--- a/seqtk_mergefa.xml	Sat Dec 09 11:14:21 2023 +0000
+++ b/seqtk_mergefa.xml	Wed Oct 16 09:08:52 2024 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
-<tool id="seqtk_mergefa" name="seqtk_mergefa" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
-    <description>merge two FASTA/Q files</description>
+<tool id="seqtk_mergefa" name="seqtk_mergefa" version="@TOOL_VERSION@+galaxy1" profile="22.05">
+    <description>Merge two FASTA/Q files into a FASTA file output</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -18,17 +18,28 @@
 '$in_fa2'
 #echo "| pigz -p ${GALAXY_SLOTS:-1} --no-name --no-time" if $in_fa1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
     ]]></command>
+    <configfiles>
+        <configfile filename="outputs.json">
+#set $ext = None
+#if $in_fa1.is_of_type('fasta.gz', 'fastq.gz')
+    #set $ext = "fasta.gz"
+#else
+    #set $ext = "fasta"
+#end if
+{"default": {"ext": "$ext"}}
+        </configfile>
+    </configfiles>
     <inputs>
         <param name="in_fa1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
         <param name="in_fa2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #2"/>
-        <param argument="-q" type="integer" value="0" label="Quality threshold"/>
+        <param argument="-q" type="integer" value="0" label="Quality threshold (for FASTQ)"/>
         <param argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Take intersection" />
-        <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Convert to lowercase when one of the input base is N" />
+        <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Pick least ambiguous, mask conflicts and uncertainties" help="Tries to pick the least ambiguous symbol from the two inputs, but masks contradictory bases in the inputs as x in the merged result and converts the merged base to lowercase where one of the input bases is an N." />
         <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Pick a random allele from het" />
         <param argument="-h" type="boolean" truevalue="-h" falsevalue="" checked="false" label="Suppress hets in the input" />
     </inputs>
-    <outputs>
-        <data name="default" format_source="in_fa1" label="${tool.name} on ${on_string}"/>
+    <outputs provided_metadata_file="outputs.json">
+        <data name="default" format="auto" label="${tool.name} on ${on_string}" />
     </outputs>
     <tests>
         <test>
@@ -52,24 +63,27 @@
     <help><![CDATA[
 **What it does**
 
-Merges two fasta files, using ambiguity codes
+This tool merges two FASTA or FASTQ files into a single FASTA file using IUPAC ambiguity codes where appropriate. 
+When differences occur between the sequences, ambiguity codes are used to represent possible variations. 
 
-::
+Example::
 
-    # seq1.fa
-    >test0
-    ACTGACTGAAA
+  >seq1
+  ACTGACTGAAA
+
+  >seq2
+  ACTGAMTGCGN
 
-    # seq2.fa
-    >test0
-    ACTGAMTGCGN
+will result in::
+
+  >seq1
+  ACTGAMTGMRN
 
-In the following the `-m` option has been set to highlight seqtk-mergefa's features.
+If the `-m` option is in use, however, the tool will pick the least ambiguous base if there is no contradiction between the symbols in the inputs. Conflicts are indicated by using x in the merged sequence and the picked base is converted to lowercase if the less specific symbol is an N to express uncertainty.
+With this logic the input sequences above will result in the merge result::
 
-::
-
-    >test0
-    ACTGACTGxxa
+  >seq1
+  ACTGACTGxxa
 
 @ATTRIBUTION@
     ]]></help>