1237,7 +1243,7 @@
                                 <option value="0" selected="True">Summed intensities + flanking</option>
                                 <option value="1">Summed intensities</option>
                             </param>
-                            <param name="comet_frag_bin_offset"  type="float" value="0.01"
+                            <param name="comet_frag_bin_offset"  type="float" value="0"
                                 label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />
                         </when>
                     </conditional>
@@ -1706,7 +1712,7 @@
                 <param name="annotation_level" label="Percent of the possible annotations relative to the most intensive peak" help="The intensity percentile to consider for annotation, e.g. 0.75 means that the 25% most intense peaks will be annotated, default is 0.75." value="0.75" type="float">
                     <validator type="in_range" min="0" max="1" />
                 </param>
-                <param name="annotation_mz_tolerance" label="Fragment ion annotation accuracy" help=" The m/z tolerance to annotate peaks, default is equal to the search settings MS2 tolerance." value="10" type="float" />
+                <param name="annotation_mz_tolerance" label="Fragment ion annotation accuracy" help=" The m/z tolerance to annotate peaks, default is equal to the search settings MS2 tolerance." value="0.5" type="float" />
                 <param name="annotation_high_resolution" label="High resolution" help="The most accurate peak will be selected within the m/z tolerance if chosen" truevalue="1" falsevalue="0" checked="true" type="boolean"/>
             </section>
 
@@ -1851,7 +1857,7 @@
                     </param>
                     <when value="no" />
                     <when value="yes">
-                        <param name="decoy_tag" type="text" value="-REVERSED" label="The decoy flag">
+                        <param name="decoy_tag" type="text" value="_REVERSED" label="The decoy flag">
                         </param>
                         <param name="decoy_type" type="select" label="Location of the decoy flag: prefix or suffix">
                             <option value="0">Prefix</option>
diff -r a6ff76e057fd -r 3ec27b4cee7c macros_basic.xml
--- a/macros_basic.xml	Tue Jul 20 08:55:11 2021 +0000
+++ b/macros_basic.xml	Thu Aug 12 14:06:52 2021 +0000
@@ -12,7 +12,7 @@
     </xml>
     <token name="@SEARCHGUI_MAJOR_VERSION@">4</token>
     <token name="@SEARCHGUI_VERSION@">4.0.41</token>
-    <token name="@SEARCHGUI_VERSION_SUFFIX@">0</token>
+    <token name="@SEARCHGUI_VERSION_SUFFIX@">1</token>
     <token name="@PEPTIDESHAKER_VERSION@">2.0.33</token>
     <token name="@PEPTIDESHAKER_VERSION_SUFFIX@">1</token>
     <xml name="citations">
diff -r a6ff76e057fd -r 3ec27b4cee7c searchgui.xml
--- a/searchgui.xml	Tue Jul 20 08:55:11 2021 +0000
+++ b/searchgui.xml	Thu Aug 12 14:06:52 2021 +0000
@@ -180,7 +180,7 @@
         <!-- Search Engine Selection -->
         <section name="search_engines_options" expanded="true" title="Search Engine Options">
             <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
-                <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA might not work into isolated environments like containers. Ms Amanda may not work either when executed into isolated environments based on MacOS X.
+                <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA might not work into isolated environments like containers. Ms Amanda may not work either when executed into isolated environments based on MacOS X (use SG 4.0.22 to solve any problem running MsAmanda).
                     MetaMorpheus only produce results when using mzML format.</help>
                 <option value="X!Tandem" selected="True">X!Tandem</option>
                 <option value="MSGF" selected="True">MS-GF+</option>