Fixes to docs or parsers (#529)

* fix genscan2gff

* fix docs or parsers

Author: rcannood

bin/agat_convert_genscan2gff.pl

@@ -276,17 +276,11 @@ =head1 OPTIONS
 
 Input genscan bed file that will be convert.
 
-=item B<--source>
+=item B<--seqid>
 
-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]
+String - Sequence ID. [default: unknown]
 
-=item B<--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]
-
-=item B<--verbose>
+=item B<--verbose> or B<-v>
 
 add verbosity
 

bin/agat_convert_mfannot2gff.pl

@@ -432,6 +432,10 @@ =head1 OPTIONS
 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).
 
+=item B<--verbose> or B<-v>
+
+add verbosity
+
 =item B<-h> or B<--help>
 
 Display this helpful text.

bin/agat_convert_sp_gff2gtf.pl

@@ -132,7 +132,7 @@ =head1 OPTIONS
 
 GTF1 (5 feature types accepted): CDS, start_codon, stop_codon, exon, intron
 
-=item B<-o> , B<--output> , B<--out> , B<--outfile> or B<--gtf>
+=item B<-o>, B<--output>, B<--out> or B<--outfile>
 
 Output GTF file. If no output file is specified, the output will be
 written to STDOUT.
@@ -143,6 +143,10 @@ =head1 OPTIONS
 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).
 
+=item B<--verbose> or B<-v>
+
+add verbosity
+
 =item B<-h> or B<--help>
 
 Display this helpful text.

bin/agat_sp_add_attribute_shortest_exon_size.pl

@@ -168,11 +168,11 @@ =head1 OPTIONS
 
 STRING: Input GTF/GFF file.
 
-=item  B<--out>, B<--output> or B<-o>
+=item B<--out>, B<--output> or B<-o>
 
 STRING: Output gff3 file where the result will be printed.
 
-=item B<-v>
+=item B<-v> or B<--verbose>
 
 BOLEAN: Verbose for debugging purpose.
 

bin/agat_sp_add_attribute_shortest_intron_size.pl

@@ -173,15 +173,15 @@ =head1 OPTIONS
 
 =over 8
 
-=item B<--gff>, B<-f>, B<--ref> or B<-reffile>
+=item B<--gff>, B<-f>, B<--ref> or B<--reffile>
 
 STRING: Input GTF/GFF file.
 
-=item  B<--out>, B<--output> or B<-o>
+=item B<--out>, B<--output> or B<-o>
 
 STRING: Output gff3 file where the result will be printed.
 
-=item B<-v>
+=item B<-v> or B<--verbose>
 
 BOLEAN: Verbose for debugging purpose.
 

bin/agat_sp_add_start_and_stop.pl

@@ -34,7 +34,7 @@
                   'o|out|output=s'   => \$opt_output,
                   'e|extend!'        => \$opt_extend,
                   'ni|na!'           => \$opt_no_iupac,
-                  'v!'               => \$verbose,
+                  'v|verbose!'       => \$verbose,
                   'c|config=s'       => \$config,
                   'h|help!'          => \$opt_help ) )
 {
@@ -632,7 +632,7 @@ =head1 OPTIONS
 
 Codon table to use. [default 1]
 
-=item  B<--out>, B<--output> or B<-o>
+=item B<--out>, B<--output> or B<-o>
 
 Output gff file updated
 
@@ -644,7 +644,7 @@ =head1 OPTIONS
 
 Boolean - no iupac / no ambiguous, avoid usage of IUPAC. By default IUPAC is used that means, NNN is seen as start and/or stop codon.
 
-=item B<-v>
+=item B<-v> or B<--verbose>
 
 Verbose for debugging purpose.
 

bin/agat_sp_clipN_seqExtremities_and_fixCoordinates.pl

@@ -250,7 +250,7 @@ =head1 OPTIONS
 
 Input GTF/GFF file.
 
-=item B<-f> or B<--fasta>
+=item B<-f>, B<--fa> or B<--fasta>
 
 Input fasta file.
 

bin/agat_sp_extract_sequences.pl

@@ -937,7 +937,7 @@ =head1 OPTIONS
 This option has to be activated with -u and/or -p option.
 /!\ using -u and -p together builds a chimeric sequence which will be the concatenation of the left and right extremities of a feature.
 
-=item B<-f> or B<--fasta>
+=item B<-f>, B<--fa> or B<--fasta>
 
 String - Input fasta file.
 

bin/agat_sp_filter_by_locus_distance.pl

@@ -275,7 +275,7 @@ =head1 OPTIONS
 The minimum inter-loci distance to allow.  No default (will not apply
 filter by default).
 
-=item B<--add> or B<--add_flag>
+=item B<--af> or B<--add_flag>
 
 Instead of filter the result into two output files, write only one and add the flag <low_dist> in the gff.(tag = Lvalue or tag = Rvalue  where L is left and R right and the value is the distance with accordingle the left or right locus)
 

bin/agat_sp_filter_feature_by_attribute_value.pl

@@ -402,7 +402,7 @@ =head1 OPTIONS
 
 Input GFF3 file that will be read
 
-=item  B<-a> or B<--attribute>
+=item B<-a> or B<--attribute>
 
 Attribute tag to specify the attribute to analyse (attribute example: tag=value).