--- a/freyja_demix.xml	Thu Jul 28 09:26:02 2022 +0000
+++ b/freyja_demix.xml	Fri Jul 07 05:51:15 2023 +0000
@@ -30,6 +30,7 @@
         --meta '$meta'
     #end if
     $confirmedonly
+    $wgisaid
     @CUSTOM_BARCODES_COMMAND@
     --covcut $depth_cutoff
     --output abundances_raw.tsv &&
@@ -73,9 +74,10 @@
                 <param name="source" value="manual"/>
                 <param name="name" value="samplename"/>
             </conditional>
-            <output name="abundances" ftype="tabular">
+            <output name="abundances">
                 <assert_contents>
-                    <has_text text="samplename"/>
+                    <has_n_columns n="2" />
+                    <has_text text="AY.48"/>
                 </assert_contents>
             </output>
         </test>
@@ -89,9 +91,10 @@
             <conditional name="sample_name">
                 <param name="source" value="auto"/>
             </conditional>
-            <output name="abundances" ftype="tabular">
+            <output name="abundances">
                 <assert_contents>
-                    <has_text text="summarized"/>
+                    <has_n_columns n="2" />
+                    <has_text text="AY.48"/>
                 </assert_contents>
             </output>
         </test>

--- a/macros.xml	Thu Jul 28 09:26:02 2022 +0000
+++ b/macros.xml	Fri Jul 07 05:51:15 2023 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.3.8</token>
+    <token name="@TOOL_VERSION@">1.4.4</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
@@ -49,6 +49,7 @@
 echo '${plot_format.plot_title}' > plot_title.txt &&
 echo '${plot_format.plot_intro}' > plot_intro.txt &&
 freyja dash
+    --mincov $plot_format.mincov
     #if $need_aggregation.choice == 'no'
         '$tsv_aggregated'
     #else
@@ -61,6 +62,8 @@
 ]]></token>
     <token name="@PLOT_COMMAND@"><![CDATA[
 freyja plot
+    $plot_format.lineages
+    --mincov $plot_format.mincov
     #if $need_aggregation.choice == 'no'
         '$tsv_aggregated'
     #else
@@ -82,6 +85,8 @@
     @DASH_COMMAND@
 #else if $plot_format.choice == 'plot'
     freyja plot
+    $plot_format.lineages
+    --mincov $plot_format.mincov
     #if $need_aggregation.choice == 'no'
         $tsv_aggregated
     #else
@@ -129,6 +134,19 @@
                checked="false"
                label="Remove unconfirmed lineages from the analysis"
                help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/>
+        <param argument="--wgisaid" type="boolean" truevalue="--wgisaid" falsevalue=""
+               checked="false"
+               label="Use larger library with non-public lineages"
+               help="Allows to use larger UShER barcodes library extended with GISAID non-public lineages"/>
+    </xml>
+    <xml name="plot_lineages">
+        <param argument="--lineages" type="boolean" truevalue="--lineages" falsevalue=""
+               checked="false" label="Use lineage specific breakdown"/>
+    </xml>
+    <xml name="plot_mincov">
+        <param argument="--mincov" type="float" min="0" max="100" value="60"
+               label="Minimum genome coverage"
+               help="Include in the plot only samples where the 'coverage' value is greater than the specified --mincov parameter. It excludes samples with coverage values below the minimum coverage threshold. By default, the minimum genome coverage is set at 60 percent."/>
     </xml>
     <token name="@HELP_HEADER@"><![CDATA[
 What it does
@@ -145,7 +163,7 @@
 ]]></token>
     <xml name="citations">
         <citations>
-            <citation type="doi">10.5281/zenodo.6585067</citation>
+            <citation type="doi">10.1038/s41586-022-05049-6</citation>
         </citations>
     </xml>
 </macros>