# HG changeset patch
# User galaxyp
# Date 1652799288 0
# Node ID b2ae586dc13bd9b86e4a089ecf9349288bcd3463
# Parent  469da8c03202cbffb55ab243c2295cdd9e23a5ae
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 0bb79ebbaf73fe6e902f6ef20cc9c9741063bf34

diff -r 469da8c03202 -r b2ae586dc13b encyclopedia_fasta_to_prosit_csv.xml
--- a/encyclopedia_fasta_to_prosit_csv.xml	Thu Apr 08 17:55:16 2021 +0000
+++ b/encyclopedia_fasta_to_prosit_csv.xml	Tue May 17 14:54:48 2022 +0000
@@ -4,7 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command detect_errors="aggressive"><![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
         EncyclopeDIA -convert -fastatoprositcsv
         -i '$i'
         -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
diff -r 469da8c03202 -r b2ae586dc13b macros.xml
--- a/macros.xml	Thu Apr 08 17:55:16 2021 +0000
+++ b/macros.xml	Tue May 17 14:54:48 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.2.2</token>
+    <token name="@TOOL_VERSION@">1.12.34</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
@@ -293,16 +293,21 @@
             </param>
             <when value="no"/>
             <when value="yes">
-                <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/>
-                <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/>
-                <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/>
+                <param argument="-percolatorVersion" type="text" value="3.01" optional="true" label="percolatorVersion">
+                     <option value="2.10">2.10</option>
+                     <option value="3.01">3.01</option>
+                     <option value="3.05">3.05</option>
+                     <validator type="regex" message="Not percolator version format">^\d([.]\d+)?$</validator>
+                </param>
+                <param argument="-percolatorProteinThreshold" type="float" value="0.01" optional="true" label="percolatorProteinThreshold"/>
+                <param argument="-percolatorThreshold" type="float" value="0.01" optional="true" label="percolatorThreshold"/>
             </when>
         </conditional>
     </xml>
     <token name="@PERCOLATOR_OPTIONS@">
     #if $options.percolator.set_percolator == 'yes'
-        #if str($options.percolator.percolatorVersionNumber)
-            -percolatorVersionNumber $options.percolator.percolatorVersionNumber
+        #if str($options.percolator.percolatorVersion)
+            -percolatorVersion $options.percolator.percolatorVersion
         #end if
         #if str($options.percolator.percolatorProteinThreshold)
             -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold
@@ -310,6 +315,8 @@
         #if str($options.percolator.percolatorThreshold)
             -percolatorThreshold $options.percolator.percolatorThreshold
         #end if
+    #else 
+        -percolatorVersion "3.01"
     #end if
     </token>
 
@@ -525,6 +532,12 @@
         @FASTA_INPUT@
         @TARGET_FASTA@
         @LIB_INPUT@
+        @MASS_LIBRARY_TOLERANCE@
+        @PERCOLATOR_OPTIONS@
+        @PEAK_OPTIONS@
+        @WINDOW_OPTIONS@
+        @MODIFICATION_OPTIONS@
+        @SEARCH_OPTIONS@
         -a $a
         -o chromatogram_library.elib
         && ls -l ./*.* inputs/*