--- a/lastal.xml	Wed Jul 22 19:50:13 2020 -0400
+++ b/lastal.xml	Thu Sep 10 16:08:15 2020 +0000
@@ -15,9 +15,20 @@
             ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
         #end if
         
-	lastal
+        lastal
 
-        -Q $lastal.Q
+        #if $query_seq.ext == 'fasta'
+            -Q 0
+        #else if $query_seq.ext == 'fastqsanger'
+            -Q 1
+        #else if $query_seq.ext == 'fastqsolexa'
+            -Q 2
+        #else if $query_seq.ext == 'fastqillumina'
+            -Q 3
+        #else if $query_seq.ext == 'pssm'
+            -Q 5            
+        #end if
+
         -f $lastal.f
         -j $lastal.j
 
@@ -68,23 +79,16 @@
             'db_files/lastdb'
         #end if
 
-        '$query_fasta'
+        '$query_seq'
 
         >'$outfile'
     ]]></command>
 
     <inputs>
         <expand macro="input_db"/>
-        <param name="query_fasta" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina,tabular" label="Queries FASTA file"/>
+        <param name="query_seq" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina,tabular" label="Query sequences"/>
 
         <section name="lastal" title="Lastal arguments" expanded="true">
-            <param argument="-Q" type="select" multiple="false" label="Query input format">
-                <option value="0" selected="true">FASTA</option>
-                <option value="1">fastq-sanger</option>
-                <option value="2">fastq-solexa</option>
-                <option value="3">fastq-illumina</option>
-                <option value="5">PSSM</option>
-            </param>            
             <param argument="-f" type="select" multiple="false" label="Output format">
                 <option value="MAF" selected="true">MAF</option>
                 <option value="TAB">TAB</option>
@@ -328,7 +332,14 @@
     </inputs>
 
     <outputs>
-        <data name="outfile" format="maf" label="LAST align from ${on_string}" />
+        <data name="outfile" format="maf" label="LAST align from ${on_string}" >
+            <change_format>
+                <when input="f" value="MAF" format="maf" />
+                <when input="f" value="TAB" format="tabular" />
+                <when input="f" value="BlastTab" format="tabular" />
+                <when input="f" value="BlastTab+" format="tabular" />
+            </change_format>
+        </data>
     </outputs>
 
     <tests>
@@ -337,7 +348,7 @@
                 <param name="db_opts_input" value="db"/>
                 <param name="database" value="humdb"/>
             </conditional>
-            <param name="query_fasta" value="fuguMito.fa" ftype="fasta"/>
+            <param name="query_seq" value="fuguMito.fa" ftype="fasta"/>
             <output name="outfile" ftype="maf" file="last_align_gen.maf" lines_diff="2"/>
         </test>
         <test>
@@ -350,9 +361,20 @@
                     <param name="lastal_protein" value="prot"/>
                 </conditional>
             </section>
-            <param name="query_fasta" value="hedgehog_prot_drosophila.fa" ftype="fasta"/>
+            <param name="query_seq" value="hedgehog_prot_drosophila.fa" ftype="fasta"/>
             <output name="outfile" ftype="maf" file="last_align_prot.maf" lines_diff="2"/>
         </test>
+        <test>
+            <conditional name="db_opts">
+                <param name="db_opts_input" value="db"/>
+                <param name="database" value="humdb-sanger"/>
+            </conditional>
+            <param name="query_seq" value="fuguMito.fq" ftype="fastqsanger"/>
+            <section name="lastal">
+                <param name="Q" value="1"/>
+            </section>
+            <output name="outfile" ftype="maf" file="last_align_fastq.maf" lines_diff="2"/>
+        </test>        
     </tests>
 
     <help>@LAST_HELP@</help>