--- a/fgbio_fastq_to_bam.xml	Wed Feb 24 13:01:53 2021 +0000
+++ b/fgbio_fastq_to_bam.xml	Thu Aug 19 15:11:08 2021 +0000
@@ -6,16 +6,11 @@
     <expand macro="requirements" />
     <version_command>fgbio --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
+        @LINK_FASTQ_INPUTS@
         fgbio FastqToBam 
-        --input 
-        #for $input in $inputs
-            '$input'
-        #end for
+        @FASTQ_INPUTS@
         --sample='$sample'
         --library='$library'
-        #if $read_structures:
-            --read-structures $read_structures
-        #end if
         --sort='$sort'
         --output '$output'
         ## optional bam header content
@@ -51,13 +46,12 @@
         #end if
     ]]></command>
     <inputs>
-        <param name="inputs" type="data" format="fastq" multiple="true" label="Fastq files corresponding to each sequencing read"/>
+        <expand macro="fastq_inputs"/>
         <param argument="--sample" type="text" value="" label="The name of the sequenced sample">
+            <validator type="empty_field"/>
         </param>
         <param argument="--library" type="text" value="" label="The name/ID of the sequenced library">
-        </param>
-        <param argument="--read-structures" type="text" value="" optional="true" label="Read structures, one for each of the FASTQ">
-            <expand macro="read_structures_validator" />
+            <validator type="empty_field"/>
         </param>
         <param argument="--sort" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sort bam by queryname" 
                help="If true, queryname sort the BAM file, otherwise preserve input order."/>