Merge pull request #5277 from rlibouba/update_lncrna_tuto

update version tools

topics/genome-annotation/tutorials/lncrna/tutorial.md

@@ -109,7 +109,7 @@ A reference annotation file in GTF or GFF3 format can be provided to StringTie w
 
 > <hands-on-title>Transcripts assembly</hands-on-title>
 >
-> {% tool [StringTie](toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.7+galaxy1) %} with the following parameters:
+> {% tool [StringTie](toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy1) %} with the following parameters:
 >    - *"Input options"*: `Short reads`
 >    - {% icon param-file %} *"Input short mapped reads"*: `SRR8534859_RNASeq_mapped.bam`
 >    - *"Specify strand information"*: Unstranded
@@ -132,7 +132,7 @@ We obtain an annotation file (GTF format) which contained all assembled transcri
 >
 > > <solution-title></solution-title>
 > >
-> > Specific features can be extracted from the GTF file using for example {% tool [Extract features from GFF data](Extract_features1) %}. By selecting `transcript` From `column 3 / Feature`, we can select only the transcript elements present in this annotation file. Assembly contains 14,877 transcripts (corresponding to the number of lines in the filtered GTF file).
+> > Specific features can be extracted from the GTF file using for example {% tool [Extract features from GFF data](Extract_features1) %}. By selecting `transcript` From `column 3 / Feature`, we can select only the transcript elements present in this annotation file. Assembly contains 17,653 transcripts (corresponding to the number of lines in the filtered GTF file).
 > >
 > {: .solution}
 >
@@ -146,11 +146,11 @@ To use FEELnc, we need to have a reference annotation file in GTF format, which
 
 > <hands-on-title>FEELnc</hands-on-title>
 >
-> 1. {% tool [gffread](toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0) %} with the following parameters:
+> 1. {% tool [gffread](toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.4+galaxy0) %} with the following parameters:
 >    - {% icon param-file %} *"Input BED, GFF3 or GTF feature file"*: `genome_annotation.gff3`
 >    - *"Feature File Output"*: `GTF`
 >
-> 2. {% tool [FEELnc](toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2) %} with the following parameters:
+> 2. {% tool [FEELnc](toolshed.g2.bx.psu.edu/repos/iuc/feelnc/feelnc/0.2.1) %} with the following parameters:
 >    - {% icon param-file %} *"Transcripts assembly"*: `Assembled transcript` (output of **StringTie** {% icon tool %})
 >    - {% icon param-file %} *"Reference annotation"*: `genome_annotation.gtf` (Output of **gffread** {% icon tool %})
 >    - {% icon param-file %} *"Genome sequence"*: `genome_assembly.fasta`
@@ -186,8 +186,8 @@ For future analyses, it would be interesting to use an updated annotation contai
 
 > <hands-on-title>Merge the annotations</hands-on-title>
 >
-> {% tool [concatenate](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1) %} with the following parameters:
->    - {% icon param-file %} *"Datasets to concatenate"*: `genome_annotation.gtf`
+> {% tool [concatenate](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/1.0.0) %} with the following parameters:
+>    - {% icon param-file %} *"Datasets to concatenate"*: `genome_annotation.gtf` (Output of **gffread** {% icon tool %})
 >    - Insert Dataset
 >    - {% icon param-file %} *"Dataset"*: `lncRNA annotation with FEELnc`
 >