Mercurial > repos > iuc > trinity_gene_to_trans_map

changeset 20:7c7fbf13aadd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
author iuc
date Tue, 08 Aug 2023 09:04:29 +0000
parents ba460ccf0006
children
files gene_to_trans_map.xml test-data/count/contig_exn50_statistic/Trinity.fasta.gz test-data/count/trinityStats/statsfile.txt
diffstat 3 files changed, 41 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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>
Binary file test-data/count/contig_exn50_statistic/Trinity.fasta.gz has changed
--- /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
+
+
+