# HG changeset patch
# User iuc
# Date 1691484724 0
# Node ID 3f52e361933808c83224ea74aae600c0bd96526d
# Parent  78b742ff461b6e31b2a4e235346a724bba4929f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce

diff -r 78b742ff461b -r 3f52e3619338 gene_to_trans_map.xml
--- a/gene_to_trans_map.xml	Tue Apr 11 19:43:57 2023 +0000
+++ b/gene_to_trans_map.xml	Tue Aug 08 08:52:04 2023 +0000
@@ -26,7 +26,7 @@
         The output file is intended to be used by the "Align reads and estimate abundance" tool.
         The same file is automatically generated when running Trinity, this tool is only intended to be used when you don't (or no longer) have access to the one produced by Trinity.
 
-        .. _Trinity: http://trinityrnaseq.github.io
+        .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
     </help>
     <expand macro="citation" />
 </tool>
diff -r 78b742ff461b -r 3f52e3619338 test-data/count/contig_exn50_statistic/Trinity.fasta.gz
Binary file test-data/count/contig_exn50_statistic/Trinity.fasta.gz has changed
diff -r 78b742ff461b -r 3f52e3619338 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 08:52:04 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
+
+
+