try to fix table

NBISweden · Apr 15, 2021 · ca9103c · ca9103c
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diff --git a/docs/tools/agat_convert_bed2gff.md b/docs/tools/agat_convert_bed2gff.md
@@ -3,7 +3,7 @@
 ## DESCRIPTION
 
 The script takes a bed file as input, and will translate it in gff format.
-The BED format is described here: https://genome.ucsc.edu/FAQ/FAQformat.html##format1
+The BED format is described [here](https://genome.ucsc.edu/FAQ/FAQformat.html##format1)
 The script converts 0-based, half-open \[start-1, end) bed file to
 1-based, closed \[start, end\] General Feature Format v3 (GFF3).
 

diff --git a/docs/tools/agat_convert_embl2gff.md b/docs/tools/agat_convert_embl2gff.md
@@ -1,4 +1,4 @@
-# gaas\_converter\_embl2gff.pl
+# agat\_converter\_embl2gff.pl
 
 ## DESCRIPTION
 
@@ -7,7 +7,7 @@ The script takes an EMBL file as input, and will translate it in gff format.
 ## SYNOPSIS
 
 ```
-gaas_converter_embl2gff.pl --embl infile.embl [ -o outfile ]
+agat_converter_embl2gff.pl --embl infile.embl [ -o outfile ]
 ```
 
 ## OPTIONS
@@ -33,4 +33,3 @@ gaas_converter_embl2gff.pl --embl infile.embl [ -o outfile ]
 - **-h** or **--help**
 
     Display this helpful text.
-
diff --git a/docs/topological-sorting-of-gff-features.md b/docs/topological-sorting-of-gff-features.md
@@ -29,13 +29,13 @@ Zhigang Lu has made a nice post about his experience trying to find a way to get
 
 ## Tests summary
 
-| tool      | option in command line | Type of sorting | Comment |
-| ------------- |:-------------:| :-------------:| -------------:|
-[AGAT](https://github.com/NBISweden/AGAT) | / | by chromosomes, by gene position, by type (mRNAs then exon, then CDS then alphabetical feature types; then mRNA2 then exon2, then CDS2 then alphabetical feature2 types) | Fix GFF/GTF if needed |
-[GenomeTools](https://github.com/genometools/genometools) | -sortlines -tidy -retainids | by chromosomes and positions then random feature type | Lines with the same chromosomes and start positions would be placed randomly, so parent feature lines might sometimes be placed after their children lines. |
-[GenomeTools](https://github.com/genometools/genometools) | -retainids | by chromosomes, by gene position, by type (mRNA then children; then mRNA2 then children2), by position (children are sorted by positions) |
-[GFF3sort](https://github.com/billzt/gff3sort) | --precise | by chromosomes and positions then attribute with Parent attribute first.  | move lines with "Parent=" attributes (case insensitive) behind lines without "Parent=" attributes. The goal of GFF3sort is not to obtain a topological sorting but rather getting something that could be indexed optimally by third part tools. |
-[gffread](https://github.com/gpertea/gffread) | | By default, chromosomes are kept in the order they were found. With --sort-alpha parameter the chromosomes (reference sequences) are sorted alphabetically | /!\ Some feature types are lost e.g. `gene`, `three_prime_UTR`, `five_prime_UTR`, etc... |
+tool | option in command line | Type of sorting | Comment
+-- | -- | -- | -- |
+[AGAT](https://github.com/NBISweden/AGAT) | / | by chromosomes, by gene position, by type (mRNAs then exon, then CDS then alphabetical feature types; then mRNA2 then exon2, then CDS2 then alphabetical feature2 types) | Fix GFF/GTF if needed
+[GenomeTools](https://github.com/genometools/genometools) | -sortlines -tidy -retainids | by chromosomes and positions then random feature type | Lines with the same chromosomes and start positions would be placed randomly, so parent feature lines might sometimes be placed after their children lines.
+[GenomeTools](https://github.com/genometools/genometools) | -retainids | by chromosomes, by gene position, by type (mRNA then children; then mRNA2 then children2), by position (children are sorted by positions) 
+[GFF3sort](https://github.com/billzt/gff3sort) | --precise | by chromosomes and positions then attribute with Parent attribute first.  | move lines with "Parent=" attributes (case insensitive) behind lines without "Parent=" attributes. The goal of GFF3sort is not to obtain a topological sorting but rather getting something that could be indexed optimally by third part tools.
+[gffread](https://github.com/gpertea/gffread) | | By default, chromosomes are kept in the order they were found. With --sort-alpha parameter the chromosomes (reference sequences) are sorted alphabetically | /!\ Some feature types are lost e.g. `gene`, `three_prime_UTR`, `five_prime_UTR`, etc...
 
 ## Example 1