# HG changeset patch
# User galaxyp
# Date 1509178594 14400
# Node ID 2439164e60610081651c7ca92c8011947e2f92e7
# Parent  ea780a2a88b2ef3f68a14fad6cac9e59ea189ba3
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit dea56622eb32b82c87dc87567dc89db3a787033d

diff -r ea780a2a88b2 -r 2439164e6061 macros.xml
--- a/macros.xml	Wed Sep 27 08:59:39 2017 -0400
+++ b/macros.xml	Sat Oct 28 04:16:34 2017 -0400
@@ -8,10 +8,10 @@
         </stdio>
     </xml>
     <token name="@GENERAL_PARAMETERS@">
-            -frag_tol "${precursor_options.fragment_tol}"
-            ### -frag_ppm
-            -prec_tol "${precursor_options.precursor_ion_tol}"
-            -prec_ppm "${precursor_options.precursor_ion_tol_units}"
+            -frag_tol '${precursor_options.fragment_tol}'
+            -frag_ppm '${precursor_options.fragment_tol_units}'
+            -prec_tol '${precursor_options.precursor_ion_tol}'
+            -prec_ppm '${precursor_options.precursor_ion_tol_units}'
 
             -min_charge $precursor_options.min_charge
             -max_charge $precursor_options.max_charge
@@ -126,7 +126,12 @@
             </param>
             <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance"
                 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
-            <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"
+            <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"
+                help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
+                <option value="1">Parts per million (ppm)</option>
+                <option value="2">Daltons</option>
+            </param>
+            <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"
                 help="Provide error value for fragment ions, based on instrument used"/>
             <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
             <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
diff -r ea780a2a88b2 -r 2439164e6061 searchgui.xml
--- a/searchgui.xml	Wed Sep 27 08:59:39 2017 -0400
+++ b/searchgui.xml	Sat Oct 28 04:16:34 2017 -0400
@@ -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>
@@ -537,7 +537,7 @@
                         label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
                     <param name="xtandem_output_spectra" help="Controls output of spectrum information"
                         label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-                    <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." -->
+                    <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." -->
                         
                     <conditional name="xtandem_refine"><!-- -xtandem_refine -->
                         <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
@@ -676,7 +676,7 @@
                         label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
                     <param name="msgf_max_pep_length" type="integer" value="30" 
                         label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
-                    <param name="msgf_termini" type="select" format="text" 
+                    <param name="msgf_termini" type="select" format="txt" 
                         label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
                         <option value="0">0 (ie non-specific cleavage)</option>
                         <option value="1">1 (ie semi-tryptic cleavage)</option>