Repository 'trinity_abundance_estimates_to_matrix'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix

Changeset 21:400691c87530 (2023-08-08)
Previous changeset 20:a009c96c5c18 (2023-04-11) Next changeset 22:ba3720d7e68b (2023-09-20)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
modified:
abundance_estimates_to_matrix.xml
added:
test-data/count/contig_exn50_statistic/Trinity.fasta.gz
test-data/count/trinityStats/statsfile.txt
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diff -r a009c96c5c18 -r 400691c87530 abundance_estimates_to_matrix.xml
--- a/abundance_estimates_to_matrix.xml Tue Apr 11 19:52:45 2023 +0000
+++ b/abundance_estimates_to_matrix.xml Tue Aug 08 09:13:04 2023 +0000
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@@ -256,7 +256,7 @@
 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
 
 
-.. _Trinity: http://trinityrnaseq.github.io
+.. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
 ]]>
     </help>
 
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diff -r a009c96c5c18 -r 400691c87530 test-data/count/contig_exn50_statistic/Trinity.fasta.gz
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Binary file test-data/count/contig_exn50_statistic/Trinity.fasta.gz has changed
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diff -r a009c96c5c18 -r 400691c87530 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 09:13:04 2023 +0000
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@@ -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
+
+
+