--- a/ppanggolin_msa.xml	Mon Jun 02 10:09:11 2025 +0000
+++ b/ppanggolin_msa.xml	Tue Sep 16 13:11:09 2025 +0000
@@ -8,8 +8,8 @@
     
     <command detect_errors="exit_code"><![CDATA[
         
-        mkdir -p "./tmp_ppanggolin/msa" &&
-        mkdir -p "./tmp_ppanggolin/tmpdir_msa" &&
+        mkdir -p ./tmp_ppanggolin/msa &&
+        mkdir -p ./tmp_ppanggolin/tmpdir_msa &&
         
         ppanggolin msa
         --pangenome '$pangenome_h5'
@@ -46,7 +46,7 @@
 
     <inputs>
     
-        <param argument="--pangenome" name="pangenome_h5" type="data" format="h5" label="Input pangenome h5 file"/>
+        <expand macro="inputs_pangenome"/>
 
         <conditional name="input_choose_partition">
             <param argument="--partition" name="choice_partition" type="select" label="Partition">
@@ -63,7 +63,7 @@
             <when value="shell"/>
             <when value="cloud"/>
             <when value="softcore">
-                <param argument="--soft_core" name="choice_soft_core" type="float" value="0.95" min="0" max="1" label="Soft core threshold to use if 'softcore' partition is chosen"/>
+                <expand macro="inputs_soft_core"/>
             </when>
             <when value="accessory"/>
             <when value="all"/>
@@ -77,42 +77,14 @@
         <param argument="--phylo" name="do_phylo" type="boolean" checked="true" label="Writes a whole genome msa file for additional phylogenetic analysis (recommended)" truevalue="--phylo" falsevalue=""/>
 
         <param argument="--single_copy" name="do_single_copy" type="boolean" checked="false" label="Report gene families that are considered 'single copy'" truevalue="--single_copy" falsevalue=""/>
-            
-        <param argument="--translation_table" type="select" label="Translation table">
-            <option value="1" selected="true">1 - Standard Code</option>
-            <option value="2">2 - Vertebrate Mitochondrial</option>
-            <option value="3">3 - Yeast Mitochondrial</option>
-            <option value="4">4 - Mold, Protozoan, and Coelenterate Mitochondrial</option>
-            <option value="5">5 - Invertebrate Mitochondrial</option>
-            <option value="6">6 - Ciliate Nuclear</option>
-            <option value="9">9 - Echinoderm Mitochondrial</option>
-            <option value="10">10 - Euplotid Nuclear</option>
-            <option value="11">11 - Bacterial and Plant Plastid</option>
-            <option value="12">12 - Alternative Yeast Nuclear</option>
-            <option value="13">13 - Ascidian Mitochondrial</option>
-            <option value="14">14 - Flatworm Mitochondrial</option>
-            <option value="15">15 - Blepharisma Nuclear</option>
-            <option value="16">16 - Chlorophycean Mitochondrial</option>
-            <option value="21">21 - Trematode Mitochondrial</option>
-            <option value="22">22 - Scenedesmus obliquus Mitochondrial</option>
-            <option value="23">23 - Thraustochytrium Mitochondrial</option>
-            <option value="24">24 - Pterobranchia Mitochondrial</option>
-            <option value="25">25 - Candidate Division SR1 and Gracilibacteria</option>
-            <option value="26">26 - Pachysolen tannophilus Nuclear</option>
-            <option value="27">27 - Karyorelict Nuclear</option>
-            <option value="28">28 - Condylostoma Nuclear</option>
-            <option value="29">29 - Mesodinium Nuclear</option>
-            <option value="30">30 - Peritrich Nuclear</option>
-            <option value="31">31 - Blastocrithidia Nuclear</option>
-            <option value="32">32 - Balanophoraceae Plastid</option>
-            <option value="33">33 - Cephalodiscidae Mitochondrial</option>
-        </param>
+
+        <expand macro="inputs_translation_table"/>
         
     </inputs>
 
     <outputs>
         <data name="archive_msa_partition_source" format="tar.gz" label="PPanGGOLiN msa on ${on_string}: archive msa ${choice_partition} ${choice_source}" />
-        <data name="partition_genome_alignment" format="aln" label="PPanGGOLiN msa on ${on_string}: ${choice_partition} genome alignment" >
+        <data name="partition_genome_alignment" format="maf" label="PPanGGOLiN msa on ${on_string}: ${choice_partition} genome alignment" >
           <filter>do_phylo is True</filter>
         </data>
     </outputs>