# HG changeset patch
# User galaxyp
# Date 1747636874 0
# Node ID 5c04f9decc01c5ed203312499b3e61db7421306a
# Parent  19e45916daf92a29f681768a0b1a4134cf1a5655
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser commit 2866078b3bef6adef82a499d9b38a56da1d372c3

diff -r 19e45916daf9 -r 5c04f9decc01 thermo_converter.xml
--- a/thermo_converter.xml	Wed Apr 21 12:23:27 2021 +0000
+++ b/thermo_converter.xml	Mon May 19 06:41:14 2025 +0000
@@ -1,11 +1,17 @@
-<tool id="thermo_raw_file_converter" name="Thermo" version="@TOOL_VERSION@+galaxy0" profile="20.05">
+<tool id="thermo_raw_file_converter" name="Thermo" version="@TOOL_VERSION@+galaxy1" profile="20.05">
     <description>RAW file converter</description>
     <macros>
         <token name="@TOOL_VERSION@">1.3.4</token>
     </macros>
+
+    <xrefs>
+        <xref type="bio.tools">ThermoRawFileParser</xref>
+    </xrefs>
+
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">thermorawfileparser</requirement>
     </requirements>
+
     <stdio>
         <regex match="ERROR" source="both" level="fatal" description="Fatal error"/>
     </stdio>
@@ -64,7 +70,6 @@
                 <param argument="--noPeakPicking" name="peakpicking_boolean" type="boolean" truevalue="" falsevalue="-p" checked="true"
                     label="Use the peak picking provided by the native thermo library" help=""/>
             </when>
-            <when value="3"/>
         </conditional>
         <param argument="--metadata" name="output_metadata_selector" type="select" label="Output metadata">
             <option value="off" selected="True">No</option>
@@ -164,7 +169,7 @@
             <param name="output_metadata_selector" value="1"/>
             <param name="ignore_instrument_errors_boolean" value="true"/>
             <param name="allDetectors" value="true"/>
-            <param name="includeExceptionData" value="--includeExceptionData"/>
+            <param name="includeExceptionData" value="true"/>
             <param name="msLevel" value="1"/>
             <output name="output" value="really_small.indexed_mzML" ftype="mzml"/>
             <output name="output_metadata" ftype="txt">