--- a/abundance_estimates_to_matrix.xml	Sun Dec 19 16:17:05 2021 +0000
+++ b/abundance_estimates_to_matrix.xml	Tue Apr 11 19:52:45 2023 +0000
@@ -1,13 +1,10 @@
-<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@">
+<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>for a de novo assembly of RNA-Seq data by Trinity</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="bio_tools"/>
-    <expand macro="requirements">
-        <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
-        <requirement type="package" version="0.44.0">kallisto</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="aggressive"><![CDATA[
         #import re
         #for $entry in $samples:
@@ -49,9 +46,9 @@
         #end if
     ]]></command>
     <inputs>
-        <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" />
-        <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" optional="true" help="Only needed for gene level estimates" />
-        <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
+        <param name="samples" type="data" format="tabular" multiple="true" label="Abundance estimates" help="output(s) from 'Align reads and estimate abundance' tool" />
+        <param argument="--gene_trans_map" type="data" format="tabular" optional="true"  label="Gene to transcript correspondence ('gene(tab)transcript' lines)" help="Only needed for gene level estimates" />
+        <param type="select" argument="--est_method" label="Abundance estimation method">
             <option value="RSEM">RSEM</option>
             <option value="eXpress">eXpress</option>
             <option value="salmon">Salmon</option>
@@ -59,7 +56,7 @@
         </param>
 
         <section name="additional_params" title="Additional Options" expanded="False">
-            <param type="select" name="cross_sample_norm" argument="--cross_sample_norm" label="Cross sample normalization">
+            <param type="select" argument="--cross_sample_norm" label="Cross sample normalization">
                 <option value="TMM">TMM</option>
                 <option value="UpperQuartile">UpperQuartile</option>
                 <option value="none">None</option>
@@ -68,26 +65,26 @@
     </inputs>
     <outputs>
         <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment isoform counts (raw counts)"/>
-        <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of isoform TPM expression values (not cross-sample normalized)"/>
+        <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: Matrix of isoform TPM expression values (not cross-sample normalized)"/>
 
         <data format="tabular" name="trans_counts_gene" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment gene counts (raw counts)">
             <filter>gene_trans_map</filter>
         </data>
-        <data format="tabular" name="TPM_no_norm_gene" label="${tool.name} on ${on_string}: matrix of gene TPM expression values (not cross-sample normalized)">
+        <data format="tabular" name="TPM_no_norm_gene" label="${tool.name} on ${on_string}: Matrix of gene TPM expression values (not cross-sample normalized)">
             <filter>gene_trans_map</filter>
         </data>
 
-        <data format="tabular" name="norm_TMM" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values">
+        <data format="tabular" name="norm_TMM" label="${tool.name} on ${on_string}: Matrix of TMM-normalized expression values">
             <filter>additional_params['cross_sample_norm'] == "TMM"</filter>
         </data>
-        <data format="tabular" name="norm_UQ" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values">
+        <data format="tabular" name="norm_UQ" label="${tool.name} on ${on_string}: Matrix of UpperQuartile-normalized expression values">
             <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter>
         </data>
 
-        <data format="tabular" name="norm_TMM_gene" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values">
+        <data format="tabular" name="norm_TMM_gene" label="${tool.name} on ${on_string}: Matrix of TMM-normalized expression values (gene)">
             <filter>additional_params['cross_sample_norm'] == "TMM" and gene_trans_map</filter>
         </data>
-        <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values">
+        <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: Matrix of UpperQuartile-normalized expression values (gene)">
             <filter>additional_params['cross_sample_norm'] == "UpperQuartile" and gene_trans_map</filter>
         </data>
     </outputs>