--- a/icescreen.xml	Tue Oct 31 16:31:33 2023 +0000
+++ b/icescreen.xml	Fri Jan 26 13:38:40 2024 +0000
@@ -1,12 +1,9 @@
 <tool id="icescreen" name="ICEscreen" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
-    <description>detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes.</description>
+    <description>detects and annotates ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Bacillota genomes.</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.2.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@TOOL_VERSION@">1.3.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
-    <xrefs>
-        <xref type="bio.tools">ICEscreen</xref>
-    </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">icescreen</requirement>
         <requirement type="package" version="3.0">zip</requirement>
@@ -23,7 +20,7 @@
             --galaxy
             --gbdir ./tmp_icescreen/source_genbank
             --outdir ./tmp_icescreen
-            --mode '${taxonomy.mode}'
+            --phylum '${taxonomy.phylum}'
             --jobs "\${GALAXY_SLOTS:-4}" > ./tmp_icescreen/ICEscreen_log.txt 2>&1
 
         && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_ME.summary > '${summary}'
@@ -49,10 +46,9 @@
     </command>
     <inputs>
         <param name="genome" type="data" format="genbank" label="Input genomes to analyze in Genbank format" help="Multi-genbank files (i.e. gbff) are supported. Each record must include the ORIGIN nucleotide sequence at the end."/>
-        <section name="taxonomy" title="Taxonomy of the genomes to analyse" expanded="False">
-            <param name="mode" type="select" label="Firmicutes is the defaut parameter" help="Streptomyces is EXPERIMENTAL and is NOT recommended.">
-                <option value="firmicutes" selected="true">Firmicutes</option>
-                <option value="streptomyces">Streptomyces</option>
+        <section name="taxonomy" title="Phylum of the genomes to analyse" expanded="True">
+            <param name="phylum" type="select" label="Bacillota is the defaut parameter">
+                <option value="bacillota" selected="true">Bacillota</option>
             </param>
         </section>
         <section name="additional_output" title="Additional output files" expanded="False">
@@ -129,7 +125,7 @@
             <param name="optional_files" value="output_log" />
             <output name="log" >
                 <assert_contents>
-                    <has_text text="firmicutes" />
+                    <has_text text="bacillota" />
                     <has_text text="Building DAG of jobs" />
                     <has_text text="Complete log" />
                     <not_has_text text="Error" />
@@ -138,22 +134,22 @@
         </test>
         <test expect_num_outputs="4">
             <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
-            <param name="mode" value="streptomyces" />
+            <param name="phylum" value="bacillota" />
             <param name="optional_files" value="output_log" />
             <output name="log" >
                 <assert_contents>
-                    <has_text text="streptomyces" />
+                    <has_text text="bacillota" />
                     <not_has_text text="Error" />
                 </assert_contents>
             </output>
         </test>
         <test expect_num_outputs="5">
             <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
-            <param name="mode" value="firmicutes" />
+            <param name="phylum" value="bacillota" />
             <param name="optional_files" value="output_zip_all_files,output_log" />
             <output name="log" >
                 <assert_contents>
-                    <has_text text="firmicutes" />
+                    <has_text text="bacillota" />
                     <not_has_text text="Error" />
                 </assert_contents>
             </output>
@@ -180,7 +176,7 @@
 
         **What it does**
 
-        ICEscreen is a bioinformatic pipeline for the detection and annotation of ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Firmicutes genomes. The full documentation is available at https://icescreen.migale.inrae.fr. The forge of the project is accessible at https://forgemia.inra.fr/ices_imes_analysis/icescreen.
+        ICEscreen is a bioinformatic pipeline for the detection and annotation of ICEs (Integrative and Conjugative Elements) and IMEs (Integrative and Mobilizable Elements) in Bacillota genomes. The full documentation is available at https://icescreen.migale.inrae.fr. The forge of the project is accessible at https://forgemia.inra.fr/ices_imes_analysis/icescreen.
 
         **Main features of ICEscreen**
 
@@ -193,8 +189,8 @@
 
         There are 3 main output results files generated by ICEscreen:
 
-        - Detected Signature Proteins table (`*_detected_SP_withMEIds.csv`): list of the signature proteins detected by the tool and their possible assignment to an ICE or IME element. It is a comma separated table of 48 columns with a one line header. Each line represents a signature protein detected by ICEscreen.
-        - Detected ICEs/IMEs table (`*_detected_ME.tsv`): list of the ICEs and IMEs elements detected by the tool, including information about the signature proteins they contain. It is a tab separated table of 21 columns, the header is at line #3. Information in this file is similar to the output file _withICEIMEIds.csv (option -m) but centered around a list of ICE / IME structures instead of a list of SPs.
+        - Detected Signature Proteins table (`*_detected_SP_withMEIds.csv`): list of the signature proteins detected by the tool and their possible assignment to an ICE or IME element. Each line represents a signature protein detected by ICEscreen.
+        - Detected ICEs/IMEs table (`*_detected_ME.tsv`): list of the ICEs and IMEs elements detected by the tool, including information about the signature proteins they contain. Information in this file is complementary to the _withICEIMEIds.csv file above with each line representing an ICE / IME structures instead of a signature protein.
         - Results summary (`*_detected_ME.summary`): this file summarizes the main parameters and statistics regarding the ICE / IME structures and the SPs.
 
         Other optional and additional output files generated by ICEscreen: