--- a/macros.xml	Thu Nov 02 11:14:39 2023 +0000
+++ b/macros.xml	Mon Feb 03 16:01:01 2025 +0000
@@ -1,22 +1,19 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.0.15</token>
+    <token name="@TOOL_VERSION@">2.1.11</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
-          <requirement type="package" version="@TOOL_VERSION@">diamond</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">diamond</requirement>
         </requirements>
     </xml>
-
     <xml name="stdio">
         <stdio>
-            <regex match="Failed to allocate" source="stderr" level="fatal_oom" />
+            <regex match="Failed to allocate" source="stderr" level="fatal_oom"/>
         </stdio>
     </xml>
-
     <xml name="version_command">
         <version_command>diamond version | cut -d" " -f 3</version_command>
     </xml>
-
     <xml name="output_type_macro">
         <conditional name="output">
             <param argument="--outfmt" type="select" label="Format of output file" help="">
@@ -26,6 +23,7 @@
                 <option value="100">DAA</option>
                 <option value="101">SAM</option>
                 <option value="102">Taxonomic classification</option>
+                <option value="104">JSON (flat)</option>
             </param>
             <when value="0"/>
             <when value="5"/>
@@ -69,20 +67,17 @@
                     <option value="cigar">Cigar</option>
                     <yield/>
                 </param>
-                <param argument="--unal" type="boolean" label="Report unaligned queries" truevalue="1" falsevalue="0" checked="false"/>
             </when>
             <when value="100">
-                <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/>
-                <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/>
             </when>
             <when value="101">
-                <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/>
-                <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/>
             </when>
-            <when value="102"/>
+            <when value="102">
+                <param argument="--include-lineage" type="boolean" truevalue="--include-lineage" falsevalue="" checked="false" label="Include lineage in the taxonomic classification format"/>
+            </when>
+            <when value="104"/>
         </conditional>
     </xml>
-
     <xml name="hit_filter_macro">
         <conditional name="hit_filter">
             <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?">
@@ -90,57 +85,50 @@
                 <option value="top">Percentage of top alignment score</option>
             </param>
             <when value="max">
-                <param name="max_target_seqs" argument="--max-target-seqs" type="integer" value="25" label="The maximum number of target sequences per query to report alignments for" 
-                    help="Setting this to 0 will report all alignments that were found." />
+                <param argument="--max-target-seqs" type="integer" value="25" label="The maximum number of target sequences per query to report alignments for" help="Setting this to 0 will report all alignments that were found."/>
             </when>
             <when value="top">
-                <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a query" 
-                    help="For example, setting this to 10 will report all alignments whose score is at most 10% lower than the best alignment score for a query." />
+                <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a query" help="For example, setting this to 10 will report all alignments whose score is at most 10% lower than the best alignment score for a query."/>
             </when>
         </conditional>
     </xml>
-
     <xml name="block_size_low_sens">
-        <param argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" 
-            help="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary 
-                disk space, but also improve performance" />
+        <param argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time"
+            help="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary                  disk space, but also improve performance"/>
     </xml>
-
     <xml name="block_size_hi_sens">
-        <param argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time" 
-            help="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary 
-                disk space, but also improve performance" />
+        <param argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time"
+            help="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary                  disk space, but also improve performance"/>
     </xml>
-
     <xml name="citations">
         <citations>
-            <citation type="doi">10.1038/nmeth.3176</citation>
+            <citation type="doi">10.1038/s41592-021-01101-x</citation>
         </citations>
     </xml>
-
-
     <xml name="output_macro">
-        <data format="txt" name="blast_pairw" label="${tool.name} on ${on_string}">
+        <data format="txt" name="blast_pairw" label="${tool.name} on ${on_string}: Blast pairwise">
             <filter>output_section["output"]["outfmt"] == "0"</filter>
         </data>
-        <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}">
+        <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}: Blast XML">
             <filter>output_section["output"]["outfmt"] == "5"</filter>
         </data>
-        <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}">
+        <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}: Blast Tabular">
             <filter>output_section["output"]["outfmt"] == "6"</filter>
         </data>
         <!-- for daa diamond appends the .daa extension -> hence from_work_dir -->
-        <data format="daa" name="daa_output" label="${tool.name} on ${on_string}" from_work_dir="output.daa">
+        <data format="daa" name="daa_output" label="${tool.name} on ${on_string}: DAA" from_work_dir="output.daa">
             <filter>output_section["output"]["outfmt"] == "100"</filter>
         </data>
-        <data format="sam" name="sam_output" label="${tool.name} on ${on_string}">
+        <data format="sam" name="sam_output" label="${tool.name} on ${on_string}: SAM">
             <filter>output_section["output"]["outfmt"] == "101"</filter>
         </data>
-        <data format="tabular" name="tax_output" label="${tool.name} on ${on_string}">
+        <data format="tabular" name="tax_output" label="${tool.name} on ${on_string}: Taxonomic classification">
             <filter>output_section["output"]["outfmt"] == "102"</filter>
         </data>
+        <data format="json" name="json_output" label="${tool.name} on ${on_string}: Json flat">
+            <filter>output_section["output"]["outfmt"] == "104"</filter>
+        </data>
     </xml>
-
     <token name="@OUTPUT_ARGS@">
         #if $output_section.output.outfmt == "0"
             --outfmt '0'
@@ -151,23 +139,18 @@
         #else if $output_section.output.outfmt == "6"
             --outfmt '6' #echo ' '.join(str($output_section.output.fields).split(','))
             --out '$blast_tabular'
-            --unal $output_section.output.unal
         #else if $output_section.output.outfmt == "100"
             --outfmt '100'
-            $output_section.output.salltitles
-            $output_section.output.sallseqid
             --out output.daa
         #else if $output_section.output.outfmt == "101"
             --outfmt '101'
-            $output_section.output.salltitles
-            $output_section.output.sallseqid
             --out '$sam_output'
         #else if $output_section.output.outfmt == "102"
             --outfmt '102'
             --out '$tax_output'
+            $output_section.output.include_lineage
         #end if
     </token>
-
     <token name="@HITFILTER_ARGS@">
         #if str($hit_filter.hit_filter_select) == 'max':
             --max-target-seqs '$hit_filter.max_target_seqs'