--- a/bbmap.xml	Sat May 18 19:14:17 2024 +0000
+++ b/bbmap.xml	Tue Aug 27 10:15:02 2024 +0000
@@ -202,7 +202,7 @@
             <param argument="untrim" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Undo trimming after mapping?" help="Untrimmed bases will be soft-clipped in cigar strings"/>
             <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/>
             <param argument="mintrimlength" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
-            <param argument="fakefastaquality" type="integer" value="-1" max="50" label="Set to a positive number 1-50 to generate fake quality strings for fasta input reads"/>
+            <param argument="fakefastaquality" type="integer" max="50" value="-1" label="Set to a positive number 1-50 to generate fake quality strings for fasta input reads"/>
             <param argument="ignorebadquality" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Keep going, rather than crashing, if a read has out-of-range quality values?"/>
             <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
             <param argument="minaveragequality" type="integer" value="0" label="Do not map reads with average quality below this value"/>
@@ -225,7 +225,7 @@
             </param>
         </section>
         <section name="pf_options" title="Post-filtering options">
-            <param argument="idfilter" type="integer" value="0" min="0" max="1" label="Specify exact minimum identity allowed for alignments to be output" help="Independent of approximate minimum alignment identity to look for"/>
+            <param argument="idfilter" type="integer" min="0" max="1" value="0" label="Specify exact minimum identity allowed for alignments to be output" help="Independent of approximate minimum alignment identity to look for"/>
             <param argument="subfilter" type="integer" value="-1" label="Ban alignments with more than this many substitutions" help="Negative value ignores"/>
             <param argument="insfilter" type="integer" value="-1" label="Ban alignments with more than this many insertions" help="Negative value ignores"/>
             <param argument="delfilter" type="integer" value="-1" label="Ban alignments with more than this many deletions" help="Negative value ignores"/>
@@ -365,4 +365,3 @@
     </help>
     <expand macro="citations"/>
 </tool>
-