From 061b593597a66929679218f7f368c0491c9a1533 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Thu, 1 Aug 2024 17:19:38 +0200
Subject: [PATCH] handle input --gff has multiple=true

---
 src/agat/agat_sq_stat_basic/config.vsh.yaml |  1 +
 src/agat/agat_sq_stat_basic/script.sh       | 12 ++++++++++--
 src/agat/agat_sq_stat_basic/test.sh         | 12 ++++++------
 3 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/src/agat/agat_sq_stat_basic/config.vsh.yaml b/src/agat/agat_sq_stat_basic/config.vsh.yaml
index 89b0d841..3ba1ef9d 100644
--- a/src/agat/agat_sq_stat_basic/config.vsh.yaml
+++ b/src/agat/agat_sq_stat_basic/config.vsh.yaml
@@ -23,6 +23,7 @@ argument_groups:
           Input GTF/GFF file. Several files can be processed at once: -i file1 -i file2
         type: file
         required: true
+        multiple: true
         direction: input
         example: input.gff
       - name: --genome_size
diff --git a/src/agat/agat_sq_stat_basic/script.sh b/src/agat/agat_sq_stat_basic/script.sh
index 2e11d0d7..038b9592 100644
--- a/src/agat/agat_sq_stat_basic/script.sh
+++ b/src/agat/agat_sq_stat_basic/script.sh
@@ -6,6 +6,14 @@
 # unset flags
 [[ "$par_inflate" == "false" ]] && unset par_inflate
 
+# Convert a list of file names to multiple -gff arguments
+input_files=""
+IFS=";" read -ra file_names <<< "$par_gff"
+for file in "${file_names[@]}"; do
+    input_files+="--gff $file "
+done
+unset IFS
+
 # take care of --genome (can originally be either a fasta file or an integer)
 if [[ -n "$par_genome_size" ]]; then
   genome_arg=$par_genome_size
@@ -15,8 +23,8 @@ fi
 
 # run agat_convert_sp_bed2gff.pl
 agat_sq_stat_basic.pl \
-  --gff "$par_gff" \
+  $input_files \
   ${genome_arg:+--genome "${genome_arg}"} \
-  -o "$par_output" \
+  --output "${par_output}" \
   ${par_inflate:+--inflate} \
   ${par_config:+--config "${par_config}"}
diff --git a/src/agat/agat_sq_stat_basic/test.sh b/src/agat/agat_sq_stat_basic/test.sh
index f3d79222..c99aa912 100644
--- a/src/agat/agat_sq_stat_basic/test.sh
+++ b/src/agat/agat_sq_stat_basic/test.sh
@@ -9,18 +9,18 @@ out_dir="${meta_resources_dir}/out_data"
 echo "> Run $meta_name with test data"
 "$meta_executable" \
   --gff "$test_dir/1.gff" \
-  --output "$out_dir/output.gff" 
-
+  --output "$out_dir/output.txt" 
+  
 echo ">> Checking output"
-[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+[ ! -f "$out_dir/output.txt" ] && echo "Output file output.txt does not exist" && exit 1
 
 echo ">> Check if output is empty"
-[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
+[ ! -s "$out_dir/output.txt" ] && echo "Output file output.txt is empty" && exit 1
 
 echo ">> Check if output matches expected output"
-diff "$out_dir/output.gff" "$test_dir/agat_sq_stat_basic_1.gff"
+diff "$out_dir/output.txt" "$test_dir/agat_sq_stat_basic_1.gff"
 if [ $? -ne 0 ]; then
-  echo "Output file output.gff does not match expected output"
+  echo "Output file output.txt does not match expected output"
   exit 1
 fi