--- a/mafft.xml	Wed Mar 20 07:34:52 2024 +0000
+++ b/mafft.xml	Thu Aug 22 19:20:24 2024 +0000
@@ -6,12 +6,8 @@
     </macros>
     <expand macro="biotools"/>
     <expand macro="requirements" />
-    <stdio>
-        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
-        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
-    </stdio>
-    <version_command><![CDATA[mafft --version]]></version_command>
-    <command><![CDATA[
+    <version_command>mafft --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
   ## Concatenate all input datasets no matter how they were provided
   bash inputs.sh &&
 
@@ -170,7 +166,7 @@
             </when>
             <when value="merge">
                 <repeat name="batches" title="Input batch" default="1" min="1">
-                    <param name="inputs" multiple="true" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>
+                    <param name="inputs" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format." multiple="true"/>
                 </repeat>
             </when>
         </conditional>
@@ -187,7 +183,7 @@
                         <option value="--kimura">Kimura</option>
                     </param>
                     <when value="--kimura">
-                        <param argument="--kimura" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix" />
+                        <param name="coefficient" argument="--kimura" type="integer" min="1" value="200" label="PAM value of the matrix" />
                     </when>
                 </conditional>
                 <expand macro="misc_scoring_scheme" />
@@ -201,7 +197,7 @@
                         <option value="custom">custom matrix</option>
                     </param>
                     <when value="--bl">
-                        <param argument="--bl" name="coefficient" type="select" display="radio" label="Coefficient of the BLOSUM matrix">
+                        <param name="coefficient" argument="--bl" type="select" label="Coefficient of the BLOSUM matrix" display="radio">
                             <option value="30">30</option>
                             <option value="45">45</option>
                             <option value="62" selected="true">62</option>
@@ -209,10 +205,10 @@
                         </param>
                     </when>
                     <when value="--jtt">
-                        <param argument="--jtt" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix" />
+                        <param name="coefficient" argument="--jtt" type="integer" min="1" value="200" label="PAM value of the matrix" />
                     </when>
                     <when value="--tm">
-                        <param argument="--tm" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix"/>
+                        <param name="coefficient" argument="--tm" type="integer" min="1" value="200" label="PAM value of the matrix"/>
                     </when>
                     <when value="custom">
                         <param argument="--aamatrix" type="data" format="txt" label="User-defined AA scoring matrix" help="The expected format of the matrix is the same as that used by BLAST."/>
@@ -267,7 +263,7 @@
                                 <option value="--fastapair">All pairwise alignments are computed with FASTA (--fastapair)</option>
                             </param>
                             <when value="--6merpair">
-                                <param argument="--retree" type="integer" value="2" min="1" max="3" label="Guide tree is build this number of times in the progressive stage."/>
+                                <param argument="--retree" type="integer" min="1" max="3" value="2" label="Guide tree is build this number of times in the progressive stage."/>
                             </when>
                             <when value="--globalpair">
                                 <expand macro="global_align_options"/>
@@ -312,7 +308,7 @@
                     </when>
                 </conditional>
                 <section name="progressive_alignment_calculation" title="Progressive alignment calculation" expanded="true">
-                    <param argument="--maxiterate" type="integer" value="0" min="0" max="1000" label="Maximum number of iterations" help="1000 for maximum quality" />
+                    <param argument="--maxiterate" type="integer" min="0" max="1000" value="0" label="Maximum number of iterations" help="1000 for maximum quality" />
                     <param argument="--fft" type="boolean" truevalue="--fft" falsevalue="--nofft" checked="True" label="Use FFT approximation in group-to-group alignment?" />
                     <param argument="--noscore" type="boolean" truevalue="" falsevalue="--noscore" checked="True" label="Check alignment score in the iterative refinement stage?" />
                 </section>
@@ -391,7 +387,7 @@
                 <param name="type" value="mafft-fftns"/>
             </conditional>
             <param name="outputFormat" value="--clustalout"/>
-            <output name="outputAlignment" ftype="clustal" file="mafft_explicit_amino_blosum80.clustal.aln" />
+            <output name="outputAlignment" ftype="clustal" file="mafft_explicit_amino_blosum80.clustal.aln" lines_diff="2" />
         </test>
         <test expect_num_outputs="1" >
             <conditional name="input">
@@ -437,7 +433,7 @@
                 </section>
             </conditional>
             <param name="outputFormat" value="--clustalout"/>
-            <output name="outputAlignment" ftype="clustal" file="mafft_custom_original.clustal.aln">
+            <output name="outputAlignment" ftype="clustal" file="mafft_custom_original.clustal.aln" lines_diff="2">
             </output>
         </test>
         <test expect_num_outputs="1">