--- a/bbmap.xml	Tue May 30 09:01:28 2023 +0000
+++ b/bbmap.xml	Tue Aug 27 10:13:16 2024 +0000
@@ -4,11 +4,11 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="edam_ontology"/>
+    <xrefs>
+        <xref type="bio.tools">bbmap</xref>
+    </xrefs>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-#import os
-#import re
-
 #if str($ref_source_cond.ref_source) == 'cached'
     #set ref = str($ref_source_cond.reference.fields.path)
 #else:
@@ -31,17 +31,15 @@
     #end if
 #else:
     #set read1 = $input_type_cond.reads_collection['forward']
-    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
     ## bbmap uses the file extension to determine the input format.
-    #set ext = $read1_identifier + '.fastq'
+    #set ext = '.fastq'
     #if $read1.ext.endswith('.gz'):
         #set ext = $ext + '.gz'
     #end if
-    #set read1_file = $read1_identifier + $ext
+    #set read1_file = 'forward' + $ext
     ln -s '${read1}' '${read1_file}' &&
     #set read2 = $input_type_cond.reads_collection['reverse']
-    #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
-    #set read2_file = $read2_identifier + $ext
+    #set read2_file = 'reverse' + $ext
     ln -s '${read2}' '${read2_file}' &&
 #end if
 
@@ -204,7 +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"/>
@@ -227,7 +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"/>
@@ -367,4 +365,3 @@
     </help>
     <expand macro="citations"/>
 </tool>
-