--- a/blast2rma.xml	Wed Nov 24 21:52:14 2021 +0000
+++ b/blast2rma.xml	Fri Dec 03 23:09:53 2021 +0000
@@ -114,8 +114,8 @@
 --lcaAlgorithm '$advanced_options.lcaAlgorithm'
 --lcaCoveragePercent $advanced_options.lcaCoveragePercent
 --readAssignmentMode '$advanced_options.readAssignmentMode'
-#if str($advanced_options.con_file_cond.conFile) == 'yes':
-    --conFile '$advanced_options.con_file_cond.conFile'
+#if $advanced_options.conFile:
+    --conFile '$advanced_options.conFile'
 #end if
 #if str($input_type_cond.input_type) == 'paired':
     && mv './tmp.rma6' '$rma6_output'
@@ -127,35 +127,14 @@
             <expand macro="blast_mode_options"/>
         </param>
         <section name="advanced_options" title="Advanced options" expanded="false">
-            <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/>
+            <expand macro="long_reads_param"/>
             <param argument="--maxMatchesPerRead" type="integer" value="100" label="Maximum matches per read"/>
-            <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/>
-            <expand macro="common_blast_params"/>
-            <param argument="--minSupportPercent" type="float" value="0.05" min="0.0" max="100.0" label="Minimum support as percent of assigned reads" help="0 value ignores"/>
-            <param argument="--minSupport" type="integer" value="0" label="Minimum support" help="0 value ignores"/>
-            <param argument="--minPercentReadCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of read length to be covered by alignments"/>
-            <param argument="--minPercentReferenceCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of reference length to be covered by alignments"/>
-            <param argument="--minReadLength" type="integer" value="0" label="Minimum read length"/>
-            <param argument="--lcaAlgorithm" type="select" label="Select the LCA algorithm to use for taxonomic assignment">
-                <option value="naive" selected="true">naive</option>
-                <option value="weighted">weighted</option>
-                <option value="longReads">longReads</option>
-            </param>
-            <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Percent for the LCA to cover"/>
-            <param argument="--readAssignmentMode" type="select" label="Select the read assignment mode">
-                <option value="alignedBases" selected="true">alignedBases</option>
-                <option value="readCount">readCount</option>
-            </param>
-            <conditional name="con_file_cond">
-                <param argument="--conFile" type="select" label="Process a file of contaminant taxa" help="One id or name per line">
-                    <option value="no" selected="true">No</option>
-                    <option value="yes">Yes</option>
-                </param>
-                <when value="no"/>
-                <when value="yes">
-                    <param argument="conFile" type="data" format="txt" label="File of contaminant taxa"/>
-                </when>
-            </conditional>
+            <expand macro="classify_param"/>
+            <expand macro="blast_params"/>
+            <expand macro="min_max_params"/>
+            <expand macro="lca_params"/>
+            <expand macro="read_assignment_mode_param"/>
+            <expand macro="con_file_param"/>
         </section>
     </inputs>
     <outputs>
@@ -178,7 +157,6 @@
             <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
             <param name="blast1" value="blast_R1.txt" ftype="txt"/>
             <param name="blastMode" value="BlastN"/>
-            <param name="conFile" value="yes"/>
             <param name="conFile" value="contaminants.txt" ftype="txt"/>
             <output name="rma6_output" ftype="rma6">
                 <assert_contents>
@@ -239,8 +217,6 @@
 This tool outputs a RealMedia Audio (RMA) file.  MEGAN uses an update of the original RMA file format known as RMA6.  This update
 requires less disk space for files.
     </help>
-    <citations>
-        <citation type="doi">https://doi.org/10.1101/050559</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>