--- a/samtools_bedcov.xml	Mon Jul 29 08:47:23 2019 -0400
+++ b/samtools_bedcov.xml	Tue Sep 28 16:11:43 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_bedcov" name="BedCov" version="2.0.2">
+<tool id="samtools_bedcov" name="Samtools bedcov" version="2.0.3" profile="@PROFILE@">
     <description>calculate read depth for a set of genomic intervals</description>
     <macros>
         <import>macros.xml</import>
@@ -14,44 +14,89 @@
                 -Q $mapq
             #end if
             $countdel
+            #set $filter = $additional_options.required_flags
+            @FLAGS@
+            -g $flags
+            #set $filter = $additional_options.skipped_flags
+            @FLAGS@
+            -G $flags
+            #if $depth_thresh:
+                -d $depth_thresh
+            #end if
             '${input_bed}'
-            #for $i in range(len( $input_bams )):
+            #for $i in range(len($input_bams)):
                 '${i}'
             #end for
             > '${output}'
     ]]></command>
     <inputs>
-        <param name="input_bed" type="data" format="bed" label="Genemic intervals (in BED format)" />
+        <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" />
         <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
         <param name="mapq" argument="-Q" type="integer" value="" optional="true" label="Minimum MAPQ" help="Only count reads with mapping quality greater than this value" />
         <param name="countdel" argument="-j" type="boolean" checked="false" truevalue="-j" falsevalue="" label="Exclude deletions and ref skips" help=" Do not include deletions (D) and ref skips (N) in bedcov computation" />
+        <param name="depth_thresh" argument="-d" type="integer" value="" min="0" optional="true" label="Depth threshold" help="Number of reference bases with coverage above and including this value will be displayed in a separate column." />
+
+        <section name="additional_options" title="Additional Filter Options">
+            <param name="required_flags" argument="-g" type="select" multiple="True" label="Require that these flags are set.">
+                <expand macro="flag_options" />
+            </param>
+
+            <param name="skipped_flags" argument="-G" type="select" multiple="True" label="Exclude reads with any of the following flags set (the default set is UNMAP,SECONDARY,QCFAIL,DUP or 0x704).">
+                <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/>
+            </param>
+        </section>
     </inputs>
     <outputs>
         <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
     </outputs>
     <tests>
+        <!-- 1) -->
         <test>
             <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             <param name="input_bams" value="eboVir3.bam" ftype="bam" />
             <output name="output" file="samtools_bedcov_out1.tab" />
         </test>
+        <!-- 2) -->
         <test>
             <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
             <output name="output" file="samtools_bedcov_out2.tab" />
         </test>
+        <!-- 3) -->
         <test>
             <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             <param name="input_bams" value="eboVir3.bam" ftype="bam" />
             <param name="mapq" value="40"/>
             <output name="output" file="samtools_bedcov_out1.tab" />
         </test>
+        <!-- 4) -->
         <test>
             <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
             <param name="countdel" value="-j" />
             <output name="output" file="samtools_bedcov_out2.tab" />
         </test>
+        <!-- 5) Testing argument -g -->
+        <test>
+            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
+            <param name="input_bams" value="eboVir3.bam" ftype="bam" />
+            <param name="required_flags" value="2,16,64" />
+            <output name="output" file="samtools_depth_out5.tab" />
+        </test>
+        <!-- 6) Testing argument -G -->
+        <test>
+            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
+            <param name="input_bams" value="eboVir3.bam" ftype="bam" />
+            <param name="skipped_flags" value="2,16,64" />
+            <output name="output" file="samtools_depth_out6.tab" />
+        </test>
+        <!-- 7) Testing depth threshold -d -->
+        <test>
+            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
+            <param name="input_bams" value="eboVir3.bam" ftype="bam" />
+            <param name="depth_thresh" value="10" />
+            <output name="output" file="samtools_bedcov_out7.tab" />
+        </test>
     </tests>
     <help>
 **What it does**