# HG changeset patch
# User iuc
# Date 1691485469 0
# Node ID 7c7fbf13aaddd8015b216bdc6d4b3ad30f81fbd4
# Parent  ba460ccf0006484e676ec33645fe56507e5be18a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce

diff -r ba460ccf0006 -r 7c7fbf13aadd gene_to_trans_map.xml
--- a/gene_to_trans_map.xml	Tue Apr 11 19:54:25 2023 +0000
+++ b/gene_to_trans_map.xml	Tue Aug 08 09:04:29 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 ba460ccf0006 -r 7c7fbf13aadd test-data/count/contig_exn50_statistic/Trinity.fasta.gz
Binary file test-data/count/contig_exn50_statistic/Trinity.fasta.gz has changed
diff -r ba460ccf0006 -r 7c7fbf13aadd 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 09:04:29 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
+
+
+