--- a/bbmerge.xml	Sat May 18 19:12:59 2024 +0000
+++ b/bbmerge.xml	Tue Aug 27 10:15:19 2024 +0000
@@ -98,7 +98,6 @@
 ]]></command>
     <inputs>
         <expand macro="input_type_cond"/>
-        
         <section name="qt_options" title="Quality and trimming options">
             <param name="qtrim" type="select" label="Select option for quality trimming ends before mapping">
                 <option value="f" selected="true">No trimming</option>
@@ -110,7 +109,6 @@
             <param argument="minlength_after_trim" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
             <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
         </section>
-        
         <section name="merge_options" title="Merging parameters">
             <param name="strictness" type="select" label="Select option for quality trimming ends before mapping">
                 <option value="xstrict">max strict</option>
@@ -128,16 +126,13 @@
             <param argument="trimnonoverlapping" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim all non-overlapping portions, leaving only consensus sequence. By default, only sequence to the right of the overlap (adapter sequence) is trimmed."/>
             <param argument="mininsert" type="integer" value="35" label="Minimum insert size to merge reads"/>
             <param argument="minoverlap" type="integer" value="12" label="Minimum number of overlapping bases to allow merging"/>
-            
             <param argument="minq" type="integer" value="9" label="Ignore bases with quality below this"/>
             <param argument="maxq" type="integer" value="41" label="Cap output quality scores at this"/>
-            
             <param argument="entropy" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Increase the minimum overlap requirement for low-complexity reads"/>
             <param argument="efilter" type="integer" value="6" label="Ban overlaps with over this many times the expected number of errors." help="Lower is more strict, -1 disables."/>
             <param argument="pfilter" type="float" value="0.00004" label="Probability filter to disallow improbable overlaps." help="Higher is stricter. 0 will disable the filter; 1 will allow only perfect overlaps."/>
             <param argument="kfilter" type="integer" value="41" label="Ban overlaps that create kmers with count below this value" help="Requires good coverage, 0 disables."/>
             <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Take quality factors into account" help="If disabled, quality values are completely ignored, both for overlap detection and filtering. May be useful for data with inaccurate quality values."/>
-            
             <conditional name="adapters">
                 <param name="selector" type="select" label="Provide adapter sequences to improve accuracy?">
                     <option value="wout_adapters" selected="true">No</option>
@@ -149,7 +144,6 @@
                     <param argument="adapter2" type="text" value="" label="Right adapter sequence"/>
                 </when>
             </conditional>
-
             <conditional name="merge_mode">
                 <param name="selector" type="select" label="Evaluate overlaps via..." help="In the ratio mode, overlaps are decided based on the ratio of matching to mismatching bases. Flat mode scores overlaps based on the total number of mismatching bases only.">
                     <option value="Ratio mode" selected="true">Ratio mode</option>
@@ -253,4 +247,3 @@
     </help>
     <expand macro="citations"/>
 </tool>
-