--- a/icescreen.xml	Sat Apr 02 21:04:43 2022 +0000
+++ b/icescreen.xml	Tue Feb 28 14:10:26 2023 +0000
@@ -1,7 +1,7 @@
 <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>
     <macros>
-        <token name="@TOOL_VERSION@">1.0.4</token>
+        <token name="@TOOL_VERSION@">1.1.1</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
@@ -45,7 +45,7 @@
         ]]>
     </command>
     <inputs>
-        <param name="genome" type="data" format="genbank" label="Input genomes to analyze in Genbank format" help=""/>
+        <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>
@@ -89,10 +89,10 @@
             <output name="detected_me" file="NC_004668_137848_164286_detected_ME.tsv" ftype="tabular" />
             <output name="detected_sp" >
                 <assert_contents>
-                    <has_text text="ICE IME Number" />
+                    <has_text text="ICE_IME_id" />
                     <has_text text="WP_002359295" />
                     <has_text text="VirB4" />
-                    <has_n_columns n="47" />
+                    <has_n_columns n="54" />
                     <has_n_lines n="5" />
                 </assert_contents>
             </output>
@@ -115,10 +115,9 @@
         <test expect_num_outputs="4">
             <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
             <param name="optional_files" value="output_zip_all_files" />
-
             <output name="outzip" >
                 <assert_contents>
-                    <has_archive_member path=".*/*_detected_SP_withMEIds.tsv"><has_text text="ICE IME Number" /></has_archive_member>
+                    <has_archive_member path=".*/*_detected_SP_withMEIds.tsv"><has_text text="ICE_IME_id" /></has_archive_member>
                 </assert_contents>
             </output>
         </test>
@@ -156,11 +155,23 @@
                 </assert_contents>
             </output>
         </test>
+        <test expect_num_outputs="3">
+            <param name="genome" value="genbank/NC_013798_298468_322494_NC_020450_643089_661957.gb" ftype="genbank" />
+            <output name="summary" file="NC_013798_298468_322494_NC_020450_643089_661957_detected_ME.summary" ftype="txt" />
+            <output name="detected_me" file="NC_013798_298468_322494_NC_020450_643089_661957_detected_ME.tsv" ftype="tabular" />
+            <output name="detected_sp" >
+                <assert_contents>
+                    <has_text text="ICE_IME_id" />
+                    <has_text text="WP_044555479.1" />
+                    <has_text text="WP_015426013.1" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
         .. class:: warningmark
 
-        This tool requires *genbank* format.
+        ICEscreen requires input files in genbank format. Multigenbank files (i.e. gbff files featuring multiple genome records back to back) are supported. Each Genbank record must include the ORIGIN nucleotide sequence.
 
 -----
 
@@ -170,7 +181,7 @@
 
         **Main features of ICEscreen**
 
-        - Detection of signature proteins (SPs) of ICEs/IMEs by using blastP on a curated resource.	BlastP allows for an accurate assignment of hits to a given ICE/IME superfamily or family. The curated resource was derived from an analysis of over 120 ICEs and IMEs in Streptococcus genomes by the DINAMIC lab.
+        - Detection of signature proteins (SPs) of ICEs/IMEs by using blastP on a curated resource. BlastP allows for an accurate assignment of hits to a given ICE/IME superfamily or family. The curated resource was derived from an analysis of over 120 ICEs and IMEs in Streptococcus genomes by the DINAMIC lab.
         - Detection of distant homologs of SPs by using HMM profiles of ICEs/IMEs protein families. The HMM profiles have been either imported from trusted resources or created and curated when needed.
         - Detection of the ICE/IME structures: ICEScreen groups together SPs that belong to the same ICE/IME structures to the best of its ability.
         - Delimitation of the elements at the gene or nucleotide level is not yet implemented and still needs manual curation.