# HG changeset patch
# User recetox
# Date 1684414847 0
# Node ID 94d6243033ec60f2cf26d5ea1aa025648b462d7f
# Parent  6fa3c0ba2e66b4c8b99a39f048c05b2beaede226
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank commit 02414aa4c20f249c2069e5e3d587e3a8cda923a8

diff -r 6fa3c0ba2e66 -r 94d6243033ec rmassbank.r
--- a/rmassbank.r	Fri Jan 28 16:31:11 2022 +0000
+++ b/rmassbank.r	Thu May 18 13:00:47 2023 +0000
@@ -21,7 +21,7 @@
 # Load libraries
 rm(list = ls(all = TRUE))
 
-suppressMessages(library("RMassBank", warn.conflicts = T, quietly = T))
+suppressMessages(library("RMassBank", warn.conflicts = TRUE, quietly = TRUE))
 
 #############################################################
 # Read arguments
diff -r 6fa3c0ba2e66 -r 94d6243033ec rmassbank.xml
--- a/rmassbank.xml	Fri Jan 28 16:31:11 2022 +0000
+++ b/rmassbank.xml	Thu May 18 13:00:47 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="rmassbank" name="RMassBank" version="@TOOL_VERSION@+galaxy0">
+<tool id="rmassbank" name="RMassBank" version="@TOOL_VERSION@+galaxy2">
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -15,7 +15,7 @@
         <exit_code range="1:"/>
         <exit_code range=":-1"/>
     </stdio>
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
          #for $infile in $param_in:
             ln -s '${infile}' '${infile.element_identifier}' &&
          #end for
@@ -208,38 +208,8 @@
             <param name="infolist" value="infolist.csv"/>
             <param name="mode" value="pH"/>
             <param name="param_in" value="1_3_Trifluoromethylphenyl_piperazin_2819_pos.mzML"/>
-            <param name="rtMargin" value="0.4"/>
-            <param name="rtShift" value="0.0"/>
-            <param name="use_version" value="2"/>
-            <param name="use_rean_peaks" value="TRUE"/>
-            <param name="add_annotation" value="TRUE"/>
-            <param name="include_sp_tags" value="FALSE"/>
-            <param name="pH" value="0"/>
-            <param name="pM" value="16"/>
-            <param name="pNa" value="32"/>
-            <param name="mH" value="50"/>
-            <param name="mFA" value="66"/>
-            <param name="electronicNoiseWidth" value="0.3"/>
-            <param name="recalibrateBy" value="dppm"/>
-            <param name="recalibrateMS1" value="common"/>
-            <param name="recalibrateMS1Window" value="15"/>
-            <param name="multiplicityFilter" value="2"/>
-            <param name="ppmHighMass" value="10"/>
-            <param name="ppmLowMass" value="15"/>
-            <param name="massRangeDivision" value="120"/>
             <param name="ppmFine" value="5"/>
-            <param name="prelimCut" value="1000"/>
-            <param name="prelimCutRatio" value="0.0"/>
-            <param name="fineCut" value="0.0"/>
-            <param name="fineCutRatio" value="0.0"/>
-            <param name="specOkLimit" value="1000"/>
-            <param name="dbeMinLimit" value="-0.5"/>
-            <param name="satelliteMzLimit" value="0.5"/>
-            <param name="satelliteIntLimit" value="0.05"/>
-            <param name="ppmFine" value="5"/>
-            <param name="mzCoarse" value="0.5"/>
-            <param name="fillPrecursorScan" value="FALSE"/>
-            <param name="unknownMass" value="charged"/>
+
             <output name="outputINI" value="mysettings_galaxy.ini" ftype="txt" lines_diff="2"/>
             <output name="csvfile" value="failedPeaks.csv" ftype="csv" lines_diff="1"/>
             <output name="pdfplot" value="plot.pdf" compare="sim_size" delta_frac="0.1"/>
@@ -257,7 +227,6 @@
     </help>
 
     <citations>
-        <citation type="doi">https://onlinelibrary.wiley.com/doi/full/10.1002/jms.3131</citation>
+        <citation type="doi">10.1002/jms.3131</citation>
     </citations>
 </tool>
-