--- a/icescreen.xml	Thu Apr 27 11:33:15 2023 +0000
+++ b/icescreen.xml	Sun Feb 23 16:52:24 2025 +0000
@@ -1,13 +1,12 @@
 <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>annotates ICEs and IMEs in Bacillota genomes</description>
+    
     <macros>
-        <token name="@TOOL_VERSION@">1.2.0</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <import>macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">icescreen</requirement>
-        <requirement type="package" version="3.0">zip</requirement>
-    </requirements>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    
     <version_command><![CDATA[
         icescreen --version
         ]]>
@@ -15,50 +14,36 @@
     <command detect_errors="aggressive"><![CDATA[
         #set $gbname = 'galaxy_genbank'
         mkdir -p ./tmp_icescreen/source_genbank
+        && mkdir -p ./tmp_icescreen/icescreen_result
         && ln -s '${genome}' ./tmp_icescreen/source_genbank/${gbname}.gb
         && icescreen
             --galaxy
             --gbdir ./tmp_icescreen/source_genbank
-            --outdir ./tmp_icescreen
-            --mode '${taxonomy.mode}'
+            --outdir ./tmp_icescreen/icescreen_result
+            --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}'
-        && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_SP_withMEIds.tsv > '${detected_sp}'
-        && cat ./tmp_icescreen/ICEscreen_results/results/${gbname}/icescreen_detection_ME/${gbname}_detected_ME.tsv > '${detected_me}'
+            
+        && cat ./tmp_icescreen/icescreen_result/ICEscreen_results/${gbname}/detected_mobile_elements/${gbname}_detected_ME.summary > '${summary}'
+        && cat ./tmp_icescreen/icescreen_result/ICEscreen_results/${gbname}/detected_mobile_elements/${gbname}_detected_SP_withMEIds.tsv > '${detected_sp}'
+        && cat ./tmp_icescreen/icescreen_result/ICEscreen_results/${gbname}/detected_mobile_elements/${gbname}_detected_ME.tsv > '${detected_me}'
 
-        #if "output_annotation_genbank" in $additional_output.optional_files:
-            && mv ./tmp_icescreen/ICEscreen_results/results/${gbname}/visualization_files/${gbname}_icescreen.gb '${gbout}'
-        #end if
-        #if "output_annotation_gff" in $additional_output.optional_files:
-            && mv ./tmp_icescreen/ICEscreen_results/results/${gbname}/visualization_files/${gbname}_icescreen.gff '${gffout}'
-        #end if
-        #if "output_annotation_embl" in $additional_output.optional_files:
-            && mv ./tmp_icescreen/ICEscreen_results/results/${gbname}/visualization_files/${gbname}_icescreen.embl '${emblout}'
-        #end if
-        #if "output_log" in $additional_output.optional_files:
-            && mv ./tmp_icescreen/ICEscreen_log.txt '${log}'
-        #end if
-        #if "output_zip_all_files" in $additional_output.optional_files:
-            && cd ./tmp_icescreen/ICEscreen_results/results/${gbname} && zip --quiet -r - -- . > '${outzip}'
-        #end if
         ]]>
     </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>
+        <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 nucleotide sequence."/>
+        <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">
             <param name="optional_files" type="select" label="Make the following optional files available in the Galaxy history" multiple="true" optional="true" display="checkboxes" >
-                <option value="output_annotation_genbank">Genome annotation in genbank format</option>
-                <option value="output_annotation_gff">Genome annotation in gff format</option>
-                <option value="output_annotation_embl">Genome annotation in embl format</option>
-                <option value="output_zip_all_files">Zip of all final and intermediate results</option>
-                <option value="output_log">ICEscreen log</option>
+                <option value="output_annotation_genbank" selected="false">Annotation in genbank format (full)</option>
+                <option value="output_annotation_gff" selected="false">Annotation in gff format (ICEs and IMEs only)</option>
+                <option value="output_annotation_embl" selected="false">Annotation in embl format (ICEs and IMEs only)</option>
+                <option value="output_tar_gz_intermediate_files" selected="false">Archive of intermediate files</option>
+                <option value="output_log" selected="false">Log file</option>
+                <option value="output_param_conf" selected="false">Param conf file</option>
             </param>
         </section>
     </inputs>
@@ -66,20 +51,23 @@
       <data format="tabular" name="detected_sp" label="${tool.name} on ${on_string}: Signature Proteins table" />
       <data format="tabular" name="detected_me" label="${tool.name} on ${on_string}: ICEs/IMEs table" />
       <data format="txt" name="summary" label="${tool.name} on ${on_string}: results summary" />
-      <data format="genbank" name="gbout" label="${tool.name} on ${on_string}: annotated genbank" >
+      <data format="genbank.gz" name="gbout" from_work_dir="./tmp_icescreen/icescreen_result/ICEscreen_results/galaxy_genbank/detected_mobile_elements/standard_genome_annotation_formats/galaxy_genbank_icescreen.gb.gz" label="${tool.name} on ${on_string}: genbank annotation (full)" >
           <filter>additional_output['optional_files'] and "output_annotation_genbank" in additional_output['optional_files']</filter>
       </data>
-      <data format="gff3" name="gffout" label="${tool.name} on ${on_string}: annotated GFF3" >
+      <data format="gff3.gz" name="gffout" from_work_dir="./tmp_icescreen/icescreen_result/ICEscreen_results/galaxy_genbank/detected_mobile_elements/standard_genome_annotation_formats/galaxy_genbank_icescreen.gff.gz" label="${tool.name} on ${on_string}: GFF3 annotation (ICEs and IMEs only)" >
           <filter>additional_output['optional_files'] and "output_annotation_gff" in additional_output['optional_files']</filter>
       </data>
-      <data format="embl" name="emblout" label="${tool.name} on ${on_string}: annotated EMBL" >
-          <filter>additional_output['optional_files'] and "output_annotation_embl" in additional_output['optional_files']</filter>
+      <data format="embl.gz" name="emblout" from_work_dir="./tmp_icescreen/icescreen_result/ICEscreen_results/galaxy_genbank/detected_mobile_elements/standard_genome_annotation_formats/galaxy_genbank_icescreen.embl.gz" label="${tool.name} on ${on_string}: EMBL annotation (ICEs and IMEs only)" >
+          <filter>additional_output['optional_files'] and "output_annotation_embl" in additional_output['optional_files']</filter>          
+      </data>
+      <data format="tar.gz" name="intermediate_tar_gz" from_work_dir="./tmp_icescreen/icescreen_result/ICEscreen_results/galaxy_genbank/tmp_intermediate_files.tar.gz" label="${tool.name} on ${on_string}: intermediate files archive">
+          <filter>additional_output['optional_files'] and "output_tar_gz_intermediate_files" in additional_output['optional_files']</filter>
       </data>
-      <data format="zip" name="outzip" label="${tool.name} on ${on_string}: all results zipped">
-          <filter>additional_output['optional_files'] and "output_zip_all_files" in additional_output['optional_files']</filter>
+      <data format="txt" name="log" from_work_dir="./tmp_icescreen/ICEscreen_log.txt" label="${tool.name} on ${on_string}: log file" >
+          <filter>additional_output['optional_files'] and "output_log" in additional_output['optional_files']</filter>
       </data>
-      <data format="txt" name="log" label="${tool.name} on ${on_string}: log file" >
-          <filter>additional_output['optional_files'] and "output_log" in additional_output['optional_files']</filter>
+      <data format="gz" name="param_conf" from_work_dir="./tmp_icescreen/icescreen_result/ICEscreen_results/galaxy_genbank/param.conf.gz" label="${tool.name} on ${on_string}: param conf file" >
+          <filter>additional_output['optional_files'] and "output_param_conf" in additional_output['optional_files']</filter>
       </data>
     </outputs>
     <tests>
@@ -100,24 +88,36 @@
         <test expect_num_outputs="4">
             <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
             <param name="optional_files" value="output_annotation_genbank" />
-            <output name="gbout" file="NC_004668_137848_164286_icescreen.gb" ftype="genbank" />
+            <output name="gbout" ftype="genbank.gz">
+                <assert_contents>
+                    <has_size value="19794" delta="100"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="4">
             <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
             <param name="optional_files" value="output_annotation_gff" />
-            <output name="gffout" file="NC_004668_137848_164286_icescreen.gff" ftype="gff3" />
+            <output name="gffout" ftype="gff3.gz">
+                <assert_contents>
+                    <has_size value="794" delta="100"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="4">
             <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
             <param name="optional_files" value="output_annotation_embl" />
-            <output name="emblout" file="NC_004668_137848_164286_icescreen.embl" ftype="embl" />
+            <output name="emblout" ftype="embl.gz">
+                <assert_contents>
+                    <has_size value="1002" delta="100"/>
+                </assert_contents>
+            </output>
         </test>
         <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" >
+            <param name="optional_files" value="output_tar_gz_intermediate_files" />
+            <output name="intermediate_tar_gz" >
                 <assert_contents>
-                    <has_archive_member path=".*/*_detected_SP_withMEIds.tsv"><has_text text="ICE_IME_id" /></has_archive_member>
+                    <has_archive_member path=".*/*_detected_SP.tsv"><has_text text="Is_hit_blast" /></has_archive_member>
                 </assert_contents>
             </output>
         </test>
@@ -126,7 +126,7 @@
             <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" />
@@ -135,22 +135,22 @@
         </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">
+        <test expect_num_outputs="6">
             <param name="genome" value="genbank/NC_004668_137848_164286.gb" ftype="genbank" />
-            <param name="mode" value="firmicutes" />
-            <param name="optional_files" value="output_zip_all_files,output_log" />
+            <param name="phylum" value="bacillota" />
+            <param name="optional_files" value="output_tar_gz_intermediate_files,output_log,output_param_conf" />
             <output name="log" >
                 <assert_contents>
-                    <has_text text="firmicutes" />
+                    <has_text text="bacillota" />
                     <not_has_text text="Error" />
                 </assert_contents>
             </output>
@@ -171,13 +171,13 @@
     <help><![CDATA[
         .. class:: warningmark
 
-        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.
+        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 nucleotide sequence.
 
 -----
 
         **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**
 
@@ -190,24 +190,22 @@
 
         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:
 
-        - Annotated Genbank, EMBL, and GFF3 files: tose files contains the annotations of the original Genbank file in addition to annotations added by ICEscreen such as ICEscreen signature proteins and mobile elements.
-        - All results zipped file: You can download this file locally and unzip it to have the complete output folder generated by the tool, including intermediate processing files. See https://icescreen.migale.inrae.fr for details.
-        - Log file (`*_detected_ME.log`): this file contains the detailed internal details used by ICEscreen to generate the results and logs of each step of the ICEscreen tool pipeline.
+        - Genbank annotation file (full): annotations of the original Genbank file as well as annotations of ICEscreen on ICEs, IMEs, and the detected signature proteins.
+        - EMBL and GFF3 annotation files (ICEs and IMEs only): annotations of ICEscreen on ICEs, IMEs, and the detected signature proteins.
+        - Intermediate files (tar.gz): You can download this file locally and uncompress it to have the intermediate files generated by the tool. See https://icescreen.migale.inrae.fr for details.
+        - Log file (`*_detected_ME.log`): this file contains the log of each step of the ICEscreen pipeline.
+        - Param conf file (`param.conf.gz`): this file contains the configuration parameters related to the ICEscreen run.
 
     ]]>
 
     </help>
-    <citations>
-        <citation type="bibtex">@UNPUBLISHED{Kim07aninterior-point,
-            author = {Julie Lao and Thomas Lacroix and Gérard Guédon and Charles Coluzzi and Nathalie Leblond-Bourget and Hélène Chiapello},
-            title = {"See our latest publication at https://icescreen.migale.inrae.fr."}
-        }
-        </citation>
-    </citations>
+
+    <expand macro="citation"/>
+    
 </tool>