update doc

NBISweden · Jan 7, 2025 · 737a28f · 737a28f
1 parent 6812637
commit 737a28f
Show file tree

Hide file tree

Showing 3 changed files with 51 additions and 4 deletions.
diff --git a/bin/agat_sp_flag_short_introns_ebi.pl b/bin/agat_sp_flag_short_introns_ebi.pl
@@ -183,7 +183,7 @@ =head1 NAME
 
 =head1 DESCRIPTION
 
-By default, the script flags short introns within coding sequences (CDS) with the <pseudo> attribute and change the <product> attribute into a <note> attribute.
+The script flags records that contain short introns (default 10bp) within coding sequences (CDS) with the <pseudo> attribute and changes the <product> attribute into a <note> attribute.
 This is useful for avoiding ERROR messages when submitting data to the EBI.
 (Typical EBI error message: ERROR: Intron usually expected to be at least 10 nt long. Please check the accuracy.)
 

diff --git a/docs/tools/agat_sp_flag_short_introns.md b/docs/tools/agat_sp_flag_short_introns.md
@@ -2,9 +2,10 @@
 
 ## DESCRIPTION
 
-The script flags the short introns with the attribute &lt;pseudo>.
-Is is usefull to avoid ERROR when submiting the data to EBI.
-(Typical EBI error message: ********ERROR: Intron usually expected to be at least 10 nt long. Please check the accuracy)
+Looking at exon features the script flags each feature of a record with the &lt;short_intron> attribute if 
+it contains an intron with a size below the &lt;--intron_size> threshold (10bp by default).
+The value of this attribute will be the size of the shortest intron found under the threshold.
+
 
 ## SYNOPSIS
 

diff --git a/docs/tools/agat_sp_flag_short_introns_ebi.md b/docs/tools/agat_sp_flag_short_introns_ebi.md
@@ -0,0 +1,46 @@
+# agat_sp_flag_short_introns_ebi.pl
+
+## DESCRIPTION
+
+The script flags records that contain short introns (default 10bp) within coding sequences (CDS) with the &lt;pseudo> attribute and changes the &lt;product> attribute into a &lt;note> attribute.
+This is useful for avoiding ERROR messages when submitting data to the EBI.
+(Typical EBI error message: ERROR: Intron usually expected to be at least 10 nt long. Please check the accuracy.)
+
+
+## SYNOPSIS
+
+```
+agat_sp_flag_short_introns_ebi.pl --gff infile --out outfile
+agat_sp_flag_short_introns_ebi.pl --help
+```
+
+## OPTIONS
+
+- **--gff**, **-f**, **--ref** or **-reffile**
+
+    Input GTF/GFF file.
+
+- **--intron_size** or **-i**
+
+    Minimum intron size, default 10. All genes with an intron < of this size will be
+    flagged with the pseudo attribute (the value will be the size of the smallest
+    intron found within the incriminated gene)
+
+- **--out**, **--output** or **-o**
+
+    Output gff3 file where the result will be printed.
+
+- **-v**
+
+    Bolean. Verbose for debugging purpose.
+
+- **-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.
+