# HG changeset patch
# User iuc
# Date 1691485618 0
# Node ID a35cba31d904d05285bbc8cbc3b305a57702936b
# Parent  aa38fa8c5815f543cb934605566dbaedf9a40164
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce

diff -r aa38fa8c5815 -r a35cba31d904 filter_low_expr_transcripts.xml
--- a/filter_low_expr_transcripts.xml	Tue Apr 11 19:51:03 2023 +0000
+++ b/filter_low_expr_transcripts.xml	Tue Aug 08 09:06:58 2023 +0000
@@ -93,7 +93,7 @@
         with "Build expression matrix for a de novo assembly of RNA-Seq data by Trinity" tool.
         It discards transcripts/isoforms having a low expression level.
 
-        .. _Trinity: http://trinityrnaseq.github.io
+        .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
     </help>
 
     <expand macro="citation" />
diff -r aa38fa8c5815 -r a35cba31d904 test-data/count/contig_exn50_statistic/Trinity.fasta.gz
Binary file test-data/count/contig_exn50_statistic/Trinity.fasta.gz has changed
diff -r aa38fa8c5815 -r a35cba31d904 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 09:06:58 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
+
+
+