# HG changeset patch
# User iuc
# Date 1691485568 0
# Node ID 65e7dea767ea0253094007c4f2c9092323bc3337
# Parent  ae501908a17f5de946672c916970b5aa0dc2a2ed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce

diff -r ae501908a17f -r 65e7dea767ea define_clusters_by_cutting_tree.xml
--- a/define_clusters_by_cutting_tree.xml	Tue Apr 11 19:50:15 2023 +0000
+++ b/define_clusters_by_cutting_tree.xml	Tue Aug 08 09:06:08 2023 +0000
@@ -81,7 +81,7 @@
 
 This tool uses the RData file produced by 'Extract and cluster differentially expressed transcripts from a Trinity assembly' tool.
 
-.. _Trinity: http://trinityrnaseq.github.io
+.. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
 ]]>
     </help>
 
diff -r ae501908a17f -r 65e7dea767ea test-data/count/contig_exn50_statistic/Trinity.fasta.gz
Binary file test-data/count/contig_exn50_statistic/Trinity.fasta.gz has changed
diff -r ae501908a17f -r 65e7dea767ea 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 09:06:08 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
+
+
+