# HG changeset patch
# User iuc
# Date 1691486036 0
# Node ID 24e94d84adc9cfe8d4833a02712a6ce97f4c0700
# Parent  c63338cf419f08d727148a43bb7a015ff664b07c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce

diff -r c63338cf419f -r 24e94d84adc9 run_de_analysis.xml
--- a/run_de_analysis.xml	Tue Apr 11 19:51:53 2023 +0000
+++ b/run_de_analysis.xml	Tue Aug 08 09:13:56 2023 +0000
@@ -171,7 +171,7 @@
 The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'.
 
 
-.. _Trinity: http://trinityrnaseq.github.io
+.. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
 ]]>
     </help>
 
diff -r c63338cf419f -r 24e94d84adc9 test-data/count/contig_exn50_statistic/Trinity.fasta.gz
Binary file test-data/count/contig_exn50_statistic/Trinity.fasta.gz has changed
diff -r c63338cf419f -r 24e94d84adc9 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 09:13:56 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
+
+
+