From 2d2bdfffde5340fbed34b858bd631225400ff5a7 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 30 Jul 2024 13:44:35 +0200
Subject: [PATCH 01/23] add config

---
 .../agat_convert_genscan2gff/config.vsh.yaml  | 97 +++++++++++++++++++
 1 file changed, 97 insertions(+)
 create mode 100644 src/agat/agat_convert_genscan2gff/config.vsh.yaml

diff --git a/src/agat/agat_convert_genscan2gff/config.vsh.yaml b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
new file mode 100644
index 00000000..c92e63f5
--- /dev/null
+++ b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
@@ -0,0 +1,97 @@
+name: agat_convert_genscan2gff
+namespace: agat
+description: |
+  The script takes a genscan file as input, and will translate it in gff
+  format. The genscan format is described here:
+  http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/gens
+  can.html /!\ vvv Known problem vvv /!\ You must have submited only DNA
+  sequence, wihtout any header!! Indeed the tool expects only DNA
+  sequences and does not crash/warn if an header is submited along the
+  sequence. e.g If you have an header ">seq" s-e-q are seen as the 3 first
+  nucleotides of the sequence. Then all prediction location are shifted
+  accordingly. (checked only on the online version
+  http://argonaute.mit.edu/GENSCAN.html. I don't know if there is the same
+  problem elsewhere.) /!\ ^^^ Known problem ^^^^ /!\
+keywords: [gene annotations, GFF conversion]
+links:
+  homepage: https://github.com/NBISweden/AGAT
+  documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_genscan2gff.html
+  issue_tracker: https://github.com/NBISweden/AGAT/issues
+  repository: https://github.com/NBISweden/AGAT
+references: 
+  doi: 10.5281/zenodo.3552717
+license: GPL-3.0
+authors:
+  - __merge__: /src/_authors/leila_paquay.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --genscan
+        alternatives: [-g]
+        description: Input genscan bed file that will be converted.
+        type: file
+        required: true
+        direction: input
+  - name: Outputs
+    arguments:       
+      - name: --output
+        alternatives: [-o, --out, --outfile, --gff]
+        description: Output GFF file. If no output file is specified, the output will be written to STDOUT.
+        type: file
+        direction: output
+        required: true
+        example: output.gff
+  - name: Arguments
+    arguments:
+      - name: --source
+        description: |
+          The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]
+        type: string
+        required: false
+        example: Stringtie
+      - name: --primary_tag
+        description: |
+          The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]
+        type: string
+        required: false
+        example: gene
+      - name: --inflate_off
+        description: |
+          By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag). Type of subfeature created based on the inflate_type parameter. If you don't want this inflating behaviour you can deactivate it by using the option --inflate_off.
+        type: boolean_false
+      - name: --inflate_type
+        description: |
+          Feature type (3rd column in gff) created when inflate parameter activated [default: exon].
+        type: string
+        required: false
+        example: exon
+      - name: --verbose
+        description: add verbosity
+        type: boolean_true
+      - name: --config
+        alternatives: [-c]
+        description: |
+          Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original 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).
+        type: file
+        required: false
+        example: custom_agat_config.yaml
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+engines:
+  - type: docker
+    image: quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0
+    setup:
+      - type: docker
+        run: |
+          agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
\ No newline at end of file

From 25ad1b01fae922a948b78f9b48fafdcb2061f1e8 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 30 Jul 2024 13:44:49 +0200
Subject: [PATCH 02/23] add help

---
 src/agat/agat_convert_genscan2gff/help.txt | 95 ++++++++++++++++++++++
 1 file changed, 95 insertions(+)
 create mode 100644 src/agat/agat_convert_genscan2gff/help.txt

diff --git a/src/agat/agat_convert_genscan2gff/help.txt b/src/agat/agat_convert_genscan2gff/help.txt
new file mode 100644
index 00000000..e465c778
--- /dev/null
+++ b/src/agat/agat_convert_genscan2gff/help.txt
@@ -0,0 +1,95 @@
+```sh
+agat_convert_genscan2gff.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_convert_genscan2gff.pl
+
+Description:
+    The script takes a genscan file as input, and will translate it in gff
+    format. The genscan format is described here:
+    http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/gens
+    can.html /!\ vvv Known problem vvv /!\ You must have submited only DNA
+    sequence, wihtout any header!! Indeed the tool expects only DNA
+    sequences and does not crash/warn if an header is submited along the
+    sequence. e.g If you have an header ">seq" s-e-q are seen as the 3 first
+    nucleotides of the sequence. Then all prediction location are shifted
+    accordingly. (checked only on the online version
+    http://argonaute.mit.edu/GENSCAN.html. I don't know if there is the same
+    pronlem elsewhere.) /!\ ^^^ Known problem ^^^^ /!\
+
+Usage:
+        agat_convert_genscan2gff.pl --genscan infile.bed [ -o outfile ]
+        agat_convert_genscan2gff.pl -h
+
+Options:
+    --genscan or -g
+            Input genscan bed file that will be convert.
+
+    --source
+            The source informs about the tool used to produce the data and
+            is stored in 2nd field of a gff file. Example:
+            Stringtie,Maker,Augustus,etc. [default: data]
+
+    --primary_tag
+            The primary_tag corresponf to the data type and is stored in 3rd
+            field of a gff file. Example: gene,mRNA,CDS,etc. [default: gene]
+
+    --inflate_off
+            By default we inflate the block fields (blockCount, blockSizes,
+            blockStarts) to create subfeatures of the main feature
+            (primary_tag). Type of subfeature created based on the
+            inflate_type parameter. If you don't want this inflating
+            behaviour you can deactivate it by using the option
+            --inflate_off.
+
+    --inflate_type
+            Feature type (3rd column in gff) created when inflate parameter
+            activated [default: exon].
+
+    --verbose
+            add verbosity
+
+    -o , --output , --out , --outfile or --gff
+            Output GFF file. If no output file is specified, the output will
+            be written to STDOUT.
+
+    -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).
+
+    -h or --help
+            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

From 00e8fbc8a39ac5ecbf380a4d688aa637a14bc239 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 30 Jul 2024 13:45:34 +0200
Subject: [PATCH 03/23] add test data and expected output adn the script to
 obtain them

---
 .../test_data/agat_convert_genscan2gff_1.gff  |  25 ++++
 .../test_data/script.sh                       |  11 ++
 .../test_data/test.genscan                    | 127 ++++++++++++++++++
 3 files changed, 163 insertions(+)
 create mode 100644 src/agat/agat_convert_genscan2gff/test_data/agat_convert_genscan2gff_1.gff
 create mode 100755 src/agat/agat_convert_genscan2gff/test_data/script.sh
 create mode 100644 src/agat/agat_convert_genscan2gff/test_data/test.genscan

diff --git a/src/agat/agat_convert_genscan2gff/test_data/agat_convert_genscan2gff_1.gff b/src/agat/agat_convert_genscan2gff/test_data/agat_convert_genscan2gff_1.gff
new file mode 100644
index 00000000..695fb46c
--- /dev/null
+++ b/src/agat/agat_convert_genscan2gff/test_data/agat_convert_genscan2gff_1.gff
@@ -0,0 +1,25 @@
+##gff-version 3
+unknown	genscan	gene	2223	4605	75.25	+	.	ID=gene_1
+unknown	genscan	mRNA	2223	4605	75.25	+	.	ID=mrna_1;Parent=gene_1
+unknown	genscan	exon	2223	3020	75.25	+	.	ID=exon_1;Parent=mrna_1
+unknown	genscan	exon	4249	4605	13.03	+	.	ID=exon_2;Parent=mrna_1
+unknown	genscan	CDS	2223	3020	75.25	+	0	ID=cds_1;Parent=mrna_1
+unknown	genscan	CDS	4249	4605	13.03	+	0	ID=cds_2;Parent=mrna_1
+unknown	genscan	gene	6829	8789	20.06	-	.	ID=gene_2
+unknown	genscan	mRNA	6829	8789	20.06	-	.	ID=mrna_2;Parent=gene_2
+unknown	genscan	exon	6829	7297	20.06	-	.	ID=exon_3;Parent=mrna_2
+unknown	genscan	exon	7730	7888	12.78	-	.	ID=exon_4;Parent=mrna_2
+unknown	genscan	exon	8029	8185	7.45	-	.	ID=exon_5;Parent=mrna_2
+unknown	genscan	exon	8278	8546	17.45	-	.	ID=exon_6;Parent=mrna_2
+unknown	genscan	exon	8647	8789	18.65	-	.	ID=exon_7;Parent=mrna_2
+unknown	genscan	CDS	6829	7297	20.06	-	1	ID=cds_3;Parent=mrna_2
+unknown	genscan	CDS	7730	7888	12.78	-	1	ID=cds_4;Parent=mrna_2
+unknown	genscan	CDS	8029	8185	7.45	-	2	ID=cds_5;Parent=mrna_2
+unknown	genscan	CDS	8278	8546	17.45	-	1	ID=cds_6;Parent=mrna_2
+unknown	genscan	CDS	8647	8789	18.65	-	0	ID=cds_7;Parent=mrna_2
+unknown	genscan	gene	10209	11924	16.18	+	.	ID=gene_3
+unknown	genscan	mRNA	10209	11924	16.18	+	.	ID=mrna_3;Parent=gene_3
+unknown	genscan	exon	10209	11313	16.18	+	.	ID=exon_8;Parent=mrna_3
+unknown	genscan	exon	11850	11924	3.27	+	.	ID=exon_9;Parent=mrna_3
+unknown	genscan	CDS	10209	11313	16.18	+	0	ID=cds_8;Parent=mrna_3
+unknown	genscan	CDS	11850	11924	3.27	+	2	ID=cds_9;Parent=mrna_3
diff --git a/src/agat/agat_convert_genscan2gff/test_data/script.sh b/src/agat/agat_convert_genscan2gff/test_data/script.sh
new file mode 100755
index 00000000..c1693653
--- /dev/null
+++ b/src/agat/agat_convert_genscan2gff/test_data/script.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+# clone repo
+if [ ! -d /tmp/agat_source ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/NBISweden/AGAT /tmp/agat_source
+fi
+
+# copy test data
+cp -r /tmp/agat_source/t/scripts_output/in/test.genscan src/agat/agat_convert_genscan2gff/test_data/test.genscan
+cp -r /tmp/agat_source/t/scripts_output/out/agat_convert_genscan2gff_1.gff src/agat/agat_convert_genscan2gff/test_data/agat_convert_genscan2gff_1.gff
+
diff --git a/src/agat/agat_convert_genscan2gff/test_data/test.genscan b/src/agat/agat_convert_genscan2gff/test_data/test.genscan
new file mode 100644
index 00000000..a88037db
--- /dev/null
+++ b/src/agat/agat_convert_genscan2gff/test_data/test.genscan
@@ -0,0 +1,127 @@
+GENSCAN 1.0	Date run:  7-Mar-120	Time: 14:46:49
+
+
+
+Sequence /tmp/03_07_20-14:46:49.fasta : 12217 bp : 42.83% C+G : Isochore 1 ( 0 - 43 C+G%)
+
+
+
+Parameter matrix: HumanIso.smat
+
+
+
+Predicted genes/exons:
+
+
+
+Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
+
+----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
+
+
+
+ 1.01 Init +   2223   3020  798  2  0   55    2   924 0.940  75.25
+
+ 1.02 Term +   4249   4605  357  0  0   26   38   307 0.976  13.03
+
+ 1.03 PlyA +   4711   4716    6                              -0.45
+
+
+
+ 2.06 PlyA -   4852   4847    6                              -0.45
+
+ 2.05 Term -   7297   6829  469  0  1   13   42   387 0.281  20.06
+
+ 2.04 Intr -   7888   7730  159  0  0   85   93   144 0.998  12.78
+
+ 2.03 Intr -   8185   8029  157  2  1   65   60   144 0.787   7.45
+
+ 2.02 Intr -   8546   8278  269  1  2   36   65   287 0.946  17.45
+
+ 2.01 Init -   8789   8647  143  2  2   94   96   176 0.550  18.65
+
+ 2.00 Prom -   9720   9681   40                              -6.55
+
+
+
+ 3.00 Prom +  10160  10199   40                             -11.84
+
+ 3.01 Init +  10209  11313 1105  2  1   66   57   269 0.512  16.18
+
+ 3.02 Intr +  11850  11924   75  1  0   80   86    57 0.507   3.27
+
+
+
+Suboptimal exons with probability > 1.000
+
+
+
+Exnum Type S .Begin ...End .Len Fr Ph B/Ac Do/T CodRg P.... Tscr..
+
+----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
+
+
+
+NO EXONS FOUND AT GIVEN PROBABILITY CUTOFF
+
+
+
+
+
+Predicted peptide sequence(s):
+
+
+
+
+
+>/tmp/03_03_20-07:33:11.fasta|GENSCAN_predicted_peptide_1|384_aa
+
+MSSKNKVSKQDIDSIVESLMKKQKSYFEPRLAQIQQVGMENVQKLSAIHAELALLTASIS
+
+TVKSDVDKLKCKVENNFSAIDGHDQAFGELELKMADMEDRSRRCNIRVIGLKERLEGFNA
+
+IQYLTHSLPKWFPALADVPVEVMSAHRIYSDAKRGDNRTLIFNVLRYTTRQAILRAAKKD
+
+PLSVDDRKVRFSPDYSNFTVKRCQAFHQAKDAARNKCLDFFLLYPATLKIKEGAQYRSFT
+
+SPKEAEDYVNSAASNHAATPASPRQHGTILTIYRRIHSLYDGERARKIQLLEQAASVALT
+
+GDNWTSVRNDNYLGVTAHFIDNVWKLRCFALEVKKKKKHSRHTAEDCAEEFIDVSNRWEI
+
+NGKLTTLGTDSALIMLAAARLLPF
+
+
+
+>/tmp/03_03_20-07:33:11.fasta|GENSCAN_predicted_peptide_2|398_aa
+
+MASTMPSSSSTEDEENTPECLNKDHYHFHHYTMEYIQDKPTNVARVGGFTDKKSIAKVER
+
+CLARERQEATEDHEAIPSTSGATSLTKKLRSRSGLPIAGSGLVLPALCIICQKKEKFINR
+
+AGKRQRDPLSKAETLTVGQLQKAAELKDDQSILLHIKDKDCVALEVQYHKGCYNQYTRFM
+
+TRPEKPEKEQNEPTFDVGYKILCERIIRQRLLVNQEVLRMGQLRMAFIELVKANEGLDAS
+
+NYSIKNLERSRRADAGSQRIQIFDPDQRTPTQWKKFLSEGTKKEALAEFLYVAWKNADLT
+
+IVGKNLCLYIAHTNQCHCVTVKEGVQSVRVVEDLLLFLHAQHAAREHKAVIIKSSDTDVA
+
+VIAVSVQTDLPCSLYVFTGTGNRTRIIDITKVSSANKI
+
+
+
+>/tmp/03_03_20-07:33:11.fasta|GENSCAN_predicted_peptide_3|394_aa
+
+MQRGRAAGINGIPPEFYVAFWEQLSPFFLHMINFSIEKGGFLRDVNTALISLLMKKDKNP
+
+TDCSSYRPLSLLNSDVKIFAKLLPLRLEPHMPELVSSDQTGFIKSRTAADNIRRLLHIIA
+
+AAPGCETPMSVLSLDAMKAFDRLEWSFLWSVLEAMGFISTFIGMVKVLYSNPSARVLTGQ
+
+TFSSLFPVSRSSRQGCPLSPALFVLSLEPLAQAVRLSNLVLPICICDTQHKLSLFADDVI
+
+VFLEHPTQSLPHFLSICEEFRKLSGFKMNWSKSALMHLNDNARKSVTPVNIPLVGQLKYL
+
+GIEVFPSLNQIVKHNYSLAFTNVLKDMDRWISLPMSIQARISIIKMNGLPRIHFVSSMVP
+
+LPPPSDYWIKISAQGVRCPLAKPFTHSPYSKTKX

From 918a17debf5642cdb1c53a659fa351af9e9a19ee Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 30 Jul 2024 13:45:44 +0200
Subject: [PATCH 04/23] add running script

---
 src/agat/agat_convert_genscan2gff/script.sh | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 src/agat/agat_convert_genscan2gff/script.sh

diff --git a/src/agat/agat_convert_genscan2gff/script.sh b/src/agat/agat_convert_genscan2gff/script.sh
new file mode 100644
index 00000000..e49050fc
--- /dev/null
+++ b/src/agat/agat_convert_genscan2gff/script.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# unset flags
+[[ "$par_inflate_off" == "true" ]] && unset par_inflate_off
+[[ "$par_verbose" == "false" ]] && unset par_verbose
+
+# run agat_convert_genscan2gff
+agat_convert_genscan2gff.pl \
+  --genscan "$par_genscan" \
+  --output "$par_output" \
+  ${par_source:+--source "${par_source}"} \
+  ${par_primary_tag:+--primary_tag "${par_primary_tag}"} \
+  ${par_inflate_off:+--inflate_off} \
+  ${par_inflate_type:+--inflate_type "${par_inflate_type}"} \
+  ${par_verbose:+--verbose} \
+  ${par_config:+--config "${par_config}"}
\ No newline at end of file

From ea05f34b8c93e3d8418d79c633bdbd2d88e421a0 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 30 Jul 2024 13:45:51 +0200
Subject: [PATCH 05/23] add test script

---
 src/agat/agat_convert_genscan2gff/test.sh | 27 +++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 src/agat/agat_convert_genscan2gff/test.sh

diff --git a/src/agat/agat_convert_genscan2gff/test.sh b/src/agat/agat_convert_genscan2gff/test.sh
new file mode 100644
index 00000000..0efb56e1
--- /dev/null
+++ b/src/agat/agat_convert_genscan2gff/test.sh
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+test_dir="${meta_resources_dir}/test_data"
+out_dir="${meta_resources_dir}/out_data"
+
+echo "> Run $meta_name with test data"
+"$meta_executable" \
+  --genscan "$test_dir/test.genscan" \
+  --output "$out_dir/output.gff" 
+
+echo ">> Checking output"
+[ ! -f "output.gff" ] && echo "Output file output.gtf does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "output.gff" ] && echo "Output file output.gtf is empty" && exit 1
+
+echo ">> Check if output matches expected output"
+diff "$out_dir/output.gff" "$test_dir/agat_convert_genscan2gff_1.gff"
+if [ $? -ne 0 ]; then
+  echo "Output file output.gff does not match expected output"
+  exit 1
+fi
+
+echo "> Test successful"
\ No newline at end of file

From 488bbd32834554993e755958443739342c69a005 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 30 Jul 2024 13:52:04 +0200
Subject: [PATCH 06/23] update changelog

---
 CHANGELOG.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c4575cb9..b1e45091 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,9 @@
 
 * `agat/agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
 
+* `agat/agat_convert_genscan2gff`: convert a genscan file into a GFF file (PR #100).
+
+
 ## MINOR CHANGES
 
 * `busco` components: update BUSCO to `5.7.1` (PR #72).

From 18ef1524fa2bcce00adcf5c3666cd35e926d3be7 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Tue, 30 Jul 2024 13:52:22 +0200
Subject: [PATCH 07/23] cleanup

---
 src/agat/agat_convert_genscan2gff/help.txt | 1 -
 src/agat/agat_convert_genscan2gff/test.sh  | 4 ++--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/agat/agat_convert_genscan2gff/help.txt b/src/agat/agat_convert_genscan2gff/help.txt
index e465c778..8a9e9f52 100644
--- a/src/agat/agat_convert_genscan2gff/help.txt
+++ b/src/agat/agat_convert_genscan2gff/help.txt
@@ -7,7 +7,6 @@ agat_convert_genscan2gff.pl --help
 |   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
  ------------------------------------------------------------------------------
 
-
 Name:
     agat_convert_genscan2gff.pl
 
diff --git a/src/agat/agat_convert_genscan2gff/test.sh b/src/agat/agat_convert_genscan2gff/test.sh
index 0efb56e1..60f0bdc1 100644
--- a/src/agat/agat_convert_genscan2gff/test.sh
+++ b/src/agat/agat_convert_genscan2gff/test.sh
@@ -12,10 +12,10 @@ echo "> Run $meta_name with test data"
   --output "$out_dir/output.gff" 
 
 echo ">> Checking output"
-[ ! -f "output.gff" ] && echo "Output file output.gtf does not exist" && exit 1
+[ ! -f "output.gff" ] && echo "Output file output.gff does not exist" && exit 1
 
 echo ">> Check if output is empty"
-[ ! -s "output.gff" ] && echo "Output file output.gtf is empty" && exit 1
+[ ! -s "output.gff" ] && echo "Output file output.gff is empty" && exit 1
 
 echo ">> Check if output matches expected output"
 diff "$out_dir/output.gff" "$test_dir/agat_convert_genscan2gff_1.gff"

From 0daefb5f5a4bdd8f7951c1d9d627c628c3886c5c Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Wed, 31 Jul 2024 10:07:26 +0200
Subject: [PATCH 08/23] fix tests

---
 src/agat/agat_convert_genscan2gff/test.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/agat/agat_convert_genscan2gff/test.sh b/src/agat/agat_convert_genscan2gff/test.sh
index 60f0bdc1..8dfad3a5 100644
--- a/src/agat/agat_convert_genscan2gff/test.sh
+++ b/src/agat/agat_convert_genscan2gff/test.sh
@@ -12,10 +12,10 @@ echo "> Run $meta_name with test data"
   --output "$out_dir/output.gff" 
 
 echo ">> Checking output"
-[ ! -f "output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
 
 echo ">> Check if output is empty"
-[ ! -s "output.gff" ] && echo "Output file output.gff is empty" && exit 1
+[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
 
 echo ">> Check if output matches expected output"
 diff "$out_dir/output.gff" "$test_dir/agat_convert_genscan2gff_1.gff"

From 98cb70639540b91b0432b2d762c778202c54d91e Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 08:38:28 +0200
Subject: [PATCH 09/23] format description

---
 src/agat/agat_convert_genscan2gff/config.vsh.yaml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/agat/agat_convert_genscan2gff/config.vsh.yaml b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
index c92e63f5..5d1b3a10 100644
--- a/src/agat/agat_convert_genscan2gff/config.vsh.yaml
+++ b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
@@ -2,16 +2,16 @@ name: agat_convert_genscan2gff
 namespace: agat
 description: |
   The script takes a genscan file as input, and will translate it in gff
-  format. The genscan format is described here:
-  http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/gens
-  can.html /!\ vvv Known problem vvv /!\ You must have submited only DNA
-  sequence, wihtout any header!! Indeed the tool expects only DNA
+  format. The genscan format is described [here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html).
+  
+  **Known problem** 
+
+  You must have submited only DNA sequence, without any header!! Indeed the tool expects only DNA
   sequences and does not crash/warn if an header is submited along the
   sequence. e.g If you have an header ">seq" s-e-q are seen as the 3 first
   nucleotides of the sequence. Then all prediction location are shifted
-  accordingly. (checked only on the online version
-  http://argonaute.mit.edu/GENSCAN.html. I don't know if there is the same
-  problem elsewhere.) /!\ ^^^ Known problem ^^^^ /!\
+  accordingly. (checked only on the [online version](http://argonaute.mit.edu/GENSCAN.html). 
+  I don't know if there is the same problem elsewhere.)
 keywords: [gene annotations, GFF conversion]
 links:
   homepage: https://github.com/NBISweden/AGAT

From c21ae867dbf9794a6deacf882f090c2dc632f8f6 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 08:40:27 +0200
Subject: [PATCH 10/23] remove unused argument --inflate-off

---
 src/agat/agat_convert_genscan2gff/config.vsh.yaml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/src/agat/agat_convert_genscan2gff/config.vsh.yaml b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
index 5d1b3a10..741dd3dd 100644
--- a/src/agat/agat_convert_genscan2gff/config.vsh.yaml
+++ b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
@@ -57,10 +57,6 @@ argument_groups:
         type: string
         required: false
         example: gene
-      - name: --inflate_off
-        description: |
-          By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag). Type of subfeature created based on the inflate_type parameter. If you don't want this inflating behaviour you can deactivate it by using the option --inflate_off.
-        type: boolean_false
       - name: --inflate_type
         description: |
           Feature type (3rd column in gff) created when inflate parameter activated [default: exon].

From 4e3a98c1a4d98f217fe332d0c0bbb908dbf774ef Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 08:47:46 +0200
Subject: [PATCH 11/23] update --config description

---
 src/agat/agat_convert_genscan2gff/config.vsh.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/agat/agat_convert_genscan2gff/config.vsh.yaml b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
index 741dd3dd..3c1725d9 100644
--- a/src/agat/agat_convert_genscan2gff/config.vsh.yaml
+++ b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
@@ -69,7 +69,7 @@ argument_groups:
       - name: --config
         alternatives: [-c]
         description: |
-          Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original 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).
+          AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).        
         type: file
         required: false
         example: custom_agat_config.yaml

From 3612a65471dc255a81db978d40c1d87dfb064e60 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 08:48:02 +0200
Subject: [PATCH 12/23] add requirements

---
 src/agat/agat_convert_genscan2gff/config.vsh.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/agat/agat_convert_genscan2gff/config.vsh.yaml b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
index 3c1725d9..c183082b 100644
--- a/src/agat/agat_convert_genscan2gff/config.vsh.yaml
+++ b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
@@ -21,6 +21,8 @@ links:
 references: 
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
+requirements:
+  - commands: [agat]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]

From d63e2674e821ce8890a5f7880ee1f617f75e7625 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 10:43:31 +0200
Subject: [PATCH 13/23] create temporary directory and clean up on exit

---
 src/agat/agat_convert_genscan2gff/test.sh | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/src/agat/agat_convert_genscan2gff/test.sh b/src/agat/agat_convert_genscan2gff/test.sh
index 8dfad3a5..e05202c4 100644
--- a/src/agat/agat_convert_genscan2gff/test.sh
+++ b/src/agat/agat_convert_genscan2gff/test.sh
@@ -4,21 +4,27 @@
 ## VIASH END
 
 test_dir="${meta_resources_dir}/test_data"
-out_dir="${meta_resources_dir}/out_data"
+
+# create temporary directory and clean up on exit
+TMPDIR=$(mktemp --tmpdir "$meta_temp_dir")
+function clean_up {
+ rm -rf "$TMPDIR"
+}
+trap clean_up EXIT
 
 echo "> Run $meta_name with test data"
 "$meta_executable" \
   --genscan "$test_dir/test.genscan" \
-  --output "$out_dir/output.gff" 
+  --output "$TMPDIR/output.gff" 
 
 echo ">> Checking output"
-[ ! -f "$out_dir/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
+[ ! -f "$TMPDIR/output.gff" ] && echo "Output file output.gff does not exist" && exit 1
 
 echo ">> Check if output is empty"
-[ ! -s "$out_dir/output.gff" ] && echo "Output file output.gff is empty" && exit 1
+[ ! -s "$TMPDIR/output.gff" ] && echo "Output file output.gff is empty" && exit 1
 
 echo ">> Check if output matches expected output"
-diff "$out_dir/output.gff" "$test_dir/agat_convert_genscan2gff_1.gff"
+diff "$TMPDIR/output.gff" "$test_dir/agat_convert_genscan2gff_1.gff"
 if [ $? -ne 0 ]; then
   echo "Output file output.gff does not match expected output"
   exit 1

From 65884578561c262a285f8dc80d3504b3c69c8a51 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 10:45:28 +0200
Subject: [PATCH 14/23] add GENSCAN in keywords

---
 src/agat/agat_convert_genscan2gff/config.vsh.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/agat/agat_convert_genscan2gff/config.vsh.yaml b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
index c183082b..512445ef 100644
--- a/src/agat/agat_convert_genscan2gff/config.vsh.yaml
+++ b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
@@ -1,8 +1,8 @@
 name: agat_convert_genscan2gff
 namespace: agat
 description: |
-  The script takes a genscan file as input, and will translate it in gff
-  format. The genscan format is described [here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html).
+  The script takes a GENSCAN file as input, and will translate it in gff
+  format. The GENSCAN format is described [here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html).
   
   **Known problem** 
 
@@ -12,7 +12,7 @@ description: |
   nucleotides of the sequence. Then all prediction location are shifted
   accordingly. (checked only on the [online version](http://argonaute.mit.edu/GENSCAN.html). 
   I don't know if there is the same problem elsewhere.)
-keywords: [gene annotations, GFF conversion]
+keywords: [gene annotations, GFF conversion, GENSCAN]
 links:
   homepage: https://github.com/NBISweden/AGAT
   documentation: https://agat.readthedocs.io/en/latest/tools/agat_convert_genscan2gff.html

From 11ce152a9f785690f086e6ee47c332aed3c5a456 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 11:08:29 +0200
Subject: [PATCH 15/23] add set -e to test

---
 src/agat/agat_convert_genscan2gff/test.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/agat/agat_convert_genscan2gff/test.sh b/src/agat/agat_convert_genscan2gff/test.sh
index e05202c4..39b0376e 100644
--- a/src/agat/agat_convert_genscan2gff/test.sh
+++ b/src/agat/agat_convert_genscan2gff/test.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+set -e
+
 ## VIASH START
 ## VIASH END
 

From 3f646ba7c9a0441d66396208f1e0df58ca1c946d Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 11:15:58 +0200
Subject: [PATCH 16/23] fix create temporary directory

---
 src/agat/agat_convert_genscan2gff/test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/agat/agat_convert_genscan2gff/test.sh b/src/agat/agat_convert_genscan2gff/test.sh
index 39b0376e..798f8251 100644
--- a/src/agat/agat_convert_genscan2gff/test.sh
+++ b/src/agat/agat_convert_genscan2gff/test.sh
@@ -8,7 +8,7 @@ set -e
 test_dir="${meta_resources_dir}/test_data"
 
 # create temporary directory and clean up on exit
-TMPDIR=$(mktemp --tmpdir "$meta_temp_dir")
+TMPDIR=$(mktemp -d --tmpdir "$meta_temp_dir")
 function clean_up {
  rm -rf "$TMPDIR"
 }

From c471b25afbff5465ab4e3c38e5d972fc1dfb622c Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 13:35:01 +0200
Subject: [PATCH 17/23] add set -eo pipefail to test

---
 src/agat/agat_convert_genscan2gff/test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/agat/agat_convert_genscan2gff/test.sh b/src/agat/agat_convert_genscan2gff/test.sh
index 798f8251..7f818b06 100644
--- a/src/agat/agat_convert_genscan2gff/test.sh
+++ b/src/agat/agat_convert_genscan2gff/test.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -e
+set -eo pipefail
 
 ## VIASH START
 ## VIASH END

From e4a814fd285460338d9a96152ba3cda15f26049d Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 13:37:00 +0200
Subject: [PATCH 18/23] add set -eo pipefail to script

---
 src/agat/agat_convert_genscan2gff/script.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/agat/agat_convert_genscan2gff/script.sh b/src/agat/agat_convert_genscan2gff/script.sh
index e49050fc..38afb084 100644
--- a/src/agat/agat_convert_genscan2gff/script.sh
+++ b/src/agat/agat_convert_genscan2gff/script.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+set -eo pipefail
+
 ## VIASH START
 ## VIASH END
 

From 30fd75ef1addf983c82f3d9efd7bd505b7805290 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 13:38:15 +0200
Subject: [PATCH 19/23] fix create temporary directory

---
 src/agat/agat_convert_genscan2gff/test.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/agat/agat_convert_genscan2gff/test.sh b/src/agat/agat_convert_genscan2gff/test.sh
index 7f818b06..a4eda31f 100644
--- a/src/agat/agat_convert_genscan2gff/test.sh
+++ b/src/agat/agat_convert_genscan2gff/test.sh
@@ -8,9 +8,9 @@ set -eo pipefail
 test_dir="${meta_resources_dir}/test_data"
 
 # create temporary directory and clean up on exit
-TMPDIR=$(mktemp -d --tmpdir "$meta_temp_dir")
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
 function clean_up {
- rm -rf "$TMPDIR"
+ [[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
 }
 trap clean_up EXIT
 

From 22a98f047d27d87112dd9fc095ce0f5222a81c7a Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 14:08:16 +0200
Subject: [PATCH 20/23] update --config description

---
 src/agat/agat_convert_genscan2gff/config.vsh.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/agat/agat_convert_genscan2gff/config.vsh.yaml b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
index 512445ef..2adce1da 100644
--- a/src/agat/agat_convert_genscan2gff/config.vsh.yaml
+++ b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
@@ -71,7 +71,7 @@ argument_groups:
       - name: --config
         alternatives: [-c]
         description: |
-          AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).        
+          AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).
         type: file
         required: false
         example: custom_agat_config.yaml

From 1a1b75036d867c126eee9de3e9d327eda6700d04 Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 15:10:42 +0200
Subject: [PATCH 21/23] cleanup changelog

---
 CHANGELOG.md | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fb1c2729..cc935b38 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,18 +21,14 @@
 
 * `agat`:
   - `agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
-  - `/agat_convert_bed2gff`: convert bed file to gff format (PR #97).
+  - `agat_convert_bed2gff`: convert bed file to gff format (PR #97).
+  - `agat_convert_embl2gff`: convert an EMBL file into GFF format (PR #99).
+  - `agat_convert_genscan2gff`: convert a genscan file into a GFF file (PR #100).
 
 * `bedtools`:
   - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).
   - `bedtools/bedtools_sort`: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98).
 
-
-* `agat/agat_convert_embl2gff`: convert an EMBL file into GFF format (PR #99).
-
-* `agat/agat_convert_genscan2gff`: convert a genscan file into a GFF file (PR #100).
-
-
 ## MINOR CHANGES
 
 * `busco` components: update BUSCO to `5.7.1` (PR #72).

From 8895d08d6f71c420145ffc1ff3000c3ceeed8b8e Mon Sep 17 00:00:00 2001
From: Leila011 <leilapaquay@gmail.com>
Date: Mon, 19 Aug 2024 15:18:23 +0200
Subject: [PATCH 22/23] cleanup changelog

---
 CHANGELOG.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cc935b38..5b63fbb1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,10 +20,10 @@
                 based on a provided sequence IDs or region coordinates file (PR #85).
 
 * `agat`:
-  - `agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
-  - `agat_convert_bed2gff`: convert bed file to gff format (PR #97).
-  - `agat_convert_embl2gff`: convert an EMBL file into GFF format (PR #99).
-  - `agat_convert_genscan2gff`: convert a genscan file into a GFF file (PR #100).
+  - `agat/agat_convert_sp_gff2gtf`: convert any GTF/GFF file into a proper GTF file (PR #76).
+  - `agat/agat_convert_bed2gff`: convert bed file to gff format (PR #97).
+  - `agat/agat_convert_embl2gff`: convert an EMBL file into GFF format (PR #99).
+  - `agat/agat_convert_genscan2gff`: convert a genscan file into a GFF file (PR #100).
 
 * `bedtools`:
   - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94).

From 1814c3e69455e0cd266f3fbba13386ddd0432d14 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 16 Sep 2024 10:16:55 +0200
Subject: [PATCH 23/23] Update deprecated variable

---
 src/agat/agat_convert_genscan2gff/test.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/agat/agat_convert_genscan2gff/test.sh b/src/agat/agat_convert_genscan2gff/test.sh
index a4eda31f..b666dacf 100644
--- a/src/agat/agat_convert_genscan2gff/test.sh
+++ b/src/agat/agat_convert_genscan2gff/test.sh
@@ -8,7 +8,7 @@ set -eo pipefail
 test_dir="${meta_resources_dir}/test_data"
 
 # create temporary directory and clean up on exit
-TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXX")
 function clean_up {
  [[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
 }
@@ -32,4 +32,4 @@ if [ $? -ne 0 ]; then
   exit 1
 fi
 
-echo "> Test successful"
\ No newline at end of file
+echo "> Test successful"