--- a/macros.xml	Fri Aug 05 15:21:27 2022 +0000
+++ b/macros.xml	Thu Mar 02 10:38:54 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">5.2.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="requirements">
         <requirements>
@@ -15,7 +15,7 @@
         </xrefs>
     </xml>
     <xml name="gene_thresholds">
-        <param name="gene_thresholds" argument="--gene-thresholds" type="text" value="0,300,1500,3000" label="Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool"/>
+        <param argument="--gene-thresholds" type="text" value="0,300,1500,3000" label="Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool"/>
     </xml>
     <xml name="citations">
         <citations>
@@ -26,7 +26,28 @@
         </citations>
     </xml>
     <xml name="min_identity_macros" token_value="">
-        <param argument="--min-identity" type="float" value="@VALUE@" min="80" max="100" label="Minimum IDY% considered as proper alignment" help="Alignments with IDY% worse than this value will be filtered. Note that all alignments
-            with IDY% less than 80.0% will be filtered regardless of this threshold. "/>
+        <param argument="--min-identity" type="float" value="@VALUE@" min="80" max="100" label="Minimum IDY% considered as proper alignment" help="Alignments with IDY% worse than this value will be filtered. Note that all alignments with IDY% less than 80.0% will be filtered regardless of this threshold. "/>
+    </xml>
+    <xml name="custom">
+        <param name="custom" type="select" label="Use customized names for the input files?" help="They will be used in reports, plots and logs">
+            <option value="true">Yes, specify custom names</option>
+            <option value="false" selected="true">No, use dataset names</option>
+        </param>
+    </xml>
+    <xml name="labelled_input">
+        <param name="input" type="data" format="fasta" label="Contigs/scaffolds file"/>
+        <param argument="--labels" type="text" value="" label="Name"/>
+    </xml>
+    <xml name="reads_option">
+        <param name="reads_option" type="select" label="Reads options" help="Currently, the supported read types are Illumina unpaired, paired-end and mate-pair reads, PacBio SMRT, and Oxford Nanopore long reads.">
+            <option value="disabled">Disabled</option>
+            <option value="single">Illumina single-end reads</option>
+            <option value="paired">Illumina paired-end reads</option>
+            <option value="paired_collection">Illumina paired-end reads in paired collection</option>
+            <option value="paired_interlaced">Illumina interlaced paired-end reads</option>
+            <option value="mate_paired">Illumina mate-pair reads</option>
+            <option value="pacbio">Pacbio SMRT reads</option>
+            <option value="nanopore">Nanopore reads</option>
+        </param>
     </xml>
 </macros>