From 07c5dd41e224cdde20aeae0f297c88f3897a0c70 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Wed, 31 Jul 2024 11:29:50 +0200
Subject: [PATCH] add help

---
 src/agat/agat_sp_add_introns/help.txt | 62 +++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100644 src/agat/agat_sp_add_introns/help.txt

diff --git a/src/agat/agat_sp_add_introns/help.txt b/src/agat/agat_sp_add_introns/help.txt
new file mode 100644
index 00000000..48dc1ace
--- /dev/null
+++ b/src/agat/agat_sp_add_introns/help.txt
@@ -0,0 +1,62 @@
+```sh
+agat_sp_add_introns.pl --help
+```
+ 
+  ------------------------------------------------------------------------------
+|   Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0                      |
+|   https://github.com/NBISweden/AGAT                                          |
+|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
+ ------------------------------------------------------------------------------
+
+
+Name:
+    agat_sp_add_introns.pl
+
+Description:
+    The script aims to add intron features to gtf/gff file without intron
+    features.
+
+Usage:
+        agat_sp_add_introns.pl --gff infile --out outFile
+        agat_sp_add_introns.pl --help
+
+Options:
+    --gff, -f, --ref or -reffile
+            Input GTF/GFF file.
+
+    --out, --output or -o
+            Output GFF3 file.
+
+    -c or --config
+            String - Input agat config file. By default AGAT takes as input
+            agat_config.yaml file from the working directory if any,
+            otherwise it takes the orignal agat_config.yaml shipped with
+            AGAT. To get the agat_config.yaml locally type: "agat config
+            --expose". The --config option gives you the possibility to use
+            your own AGAT config file (located elsewhere or named
+            differently).
+
+    --help or -h
+            Display this helpful text.
+
+Feedback:
+  Did you find a bug?:
+    Do not hesitate to report bugs to help us keep track of the bugs and
+    their resolution. Please use the GitHub issue tracking system available
+    at this address:
+
+                https://github.com/NBISweden/AGAT/issues
+
+     Ensure that the bug was not already reported by searching under Issues.
+     If you're unable to find an (open) issue addressing the problem, open a new one.
+     Try as much as possible to include in the issue when relevant:
+     - a clear description,
+     - as much relevant information as possible,
+     - the command used,
+     - a data sample,
+     - an explanation of the expected behaviour that is not occurring.
+
+  Do you want to contribute?:
+    You are very welcome, visit this address for the Contributing
+    guidelines:
+    https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
\ No newline at end of file