# HG changeset patch
# User iuc
# Date 1706276320 0
# Node ID d45c95f382d3a2e8664189a2c593c09dedeb0458
# Parent  85c9849b429e9277209e4a49aca6ee044e5bc598
planemo upload for repository https://forgemia.inra.fr/ices_imes_analysis/icescreen commit bc68b3c32a23a39507f54cb6b4453676174712d6

diff -r 85c9849b429e -r d45c95f382d3 icescreen.xml
--- 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:
diff -r 85c9849b429e -r d45c95f382d3 test-data/NC_004668_137848_164286_detected_ME.tsv
--- a/test-data/NC_004668_137848_164286_detected_ME.tsv	Tue Oct 31 16:31:33 2023 +0000
+++ b/test-data/NC_004668_137848_164286_detected_ME.tsv	Fri Jan 26 13:38:40 2024 +0000
@@ -1,2 +1,2 @@
-ICE_IME_id	Segment_number	Genome_accession	Category_of_element	Category_of_integrase	Host_ICE_IME_ids	Guest_ICE_IME_ids	Colocalized_ICE_IME_ids	ICEline_format	ICE_consensus_superfamily_SP_conj_module	ICE_consensus_family_SP_conj_module	IME_relaxase_family_domains_blast	HMM_family_SP_conj_module	Integrase_upstream	Integrase_downstream	Relaxase	Coupling_protein	VirB4	List_SP_ordered_genomic_position	Other_potential_SP_conj_module_need_manual_curation_and_review	Other_potential_integrase_need_manual_curation_and_review	Comments_regarding_structure
-ID_1	1	NC_004668.1	Complete ICE (C+R+V+I)	one integrase Tyr	-	-	-	C3.R1:V7.I	Tn916	ICESt3	-	C:TcpA, R:MOBT, V:VirB4	-	EF_RS00760	EF_RS00650	EF_RS00630	EF_RS00720	EF_RS00630, EF_RS00650, EF_RS00720, EF_RS00760	-	-	Downstream integrase EF_RS00760 has been associated to the structure ID_1 pre-merging because it is adjacent to the conj module and there is no upstream/downstream ambiguity. 
+ICE_IME_id	Segment_number	Genome_accession	Category_of_element	Category_of_integrase	Host_ICE_IME_ids	Guest_ICE_IME_ids	Colocalized_ICE_IME_ids	ICEline_format	ICE_consensus_superfamily_SP_conj_module	ICE_consensus_family_SP_conj_module	IME_relaxase_family_domains_blast	HMM_family_SP_conj_module	Integrase_upstream	Integrase_downstream	Relaxase	Coupling_protein	VirB4	List_SP_ordered_genomic_position	Start_of_most_upstream_SP	Stop_of_most_downstream_SP	Other_potential_SP_conj_module_need_manual_curation_and_review	Other_potential_integrase_need_manual_curation_and_review	Comments_regarding_structure
+ID_1	1	NC_004668.1	Complete ICE (C+R+V+I)	one integrase Tyr	-	-	-	C3.R1:V7.I	Tn916	ICESt3	-	C:TcpA, R:MOBT, V:VirB4	-	EF_RS00760	EF_RS00650	EF_RS00630	EF_RS00720	EF_RS00630, EF_RS00650, EF_RS00720, EF_RS00760	1	26439	-	-	Downstream integrase EF_RS00760 has been associated to the structure ID_1 pre-merging because it is adjacent to the conj module and there is no upstream/downstream ambiguity. 
diff -r 85c9849b429e -r d45c95f382d3 test-data/NC_013798_298468_322494_NC_020450_643089_661957_detected_ME.tsv
--- a/test-data/NC_013798_298468_322494_NC_020450_643089_661957_detected_ME.tsv	Tue Oct 31 16:31:33 2023 +0000
+++ b/test-data/NC_013798_298468_322494_NC_020450_643089_661957_detected_ME.tsv	Fri Jan 26 13:38:40 2024 +0000
@@ -1,3 +1,3 @@
-ICE_IME_id	Segment_number	Genome_accession	Category_of_element	Category_of_integrase	Host_ICE_IME_ids	Guest_ICE_IME_ids	Colocalized_ICE_IME_ids	ICEline_format	ICE_consensus_superfamily_SP_conj_module	ICE_consensus_family_SP_conj_module	IME_relaxase_family_domains_blast	HMM_family_SP_conj_module	Integrase_upstream	Integrase_downstream	Relaxase	Coupling_protein	VirB4	List_SP_ordered_genomic_position	Other_potential_SP_conj_module_need_manual_curation_and_review	Other_potential_integrase_need_manual_curation_and_review	Comments_regarding_structure
-ID_1	1	NC_013798.1	Complete ICE (V+C+R+D)	one integrase DDE	-	-	-	V8.C7.R2.D	Tn5252	TnGBS2	-	C:VirD4, R:MOBP, V:VirB4	-	GALLO_RS01755	GALLO_RS01740	GALLO_RS01695	GALLO_RS01650	GALLO_RS01650, GALLO_RS01695, GALLO_RS01740, GALLO_RS01755	-	-	Downstream integrase GALLO_RS01755 has been associated to the structure ID_1 pre-merging because it is adjacent to the conj module and there is no upstream/downstream ambiguity. 
-ID_2	2	NC_020450.1	Complete ICE (C+R+V+I)	one integrase Tyr	-	-	-	C1.R1:V5.I	Tn916	-	-	C:TcpA, R:MOBT, V:VirB4	-	LILO_RS03350	LILO_RS03260	LILO_RS03250	LILO_RS03320	LILO_RS03250, LILO_RS03260, LILO_RS03320, LILO_RS03350	-	-	Downstream integrase LILO_RS03350 has been associated to the structure ID_2 pre-merging because it is adjacent to the conj module and there is no upstream/downstream ambiguity. 
+ICE_IME_id	Segment_number	Genome_accession	Category_of_element	Category_of_integrase	Host_ICE_IME_ids	Guest_ICE_IME_ids	Colocalized_ICE_IME_ids	ICEline_format	ICE_consensus_superfamily_SP_conj_module	ICE_consensus_family_SP_conj_module	IME_relaxase_family_domains_blast	HMM_family_SP_conj_module	Integrase_upstream	Integrase_downstream	Relaxase	Coupling_protein	VirB4	List_SP_ordered_genomic_position	Start_of_most_upstream_SP	Stop_of_most_downstream_SP	Other_potential_SP_conj_module_need_manual_curation_and_review	Other_potential_integrase_need_manual_curation_and_review	Comments_regarding_structure
+ID_1	1	NC_013798.1	Complete ICE (V+C+R+D)	one integrase DDE	-	-	-	V8.C7.R2.D	Tn5252	TnGBS2	-	C:VirD4, R:MOBP, V:VirB4	-	GALLO_RS01755	GALLO_RS01740	GALLO_RS01695	GALLO_RS01650	GALLO_RS01650, GALLO_RS01695, GALLO_RS01740, GALLO_RS01755	2	24026	-	-	Downstream integrase GALLO_RS01755 has been associated to the structure ID_1 pre-merging because it is adjacent to the conj module and there is no upstream/downstream ambiguity. 
+ID_2	2	NC_020450.1	Complete ICE (C+R+V+I)	one integrase Tyr	-	-	-	C1.R1:V5.I	Tn916	-	-	C:TcpA, R:MOBT, V:VirB4	-	LILO_RS03350	LILO_RS03260	LILO_RS03250	LILO_RS03320	LILO_RS03250, LILO_RS03260, LILO_RS03320, LILO_RS03350	2	18868	-	-	Downstream integrase LILO_RS03350 has been associated to the structure ID_2 pre-merging because it is adjacent to the conj module and there is no upstream/downstream ambiguity.