--- a/trinity.xml	Sun Dec 19 16:25:47 2021 +0000
+++ b/trinity.xml	Tue Apr 11 19:57:45 2023 +0000
@@ -1,12 +1,11 @@
-<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@+galaxy2">
+<tool id="trinity" name="Trinity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>de novo assembly of RNA-Seq data</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="bio_tools"/>
     <expand macro="requirements">
-        <requirement type="package" version="8.32">coreutils</requirement>
-        <requirement type="package" version="3.2.3">rsync</requirement>
+        <requirement type="package" version="3.2.7">rsync</requirement>
     </expand>
     <command detect_errors="aggressive"><![CDATA[
         if [ -z "\$GALAXY_MEMORY_MB" ] ; then
@@ -54,7 +53,9 @@
         #end if
 
         Trinity --no_version_check
-
+        --output ./trinity_out_dir
+        ## do not try to run the high-mem normalization stats generator in parallel for paired-end fastqs
+        --no_parallel_norm_stats
         ## Inputs
         #if $pool.pool_mode == "Yes":
             #if str($pool.inputs.paired_or_single) == "single":
@@ -65,7 +66,7 @@
                     --seqType fq
                 #end if
 
-                #if $pool.inputs.strand.is_strand_specific:
+                #if $pool.inputs.strand.is_strand_specific == 'true':
                     --SS_lib_type $pool.inputs.strand.library_type
                 #end if
             #elif str($pool.inputs.paired_or_single) == "paired":
@@ -110,12 +111,12 @@
                     --seqType fq
                 #end if
 
-                #if $pool.inputs.strand.is_strand_specific:
+                #if $pool.inputs.strand.is_strand_specific == 'true':
                     --SS_lib_type $pool.inputs.strand.library_type
                 #end if
             #end if
         #end if
-        $norm
+        $no_normalize_reads
 
         ## Additional parameters.
         #if $additional_params.min_contig_length:
@@ -179,17 +180,7 @@
                     </param>
                     <when value="single">
                         <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Single-end reads" help=""/>
-                        <conditional name="strand">
-                            <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
-                            <when value="false">
-                            </when>
-                            <when value="true">
-                                <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
-                                    <option value="F">F</option>
-                                    <option value="R">R</option>
-                                </param>
-                            </when>
-                        </conditional>
+                        <expand macro="is_strand_specific_f_r"/>
                     </when>
                     <when value="paired">
                         <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Left/Forward strand reads" />
@@ -210,17 +201,7 @@
                     </param>
                     <when value="unmerged_single_collection">
                         <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Single-end reads" help="Elements of collection will NOT be merged"/>
-                        <conditional name="strand">
-                            <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
-                            <when value="false">
-                            </when>
-                            <when value="true">
-                                <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
-                                    <option value="F">F</option>
-                                    <option value="R">R</option>
-                                </param>
-                            </when>
-                        </conditional>
+                        <expand macro="is_strand_specific_f_r"/>
                     </when>
                     <when value="unmerged_paired_collection">
                         <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger,fastqsanger.gz" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/>
@@ -229,9 +210,9 @@
                 </conditional>
             </when>
         </conditional>
-        <param name="norm" type="boolean" argument="--no_normalize_reads" truevalue="" falsevalue="--no_normalize_reads" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
+        <param argument="--no_normalize_reads" type="boolean" truevalue="" falsevalue="--no_normalize_reads" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
         <section name="additional_params" title="Additional Options" expanded="False">
-            <param name="min_contig_length" argument="--min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
+            <param argument="--min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
 
             <conditional name="guided">
                 <param name="is_guided" type="select" label="Use the genome guided mode?" help="If you already mapped the reads to the genome, Trinity can use this information">
@@ -241,21 +222,21 @@
                 <when value="no">
                 </when>
                 <when value="yes">
-                    <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
-                    <param name="genome_guided_max_intron" argument="--genome_guided_max_intron" type="integer" value="" min="1" label="Maximum allowed intron length (also maximum fragment span on genome)"/>
-                    <param name="genome_guided_min_coverage" argument="--genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
-                    <param name="genome_guided_min_reads_per_partition" argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
+                    <param argument="--genome_guided_bam" type="data" format="bam" label="Coordinate-sorted BAM file" />
+                    <param argument="--genome_guided_max_intron" type="integer" value="" min="1" label="Maximum allowed intron length (also maximum fragment span on genome)"/>
+                    <param argument="--genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
+                    <param argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
                 </when>
             </conditional>
 
-            <param name="long_reads" argument="--long_reads" type="data" format="fasta" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
-
-            <param name="min_kmer_cov" argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
+            <param argument="--long_reads" type="data" format="fasta" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads"
+                help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
+            <param argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
         </section>
     </inputs>
     <outputs>
-        <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
-        <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map" from_work_dir="trinity_out_dir/Trinity.fasta.gene_trans_map"/>
+        <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir.Trinity.fasta"/>
+        <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map" from_work_dir="trinity_out_dir.Trinity.fasta.gene_trans_map"/>
     </outputs>
     <tests>
         <test>
@@ -268,7 +249,7 @@
                 </collection>
             </param>
             <param name="is_strand_specific" value="true"/>
-            <param name="norm" value="true"/>
+            <param name="no_normalize_reads" value="true"/>
             <param name="library_type" value="RF"/>
             <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
             <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" />
@@ -283,7 +264,7 @@
                 </collection>
             </param>
             <param name="is_strand_specific" value="true"/>
-            <param name="norm" value="true"/>
+            <param name="no_normalize_reads" value="true"/>
             <param name="library_type" value="RF"/>
             <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" />
             <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" />
@@ -293,7 +274,7 @@
             <param name="paired_or_single" value="unmerged_single_collection"/>
             <param name="input" value="reads.left.fq" ftype="fastqsanger"/>
             <param name="is_strand_specific" value="true"/>
-            <param name="norm" value="false"/>
+            <param name="no_normalize_reads" value="false"/>
             <param name="library_type" value="F"/>
             <output name="assembled_transcripts" file="raw/Trinity_single_unmerged_1.fasta" compare="sim_size" delta="500" />
             <output name="gene_to_trans" file="raw/Trinity_single_unmerged_1.map" compare="sim_size" />
@@ -304,7 +285,7 @@
             <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
             <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
             <param name="is_strand_specific" value="true"/>
-            <param name="norm" value="false"/>
+            <param name="no_normalize_reads" value="false"/>
             <param name="library_type" value="RF"/>
             <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
             <output name="gene_to_trans" file="raw/Trinity.map" compare="sim_size" />
@@ -315,7 +296,7 @@
             <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
             <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
             <param name="is_strand_specific" value="true"/>
-            <param name="norm" value="true"/>
+            <param name="no_normalize_reads" value="true"/>
             <param name="library_type" value="RF"/>
             <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
             <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" />
@@ -340,7 +321,7 @@
                 </collection>
             </param>
             <param name="is_strand_specific" value="true"/>
-            <param name="norm" value="true"/>
+            <param name="no_normalize_reads" value="true"/>
             <param name="library_type" value="RF"/>
             <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
             <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" />