# HG changeset patch
# User iuc
# Date 1572610222 14400
# Node ID b34de8dc0f64e05f3f92c6baff536664967d71a3
# Parent  3abd51c4b151af5bde9fb287804b296879cf7478
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 3b8670ad0ce9dd90d6a24429bca131362e56d17d"

diff -r 3abd51c4b151 -r b34de8dc0f64 macros.xml
--- a/macros.xml	Wed Oct 17 12:59:45 2018 -0400
+++ b/macros.xml	Fri Nov 01 08:10:22 2019 -0400
@@ -7,7 +7,7 @@
         </requirements>
     </xml>
 
-    <token name="@WRAPPER_VERSION@">2.8.4</token>
+    <token name="@WRAPPER_VERSION@">2.8.5</token>
 
     <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
         #if $pool.inputs.strand.is_strand_specific:
diff -r 3abd51c4b151 -r b34de8dc0f64 super_transcripts.xml
--- a/super_transcripts.xml	Wed Oct 17 12:59:45 2018 -0400
+++ b/super_transcripts.xml	Fri Nov 01 08:10:22 2019 -0400
@@ -18,8 +18,8 @@
     <tests>
         <test>
             <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/>
-            <output name="seqs" file="supertranscripts/trinity_genes.fasta" />
-            <output name="annotation" file="supertranscripts/trinity_genes.gtf" />
+            <output name="seqs" file="supertranscripts/trinity_genes.fasta" sort="True" />
+            <output name="annotation" file="supertranscripts/trinity_genes.gtf" sort="True" />
             <output name="malign" file="supertranscripts/trinity_genes.malign" />
         </test>
     </tests>
diff -r 3abd51c4b151 -r b34de8dc0f64 test-data/count/contig_exn50_statistic/ExN50.stats
--- a/test-data/count/contig_exn50_statistic/ExN50.stats	Wed Oct 17 12:59:45 2018 -0400
+++ b/test-data/count/contig_exn50_statistic/ExN50.stats	Fri Nov 01 08:10:22 2019 -0400
@@ -1,4 +1,5 @@
 Ex	ExN50	num_transcripts
 33	541	1
 67	541	2
+99	380	3
 100	279	7
diff -r 3abd51c4b151 -r b34de8dc0f64 test-data/supertranscripts/trinity_genes.fasta
--- a/test-data/supertranscripts/trinity_genes.fasta	Wed Oct 17 12:59:45 2018 -0400
+++ b/test-data/supertranscripts/trinity_genes.fasta	Fri Nov 01 08:10:22 2019 -0400
@@ -1,14 +1,14 @@
->TRINITY_DN1_c0_g1
-CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG
+>TRINITY_DN2_c3_g1
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA
 >TRINITY_DN0_c0_g1
 AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
 >TRINITY_DN2_c0_g1
 TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
->TRINITY_DN2_c1_g1
-GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG
+>TRINITY_DN3_c0_g1
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
 >TRINITY_DN2_c2_g1
 ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGAGTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
->TRINITY_DN2_c3_g1
-GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA
->TRINITY_DN3_c0_g1
-ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
+>TRINITY_DN2_c1_g1
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG
+>TRINITY_DN1_c0_g1
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG
diff -r 3abd51c4b151 -r b34de8dc0f64 test-data/supertranscripts/trinity_genes.gtf
--- a/test-data/supertranscripts/trinity_genes.gtf	Wed Oct 17 12:59:45 2018 -0400
+++ b/test-data/supertranscripts/trinity_genes.gtf	Fri Nov 01 08:10:22 2019 -0400
@@ -1,14 +1,14 @@
-TRINITY_DN1_c0_g1	Trinity_gene	exon	1	380	.	+	.	gene_id "TRINITY_DN1_c0_g1"; transcript_id "TRINITY_DN1_c0_g1_i1"
+TRINITY_DN2_c3_g1	Trinity_gene	exon	1	202	.	+	.	gene_id "TRINITY_DN2_c3_g1"; transcript_id "TRINITY_DN2_c3_g1_i1"
 
 TRINITY_DN0_c0_g1	Trinity_gene	exon	1	229	.	+	.	gene_id "TRINITY_DN0_c0_g1"; transcript_id "TRINITY_DN0_c0_g1_i1"
 
 TRINITY_DN2_c0_g1	Trinity_gene	exon	1	279	.	+	.	gene_id "TRINITY_DN2_c0_g1"; transcript_id "TRINITY_DN2_c0_g1_i1"
 
-TRINITY_DN2_c1_g1	Trinity_gene	exon	1	541	.	+	.	gene_id "TRINITY_DN2_c1_g1"; transcript_id "TRINITY_DN2_c1_g1_i1"
+TRINITY_DN3_c0_g1	Trinity_gene	exon	1	216	.	+	.	gene_id "TRINITY_DN3_c0_g1"; transcript_id "TRINITY_DN3_c0_g1_i1"
 
 TRINITY_DN2_c2_g1	Trinity_gene	exon	1	240	.	+	.	gene_id "TRINITY_DN2_c2_g1"; transcript_id "TRINITY_DN2_c2_g1_i1"
 
-TRINITY_DN2_c3_g1	Trinity_gene	exon	1	202	.	+	.	gene_id "TRINITY_DN2_c3_g1"; transcript_id "TRINITY_DN2_c3_g1_i1"
+TRINITY_DN2_c1_g1	Trinity_gene	exon	1	541	.	+	.	gene_id "TRINITY_DN2_c1_g1"; transcript_id "TRINITY_DN2_c1_g1_i1"
 
-TRINITY_DN3_c0_g1	Trinity_gene	exon	1	216	.	+	.	gene_id "TRINITY_DN3_c0_g1"; transcript_id "TRINITY_DN3_c0_g1_i1"
+TRINITY_DN1_c0_g1	Trinity_gene	exon	1	380	.	+	.	gene_id "TRINITY_DN1_c0_g1"; transcript_id "TRINITY_DN1_c0_g1_i1"