--- a/macros.xml	Tue Mar 22 16:09:47 2022 +0000
+++ b/macros.xml	Thu May 26 16:46:13 2022 +0000
@@ -1,16 +1,17 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.9.3</token>
+    <token name="@TOOL_VERSION@">0.9.4</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="4.1.0">r-base</requirement>
             <requirement type="package" version="4.0.1">r-arrow</requirement>
-            <requirement type="package" version="0.9.3">r-recetox-aplcms</requirement>
+            <requirement type="package" version="0.9.4">r-recetox-aplcms</requirement>
             <requirement type="package" version="1.0.7">r-dplyr</requirement>
         </requirements>
     </xml>
 
     <xml name="creator">
         <creator>
+            <yield />  
             <person
                 givenName="Martin"
                 familyName="Čech"
@@ -49,9 +50,7 @@
 
     <xml name="noise_filtering">
         <section name="noise_filtering" title="Noise filtering and peak detection">
-            <param name="min_exp" type="integer" min="1" value="2"
-                   label="min_exp"
-                   help="If a feature is to be included in the final feature table, it must be present in at least this number of spectra." />
+            <yield />
             <param name="min_pres" type="float" value="0.5"
                    label="min_pres"
                    help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
@@ -146,6 +145,22 @@
                    help="The minimum number of raw data points to be considered as a true feature." />
         </section>
     </xml>
+    <xml name="multibatch_processing">
+        <section name="multibatch_processing" title="Multibatch processing">
+            <param name="min_within_batch_prop_detect" type="float" min="0" max="1" value="0.1"
+                   label="minimum_batchwise_prop_detect"
+                   help="The minimum detection frequency (relative) of a feature for it to be included in the final feature table." />
+            <param name="min_batch_prop" type="float" min="0" max="1" value="0.5"
+                   label="minimum_batch_prop"
+                   help="The minimum proportion of batches that must have a given feature. The features that are less abundant than the value won't be reported." />
+            <param name="batch_align_mz_tol" type="float" min="0" value="0.00001"
+                   label="batch_align_mz_tol"
+                   help="The m/z tolerance level for peak alignment within batch." />
+            <param name="batch_align_chr_tol" type="float" min="0" value="50.0"
+                   label="batch_align_chr_tol"
+                   help="The retention time tolerance level for peak alignment within batch." />
+        </section>
+    </xml>
     <xml name="output_format">
        <section name="output_format" title="Output Format">
               <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" />
@@ -155,12 +170,8 @@
     <xml name="unsupervised_outputs">
         <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" />
         <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" />
-        <collection  name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}">
-            <discover_datasets pattern="__designation__" directory="corrected" format="parquet" />
-        </collection >
-        <collection  name="extracted_features" type="list" label="${tool.name} extracted_features on ${on_string}">
-            <discover_datasets pattern="__designation__" directory="extracted" format="parquet" />
-        </collection >
+        <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/>
+        <yield />
     </xml>
 
     <xml name="citations">
@@ -169,6 +180,7 @@
             <citation type="doi">10.1186/1471-2105-11-559</citation>
             <citation type="doi">10.1021/pr301053d</citation>
             <citation type="doi">10.1093/bioinformatics/btu430</citation>
+            <yield />
         </citations>
     </xml>
 
@@ -194,6 +206,20 @@
         ]]>
     </token>
 
+    <token name="@HELP_two-step-hybrid@">
+        <![CDATA[
+              This is the **Two-Step Hybrid** version of **apLCMS**. This tool is improved upon the Hybrid version by accounting for the batch
+              effects in multi-batch experiments. As in the Hybrid version, this tool incorporates 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@
+        ]]>
+    </token>
+
     <token name="@GENERAL_HELP@">
         apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time
         tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.