--- a/recetox_aplcms_hybrid.xml	Thu Oct 21 15:03:51 2021 +0000
+++ b/recetox_aplcms_hybrid.xml	Fri Jan 28 16:26:36 2022 +0000
@@ -1,14 +1,15 @@
 <tool id="recetox_aplcms_hybrid" name="RECETOX apLCMS Hybrid" version="@TOOL_VERSION@+galaxy2">
     <description>generate a feature table from LC/MS spectra</description>
     <macros>
-        <import>recetox_aplcms_macros.xml</import>
+        <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="creator"/>
+
+    <expand macro="requirements"/>
     <command detect_errors="aggressive"><![CDATA[
         sh ${symlink_inputs} &&
         Rscript  -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")'
     ]]></command>
-    <expand macro="creator" />
     <configfiles>
         <configfile name="symlink_inputs">
             #for $infile in $files
@@ -57,46 +58,43 @@
     </configfiles>
 
     <expand macro="inputs">
-        <expand macro="history_db" />
-        <expand macro="noise_filtering" />
-        <expand macro="feature_detection" />
-        <expand macro="peak_alignment" />
-        <expand macro="weak_signal_recovery" />
-        <expand macro="output_format" />
+        <expand macro="history_db"/>
+        <expand macro="noise_filtering"/>
+        <expand macro="feature_detection"/>
+        <expand macro="peak_alignment"/>
+        <expand macro="weak_signal_recovery"/>
+        <expand macro="output_format"/>
     </expand>
 
     <outputs>
-        <expand macro="unsupervised_outputs" />
-        <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}" />
-        <data name="feature_known_table_pairing" format="tabular" label="${tool.name} feature_known_table_pairing on ${on_string}" hidden="true" />
+        <expand macro="unsupervised_outputs"/>
+        <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/>
+        <data name="feature_known_table_pairing" format="tabular"
+              label="${tool.name} feature_known_table_pairing on ${on_string}" hidden="true"/>
     </outputs>
 
     <tests>
         <test>
-            <param name="known_table" value="known_table.parquet" ftype="parquet" />
-            <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" />
-            <output name="recovered_feature_sample_table" file="hybrid_recovered_feature_sample_table.parquet" ftype="parquet" />
+            <param name="known_table" value="known_table.parquet" ftype="parquet"/>
+            <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
+            <output name="recovered_feature_sample_table" file="hybrid_recovered_feature_sample_table.parquet"
+                    ftype="parquet"/>
         </test>
         <test>
-            <param name="known_table" value="known_table.parquet" ftype="parquet" />
-            <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" />
+            <param name="known_table" value="known_table.parquet" ftype="parquet"/>
+            <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
             <section name="output_format">
-                <param name="out_format" value="recetox" />
+                <param name="out_format" value="recetox"/>
             </section>
-            <output name="recovered_feature_sample_table" file="hybrid.recetox.parquet" ftype="parquet" />
+            <output name="recovered_feature_sample_table" file="hybrid.recetox.parquet" ftype="parquet"/>
         </test>
     </tests>
 
     <help>
-        This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
-        detected features on the same machinery to help detect and quantify lower-intensity peaks.
-
-        CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
-        system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
-        technique, such as human serum.
-
-        @GENERAL_HELP@
+        <![CDATA[
+            @HELP_hybrid@
+        ]]>
     </help>
 
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>