--- a/analyze_diff_expr.xml	Sun Dec 19 16:21:54 2021 +0000
+++ b/analyze_diff_expr.xml	Tue Apr 11 19:55:15 2023 +0000
@@ -1,15 +1,10 @@
-<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@">
+<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>from a Trinity assembly</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="bio_tools"/>
-    <expand macro="requirements">
-        <requirement type="package" version="2.18.0">bioconductor-qvalue</requirement>
-        <requirement type="package" version="1.36.0">bioconductor-goseq</requirement>
-        <requirement type="package" version="2.0.8">r-cluster</requirement>
-        <requirement type="package" version="1.1.25">r-fastcluster</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="aggressive"><![CDATA[
     ## DE results input files must be in the working directory and have suffix .DE_results
     #import re
@@ -35,8 +30,8 @@
     analyze_diff_expr.pl
         --matrix '${matrix}'
         --samples '${samples}'
-        -P ${p}
-        -C ${c}
+        -P ${P}
+        -C ${C}
 
         #if str( $additional_params.max_DE_genes_per_comparison ):
             --max_DE_genes_per_comparison ${additional_params.max_DE_genes_per_comparison}
@@ -57,26 +52,26 @@
         --output results
     ]]></command>
     <inputs>
-        <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="Raw counts matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool"/>
-        <param format="tabular" name="samples" argument="--samples" type="data" label="Sample description" help="File describing samples and replicates"/>
-        <param format="tabular" name="DE_results" type="data_collection" collection_type="list" label="Differential expression results" help="Generated by 'Differential expression analysis using a Trinity assembly' tool"/>
-        <param name="p" type="float" argument="-P" value="0.001" label="p-value cutoff for FDR"/>
-        <param name="c" type="float" argument="-C" value="2" label="min abs(log2(a/b)) fold change" help="Default: 2 (meaning 2^(2) or 4-fold"/>
+        <param argument="--matrix" format="tabular" type="data" label="Expression matrix" help="Raw counts matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool"/>
+        <param argument="--samples" format="tabular" type="data" label="Sample description" help="File describing samples and replicates"/>
+        <param name="DE_results" format="tabular" type="data_collection" collection_type="list" label="Differential expression results" help="Generated by 'Differential expression analysis using a Trinity assembly' tool"/>
+        <param argument="-P" type="float" value="0.001" label="p-value cutoff for FDR"/>
+        <param argument="-C" type="float" value="2" label="min abs(log2(a/b)) fold change" help="Default: 2 (meaning 2^(2) or 4-fold"/>
         <section name="additional_params" title="Additional Options" expanded="False">
-            <param name="max_DE_genes_per_comparison" argument="--max_DE_genes_per_comparison" type="integer" value="" optional="true" label="Maximum differential expression genes per comparison" help="Extract only up to the top number of DE features within each pairwise comparison. This is useful when you have massive numbers of DE features but still want to make useful heatmaps and other plots with more manageable numbers of data points."/>
-            <param name="order_columns_by_samples_file" argument="--order_columns_by_samples_file" type="boolean" checked="false" truevalue="--order_columns_by_samples_file" falsevalue="" label="Order columns by samples file" help="Instead of clustering samples or replicates hierarchically based on gene expression patterns, order columns according to order in the --samples file."/>
-            <param name="max_genes_clust" argument="--max_genes_clust" type="integer" value="10000" label="Maximum genes in cluster" help="If more than 10000, heatmaps are not generated, since too time consuming"/>
+            <param argument="--max_DE_genes_per_comparison" type="integer" value="" optional="true" label="Maximum differential expression genes per comparison" help="Extract only up to the top number of DE features within each pairwise comparison. This is useful when you have massive numbers of DE features but still want to make useful heatmaps and other plots with more manageable numbers of data points."/>
+            <param argument="--order_columns_by_samples_file" type="boolean" checked="false" truevalue="--order_columns_by_samples_file" falsevalue="" label="Order columns by samples file" help="Instead of clustering samples or replicates hierarchically based on gene expression patterns, order columns according to order in the --samples file."/>
+            <param argument="--max_genes_clust" type="integer" value="10000" label="Maximum genes in cluster" help="If more than 10000, heatmaps are not generated, since too time consuming"/>
             <conditional name="GO_enrichment">
-                <param type="select" name="examine_GO_enrichment" argument="--examine_GO_enrichment" label="Run GO enrichment analysis" help="To examine GO enrichment, you must first run Trinotate and then extract all GO assignments for each gene feature, with the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl">
+                <param argument="--examine_GO_enrichment" type="select" label="Run GO enrichment analysis" help="To examine GO enrichment, you must first run Trinotate and then extract all GO assignments for each gene feature, with the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl">
                     <option value="no">No</option>
                     <option value="yes">Yes</option>
                 </param>
                 <when value="no">
                 </when>
                 <when value="yes">
-                    <param format="tabular" name="DE_matrices" type="data_collection" collection_type="list" label="Differential expression count matrices" help="Generated by 'Differential expression analysis using a Trinity assembly' tool. If not, be careful that the file names are identical to the file names of differential expression results, with extension '.count_matrix' instead of '.DE_results'."/>
-                    <param format="tabular" name="GO_annots" argument="--GO_annots" type="data" label="Extracted GO assignments file" help="Generated by the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl. Must have 2 columns: feature_id GO:000001,GO:00002,..."/>
-                    <param format="tabular" name="gene_lengths" argument="--gene_lengths" type="data" label="Gene length file" help="Must have 2 columns: feature_id length"/>
+                    <param name="DE_matrices" format="tabular" type="data_collection" collection_type="list" label="Differential expression count matrices" help="Generated by 'Differential expression analysis using a Trinity assembly' tool. If not, be careful that the file names are identical to the file names of differential expression results, with extension '.count_matrix' instead of '.DE_results'."/>
+                    <param argument="--GO_annots" format="tabular" type="data" label="Extracted GO assignments file" help="Generated by the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl. Must have 2 columns: feature_id GO:000001,GO:00002,..."/>
+                    <param argument="--gene_lengths" format="tabular" type="data" label="Gene length file" help="Must have 2 columns: feature_id length"/>
                 </when>
         </conditional>
         </section>
@@ -93,7 +88,7 @@
             <data format="tabular" name="results_matrix_log2_sample_cor" from_work_dir="results.matrix.log2.sample_cor.dat"/>
             <data format="pdf" name="results_matrix_log2_sample_cor_matrix" from_work_dir="results.matrix.log2.sample_cor_matrix.pdf"/>
         </collection>
-        <data format="rdata" name="rdata" label="${tool.name} on ${on_string}: RData file" from_work_dir="results.matrix.RData"/>
+        <data name="rdata" format="rdata" label="${tool.name} on ${on_string}: RData file" from_work_dir="results.matrix.RData"/>
         <collection name="GOseq_enrichment" type="list" label="${tool.name} on ${on_string}: GOseq enriched and depleted categories">
             <filter>additional_params['GO_enrichment']['examine_GO_enrichment'] == 'yes'</filter>
             <discover_datasets pattern="(?P&lt;name&gt;.+\.subset\.GOseq\.(enriched|depleted))$" ext="tabular" />