# HG changeset patch
# User iuc
# Date 1691484956 0
# Node ID b4094dad3f41db5aaf95b174ed3417ee56b60c8c
# Parent  1a7b4d2a891634f60105c43f4ace2bac2a20ae3b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce

diff -r 1a7b4d2a8916 -r b4094dad3f41 super_transcripts.xml
--- a/super_transcripts.xml	Tue Apr 11 19:43:04 2023 +0000
+++ b/super_transcripts.xml	Tue Aug 08 08:55:56 2023 +0000
@@ -29,7 +29,7 @@
 
         A SuperTranscript is constructed by collapsing unique and common sequence regions among splicing isoforms into a single linear sequence.
 
-        .. _Trinity: http://trinityrnaseq.github.io
+        .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
     </help>
 
     <expand macro="citation" />
diff -r 1a7b4d2a8916 -r b4094dad3f41 test-data/count/contig_exn50_statistic/Trinity.fasta.gz
Binary file test-data/count/contig_exn50_statistic/Trinity.fasta.gz has changed
diff -r 1a7b4d2a8916 -r b4094dad3f41 test-data/count/trinityStats/statsfile.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/trinityStats/statsfile.txt	Tue Aug 08 08:55:56 2023 +0000
@@ -0,0 +1,40 @@
+
+
+################################
+## Counts of transcripts, etc.
+################################
+Total trinity 'genes':	7
+Total trinity transcripts:	7
+Percent GC: 42.12
+
+########################################
+Stats based on ALL transcript contigs:
+########################################
+
+	Contig N10: 541
+	Contig N20: 541
+	Contig N30: 380
+	Contig N40: 380
+	Contig N50: 279
+
+	Median contig length: 240
+	Average contig: 298.14
+	Total assembled bases: 2087
+
+
+#####################################################
+## Stats based on ONLY LONGEST ISOFORM per 'GENE':
+#####################################################
+
+	Contig N10: 541
+	Contig N20: 541
+	Contig N30: 380
+	Contig N40: 380
+	Contig N50: 279
+
+	Median contig length: 240
+	Average contig: 298.14
+	Total assembled bases: 2087
+
+
+