--- a/ExtractCgMLST.xml	Sat Apr 13 16:09:08 2024 +0000
+++ b/ExtractCgMLST.xml	Sat May 11 22:50:28 2024 +0000
@@ -5,28 +5,24 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        mkdir 'input' &&
-        #for $file in $input_file
-        ln -sf '$file' 'input/${file.element_identifier}.tsv' &&
-        #end for
         chewBBACA.py ExtractCgMLST
         --t $threshold
-        #if str($genes2remove) != 'false'
-            --r 'input/paralogous_counts.tsv'
+        #if $genes2remove:
+            --r '$genes2remove'
         #end if 
         #if $genomes2remove:
             --g '$genomes2remove'
         #end if 
-        -i 'input/results_alleles.tsv' -o 'output'
+        -i '$input_file' -o 'output'
     ]]></command>
     <inputs>
-        <param name="input_file" type="data_collection" collection_type="list" label="AlleleCall Results" format="tabular"/>
+        <param argument="--input-file" type="data" label="Allelic Profiles" format="tabular"/>
         <section name="advanced" title="Advanced options">
             <param argument="--genomes2remove" type="data" format="txt" label="Genomes/rows to remove from the matrix" optional="true" help="One genome identifier per line"/>
             <param argument="--threshold" type="text" value="0.95 0.99 1" label="threshold" help="Genes that constitute the core genome must be in a proportion of genomes that is at least equal to this value. Users can provide multiple values as a space-separated list.">
                 <validator type="regex">[ .0-9]+</validator>
             </param>
-            <param name="genes2remove" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove paralogous counts?" help="the list of genes listed in the &quot;paralogous_counts.tsv&quot; file created by the AlleleCall process. --genes2remove"/>
+            <param argument="--genes2remove" type="data" format="tabular" label="List of genes  to exclude from analysis" optional="true" help="the list of genes listed in the &quot;paralogous_counts.tsv&quot; file created by the AlleleCall process."/>
         </section>
     </inputs>
     <outputs>
@@ -36,11 +32,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="input_file">
-                <collection type="list">
-                    <element name="results_alleles" value="results_alleles.tsv" ftype="tabular"/>
-                </collection>
-            </param>
+            <param name="input_file" value="results_alleles.tsv"/>
             <output_collection name="output_collection" type="list">
                 <element name="missing_loci_stats">
                     <assert_contents>