--- a/repenrich.xml	Sat Mar 09 22:32:46 2024 +0000
+++ b/repenrich.xml	Mon Mar 18 09:39:44 2024 +0000
@@ -30,16 +30,18 @@
         #else:
             #if $seq_method.input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):
                 gunzip < '$seq_method.input_fastq' > '${input_base}.fastq' &&
-                gunzip < '$seq_method.input2_fastq' > '${input_base}_2.fastq' &&                
+                gunzip < '$seq_method.input2_fastq' > '${input_base}_2.fastq' &&
             #else:
                 ln -f -s '$seq_method.input_fastq' '${input_base}.fastq' &&
                 ln -f -s '$seq_method.input2_fastq' '${input_base}_2.fastq' &&
             #end if
         #end if
-        
         ln -f -s '$genome' '${baseReference}.fa' &&
         bowtie-build '$genome' ${baseReference} &&
-        python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} &&
+        python $__tool_directory__/RepEnrich_setup.py
+            --annotation_file $repeatmasker
+            --genomefasta ${baseReference}.fa
+            --setup_folder setup_folder_${baseReference} &&
         #if $seq_method.seq_method_list == "single-read":
             bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&
             TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&
@@ -56,9 +58,25 @@
         samtools view -@ \${GALAXY_SLOTS:-4} -bS '${input_base}_unique.sam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o '${input_base}_unique.bam' &&
         samtools index ${input_base}_unique.bam &&
         #if $seq_method.seq_method_list == "single-read":
-            python $__tool_directory__/RepEnrich.py $repeatmasker ${input_base} ${input_base} setup_folder_${baseReference} ${input_base}_multimap.fastq ${input_base}_unique.bam --cpus "\${GALAXY_SLOTS:-4}" &&
+            python $__tool_directory__/RepEnrich.py
+                --annotation_file $repeatmasker
+                --outputfolder ${input_base}
+                --outputprefix ${input_base}
+                --setup_folder setup_folder_${baseReference}
+                --fastqfile ${input_base}_multimap.fastq
+                --alignment_bam ${input_base}_unique.bam
+                --cpus "\${GALAXY_SLOTS:-4}" &&
         #else:
-            python $__tool_directory__/RepEnrich.py $repeatmasker ${input_base} ${input_base} setup_folder_${baseReference} ${input_base}_multimap_1.fastq --fastqfile2 ${input_base}_multimap_2.fastq ${input_base}_unique.bam --cpus "\${GALAXY_SLOTS:-4}" --pairedend TRUE &&
+            python $__tool_directory__/RepEnrich.py
+                --annotation_file $repeatmasker
+                --outputfolder ${input_base}
+                --outputprefix ${input_base}
+                --setup_folder setup_folder_${baseReference}
+                --fastqfile ${input_base}_multimap_1.fastq
+                --fastqfile2 ${input_base}_multimap_2.fastq
+                --alignment_bam ${input_base}_unique.bam
+                --cpus "\${GALAXY_SLOTS:-4}"
+                --pairedend TRUE &&
         #end if
         cp $input_base/${input_base}_class_fraction_counts.txt class_fraction_counts.tabular &&
         cp $input_base/${input_base}_family_fraction_counts.txt family_fraction_counts.tabular &&
@@ -227,15 +245,10 @@
 
 .. class:: infomark
 
-For more information on the tools, please visit our `code repository`_.
-
-If you would like to give us feedback or you run into any trouble, please send an email to artbio.ibps@gmail.com 
-
-This tool wrapper is developed by the `ARTbio team`_ at the `Institut de Biologie Paris Seine (IBPS)`_.
+For more information on the tools, or giving us feedback, please visit our `code repository`_.
 
 .. _code repository: https://github.com/ARTbio/tools-artbio/tree/master/tools/
 .. _ARTbio team: http://artbio.fr
-.. _Institut de Biologie Paris Seine (IBPS): http://www.ibps.upmc.fr/en/core-facilities/bioinformatics
 
     </help>