--- a/umi-tools_extract.xml	Wed Jan 29 10:09:09 2025 +0000
+++ b/umi-tools_extract.xml	Fri Feb 28 20:41:17 2025 +0000
@@ -83,7 +83,7 @@
     ]]></command>
     <inputs>
         <expand macro="input_types">
-                <param argument="--reconcile-pairs" type="boolean" truevalue="--reconcile-pairs" falsevalue="" checked="false" label="Allow unpaired reads" help="Allow the presences of reads in read2 input that are not present in read1 input. This allows cell barcode filtering of read1s without considering read2s" />
+            <param argument="--reconcile-pairs" type="boolean" truevalue="--reconcile-pairs" falsevalue="" checked="false" label="Allow unpaired reads" help="Allow the presences of reads in read2 input that are not present in read1 input. This allows cell barcode filtering of read1s without considering read2s" />
         </expand>
         <expand macro="fastq_barcode_extraction_options_macro"/>
 
@@ -134,8 +134,8 @@
             <conditional name="extract_method_cond">
                 <param name="prime3" value="true" />
             </conditional>
-            <param name="quality_selector" value="true" />
-            <param name="quality_filter_threshold" value="10" />
+            <param name="quality|quality_selector" value="true" />
+            <param name="quality|quality_filter_threshold" value="10" />
             <param name="log" value="true"/>
             <output name="out" file="out_SE.fastq" ftype="fastqsanger" />
             <output name="out_log" >
@@ -166,7 +166,6 @@
         <test expect_num_outputs="4">
             <conditional name="input_type_cond">
                 <param name="input_type" value="paired_collection" /> <!-- same as before, but uncompressed -->
-                <param name="paired_type" value="no" />
                 <param name="input_readpair">
                     <collection type="paired" >
                         <element name="forward" ftype="fastqsanger" value="t_R1.fastq" />
@@ -194,7 +193,7 @@
                 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastqsanger.gz" />
                 <param name="bc_pattern" value="CCCCCCNNNNNNNNNN" />
             </conditional>
-            <param name="extract_method" value="string" />
+            <param name="extract_method_cond|extract_method" value="string" />
             <param name="whitelist" value="scrb_seq_barcodes" />
             <param name="log" value="true"/>
             <output name="out2" file="scrb_extract.fastq.gz" decompress="true"  ftype="fastqsanger.gz" />
@@ -206,7 +205,7 @@
                 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastqsanger.gz" />
                 <param name="bc_pattern" value="^(?P&lt;cell_1&gt;.{6})(?P&lt;umi_1&gt;.{10})" />
             </conditional>
-            <param name="extract_method" value="regex" />
+            <param name="extract_method_cond|extract_method" value="regex" />
             <param name="whitelist" value="scrb_seq_barcodes" />
             <param name="log" value="true"/>
             <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastqsanger.gz" />
@@ -218,7 +217,7 @@
                 <param name="input_read2" value="read_R2.200.gz" ftype="fastqsanger.gz" />
                 <param name="bc_pattern" value="NNNNNNCCCCCC" />
             </conditional>
-            <param name="extract_method" value="string" />
+            <param name="extract_method_cond|extract_method" value="string" />
             <output name="out" file="read_R1.200_extracted.fastq.gz" ftype="fastqsanger.gz" decompress="true" lines_diff="1" />
             <output name="out2" file="read_R2.200_extracted.fastq.gz" ftype="fastqsanger.gz" decompress="true" lines_diff="1" />
         </test>