--- a/salmonquantmerge.xml	Fri Jun 23 17:01:36 2023 +0000
+++ b/salmonquantmerge.xml	Wed Oct 29 10:45:39 2025 +0000
@@ -3,12 +3,48 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
-        @qmerge@
+    #import re
+
+    #for $counter, $input_data in enumerate($quantfiles):
+        rank_of_series=$counter
+        mkdir ${counter}.quantmerge &&
+        ln -s '$input_data.quants' ${counter}.quantmerge/quant.sf &&
+    #end for
+    salmon --no-version-check quantmerge
+        --quants *.quantmerge
+        --names
+        #for $counter, $input_data in enumerate($quantfiles):
+            #if $input_data.names and re.sub(' ', '', '$input_data.names') != '':
+                '${input_data.names}'
+            #else:
+                #set $identifier=re.sub('[^\w\-\s]', '_', str($input_data.quants.element_identifier))
+                "$identifier"
+            #end if
+        #end for
+        --column '${column}'
+        ${genes}
+        #if $missing:
+            --missing '${missing}'
+        #end if
+        -o qmergeout.tab
     ]]></command>
     <inputs>
-        <expand macro="quantmerge"/>
+        <repeat name="quantfiles" title="Quant file and names">
+            <param argument="--quants" type="data" format="tsv,tabular" label="Salmon quant tabular output files"/>
+            <param argument="--names" type="text" label="One-word sample names" optional="True"/>
+        </repeat>
+        <param argument="--column" type="select" label="Columns" help="Name of columns that will be merged in the output file">
+            <option value="len" selected="True">Length</option>
+            <option value="elen">Effective Length</option>
+            <option value="tpm">Transcripts per Million</option>
+            <option value="numreads">NumReads</option>
+        </param>
+        <param argument="--genes" type="boolean" truevalue="--genes" falsevalue="" checked="False" label="Genes" help="Use gene quantifications instead of transcript"/>
+        <param argument="--missing" type="integer" label="Missing" optional="True" help="The value of missing values"/>
     </inputs>
     <outputs>
         <data name="mergedfile" format="tabular" label="${tool.name} on ${on_string}" from_work_dir="qmergeout.tab"/>