--- a/align_and_estimate_abundance.xml	Sun Dec 19 16:23:51 2021 +0000
+++ b/align_and_estimate_abundance.xml	Tue Apr 11 19:56:08 2023 +0000
@@ -1,12 +1,11 @@
-<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@+galaxy1">
+<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>on a 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="1.3.2">rsem</requirement>
-        <requirement type="package" version="0.46.0">kallisto</requirement>
+        <requirement type="package" version="1.3.3">rsem</requirement>
     </expand>
     <command detect_errors="aggressive"><![CDATA[
         ln -f -s '$transcripts' input.fa &&
@@ -59,11 +58,11 @@
                 --left paired_left.fq.gz --right paired_right.fq.gz --seqType fq
             #end if
 
-            #if $inputs.strand.is_strand_specific:
+            #if $inputs.strand.is_strand_specific == 'true':
                 --SS_lib_type $inputs.strand.library_type
             #end if
 
-            --max_ins_size $inputs.paired_fragment_length
+            --max_ins_size $inputs.max_ins_size
 
         #else:
             #if $inputs.input.is_of_type('fasta'):
@@ -74,35 +73,35 @@
                 --single single.fq.gz --seqType fq
             #end if
 
-            #if $inputs.strand.is_strand_specific:
+            #if $inputs.strand.is_strand_specific == 'true':
                 --SS_lib_type $inputs.strand.library_type
             #end if
         #end if
 
         ## Additional parameters.
         --gene_trans_map gene_to_trans.map
-
         --prep_reference
-
         --output_dir output
 
         ## CPU
         --thread_count \${GALAXY_SLOTS:-4}
     ]]></command>
     <inputs>
-        <param format="fasta" name="transcripts" argument="--transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/>
+        <param format="fasta" argument="--transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/>
         <conditional name="inputs">
             <param name="paired_or_single" type="select" label="Paired or Single-end data?">
                 <option value="paired">Paired</option>
                 <option value="single">Single</option>
             </param>
             <when value="paired">
-                <param format="fasta,fastqsanger,fastqsanger.gz" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/>
-                <param format="fasta,fastqsanger,fastqsanger.gz" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/>
+                <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Left/Forward strand reads" />
+                <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Right/Reverse strand reads" />
                 <conditional name="strand">
-                    <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
-                    <when value="false">
-                    </when>
+                    <param name="is_strand_specific" type="select" label="Strand specific data">
+                        <option value="false">No</option>
+                        <option value="true">Yes</option>
+                    </param>
+                    <when value="false"/>
                     <when value="true">
                         <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
                             <option value="FR">Forward-Reverse</option>
@@ -110,14 +109,16 @@
                         </param>
                     </when>
                 </conditional>
-                <param name="paired_fragment_length" argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/>
+                <param argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="Bowtie -X parameter"/>
             </when>
             <when value="single">
                 <param format="fasta,fastqsanger,fastqsanger.gz" argument="--single" name="input" type="data" 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>
+                    <param name="is_strand_specific" type="select" label="Strand specific data">
+                        <option value="false">No</option>
+                        <option value="true">Yes</option>
+                    </param>
+                    <when value="false"/>
                     <when value="true">
                         <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
                             <option value="F">F</option>
@@ -129,21 +130,19 @@
         </conditional>
 
         <conditional name="method">
-            <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
+            <param type="select" argument="--est_method" label="Abundance estimation method">
                 <option value="RSEM">RSEM</option>
                 <option value="salmon">Salmon</option>
                 <option value="kallisto">Kallisto</option>
             </param>
             <when value="RSEM">
-                <param type="select" name="aln_method" argument="--aln_method" label="Alignment method">
+                <param type="select" argument="--aln_method" label="Alignment method">
                     <option value="bowtie">Bowtie</option>
                     <option value="bowtie2">Bowtie2</option>
                 </param>
             </when>
-            <when value="salmon">
-            </when>
-            <when value="kallisto">
-            </when>
+            <when value="salmon"/>
+            <when value="kallisto"/>
         </conditional>
 
         <section name="additional_params" title="Additional Options" expanded="False">
@@ -152,35 +151,31 @@
                     <option value="yes">Yes</option>
                     <option value="no">No</option>
                 </param>
-                <when value="yes">
-                </when>
+                <when value="yes" />
                 <when value="no">
-                    <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" />
+                    <param argument="--gene_trans_map" type="data" format="tabular" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" />
                 </when>
             </conditional>
-
         </section>
     </inputs>
     <outputs>
-        <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/RSEM.isoforms.results">
-            <filter>method['est_method'] == "RSEM"</filter>
-        </data>
-        <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/RSEM.genes.results">
+        <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts (RSEM)" from_work_dir="output/RSEM.isoforms.results">
             <filter>method['est_method'] == "RSEM"</filter>
         </data>
-
-
-        <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/quant.sf">
+        <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts (RSEM)" from_work_dir="output/RSEM.genes.results">
+            <filter>method['est_method'] == "RSEM"</filter>
+        </data>
+        <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts (Salmon)" from_work_dir="output/quant.sf">
             <filter>method['est_method'] == "salmon"</filter>
         </data>
-        <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes">
+        <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts (Salmon)" from_work_dir="output/quant.sf.genes">
             <filter>method['est_method'] == "salmon"</filter>
         </data>
 
-        <data format="tabular" name="isoforms_counts_kallisto" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/abundance.tsv">
+        <data format="tabular" name="isoforms_counts_kallisto" label="${tool.name} on ${on_string}: isoforms counts (Kallisto)" from_work_dir="output/abundance.tsv">
             <filter>method['est_method'] == "kallisto"</filter>
         </data>
-        <data format="tabular" name="genes_counts_kallisto" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/abundance.tsv.genes">
+        <data format="tabular" name="genes_counts_kallisto" label="${tool.name} on ${on_string}: genes counts (Kallisto)" from_work_dir="output/abundance.tsv.genes">
             <filter>method['est_method'] == "kallisto"</filter>
         </data>
     </outputs>