# HG changeset patch
# User iuc
# Date 1572610189 14400
# Node ID 6d6b72d141701285a1c82fd25c0de4604908ae68
# Parent  478f36effca1722801dd4fde8368341739abd359
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 3b8670ad0ce9dd90d6a24429bca131362e56d17d"

diff -r 478f36effca1 -r 6d6b72d14170 align_and_estimate_abundance.xml
--- a/align_and_estimate_abundance.xml	Wed Oct 17 12:57:01 2018 -0400
+++ b/align_and_estimate_abundance.xml	Fri Nov 01 08:09:49 2019 -0400
@@ -4,9 +4,8 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.3.0">rsem</requirement>
-        <requirement type="package" version="1.5.1">express</requirement>
-        <requirement type="package" version="0.43.1">kallisto</requirement>
+        <requirement type="package" version="1.3.2">rsem</requirement>
+        <requirement type="package" version="0.46.0">kallisto</requirement>
     </expand>
     <command detect_errors="aggressive"><![CDATA[
         ln -f -s '$transcripts' input.fa &&
@@ -40,7 +39,7 @@
         --transcripts input.fa
 
         --est_method $method.est_method
-        #if $method.est_method == "RSEM" or $method.est_method == "eXpress":
+        #if $method.est_method == "RSEM":
             --aln_method $method.aln_method
         #else if $method.est_method == "salmon":
             --salmon_idx_type $method.salmon_idx_type
@@ -124,7 +123,6 @@
         <conditional name="method">
             <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
                 <option value="RSEM">RSEM</option>
-                <option value="eXpress">eXpress</option>
                 <option value="salmon">Salmon</option>
                 <option value="kallisto">Kallisto</option>
             </param>
@@ -134,12 +132,6 @@
                     <option value="bowtie2">Bowtie2</option>
                 </param>
             </when>
-            <when value="eXpress">
-                <param type="select" name="aln_method" argument="--aln_method" label="Alignment method">
-                    <option value="bowtie">Bowtie</option>
-                    <option value="bowtie2">Bowtie2</option>
-                </param>
-            </when>
             <when value="salmon">
                 <param type="select" name="salmon_idx_type" argument="--salmon_idx_type" label="Index type">
                     <option value="quasi">Quasi</option>
@@ -173,12 +165,6 @@
             <filter>method['est_method'] == "RSEM"</filter>
         </data>
 
-        <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/results.xprs">
-            <filter>method['est_method'] == "eXpress"</filter>
-        </data>
-        <data format="tabular" name="genes_counts_express" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/results.xprs.genes">
-            <filter>method['est_method'] == "eXpress"</filter>
-        </data>
 
         <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/quant.sf">
             <filter>method['est_method'] == "salmon"</filter>
@@ -248,29 +234,6 @@
             <param name="transcripts" value="raw/Trinity.fasta"/>
             <param name="gene_to_trans" value="raw/Trinity.map" />
             <param name="library_type" value="RF"/>
-            <param name="est_method" value="eXpress"/>
-            <param name="aln_method" value="bowtie"/>
-            <param name="has_gene_map" value="yes"/>
-            <output name="isoforms_counts_express">
-                <assert_contents>
-                    <has_line_matching expression=".*&#009;TRINITY_DN2_c3_g1_i1&#009;.*" />
-                    <has_n_columns n="15" />
-                </assert_contents>
-            </output>
-            <output name="genes_counts_express">
-                <assert_contents>
-                    <has_line_matching expression="NA&#009;TRINITY_DN3_c0_g1.*" />
-                    <has_n_columns n="15" />
-                </assert_contents>
-            </output>
-        </test>
-        <test>
-            <param name="paired_or_single" value="paired"/>
-            <param name="left_input" value="reads.left.fq"/>
-            <param name="right_input" value="reads.right.fq"/>
-            <param name="transcripts" value="raw/Trinity.fasta"/>
-            <param name="gene_to_trans" value="raw/Trinity.map" />
-            <param name="library_type" value="RF"/>
             <param name="est_method" value="salmon"/>
             <param name="aln_method" value="bowtie"/>
             <param name="has_gene_map" value="yes"/>
diff -r 478f36effca1 -r 6d6b72d14170 macros.xml
--- a/macros.xml	Wed Oct 17 12:57:01 2018 -0400
+++ b/macros.xml	Fri Nov 01 08:09:49 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 478f36effca1 -r 6d6b72d14170 test-data/count/contig_exn50_statistic/ExN50.stats
--- a/test-data/count/contig_exn50_statistic/ExN50.stats	Wed Oct 17 12:57:01 2018 -0400
+++ b/test-data/count/contig_exn50_statistic/ExN50.stats	Fri Nov 01 08:09:49 2019 -0400
@@ -1,4 +1,5 @@
 Ex	ExN50	num_transcripts
 33	541	1
 67	541	2
+99	380	3
 100	279	7
diff -r 478f36effca1 -r 6d6b72d14170 test-data/supertranscripts/trinity_genes.fasta
--- a/test-data/supertranscripts/trinity_genes.fasta	Wed Oct 17 12:57:01 2018 -0400
+++ b/test-data/supertranscripts/trinity_genes.fasta	Fri Nov 01 08:09:49 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 478f36effca1 -r 6d6b72d14170 test-data/supertranscripts/trinity_genes.gtf
--- a/test-data/supertranscripts/trinity_genes.gtf	Wed Oct 17 12:57:01 2018 -0400
+++ b/test-data/supertranscripts/trinity_genes.gtf	Fri Nov 01 08:09:49 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"