--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/covacs_mpileup.xml	Fri Nov 09 06:02:52 2018 -0500
@@ -0,0 +1,76 @@
+ <tool id="covacs_mpileup" name="covacs_mpileup" version="1.9">
+  <description>samtools mpileup wrapper for covacs</description>
+  <macros>
+	<import>bed_macros.xml</import>
+	<import>covacs_macros.xml</import>
+  </macros>
+  <requirements>
+  	<requirement type="package" version="1.9" >samtools</requirement>
+  </requirements>
+  <command>
+    <![CDATA[
+
+
+       samtools mpileup 
+	 -C $adjust 
+	#if $bed_source.bed_source_selector == "history" and $bed_source.bed_history
+	  -l $bed_source.bed_history
+	  #end if
+  	  #if $bed_source.bed_source_selector == "cached"
+   	  -l $bed_source.bed_cached.fields.path
+    	 #end if
+
+	-d $depth
+	-q $MappingQuality
+	-Q $BaseQuality
+	#if $reference_source.reference_source_selector == "cached"
+                -f $reference_source.ref_file.fields.path
+        #end if
+	
+	#if $reference_source.reference_source_selector == "history"
+	
+         -f $reference_source.ref_file_h
+	
+	#end if
+
+	$input1 -A -o $output 2>$log
+
+	
+
+
+
+	]]>
+  </command>
+  <inputs>
+    <param format="bam" name="input1" label="bam-input" type="data" optional="true" />
+    <param name="adjust" type="integer" optional="true" value="50" help="adjust mapping quality"/>
+    <expand macro="bed_loc"/>
+    <param name="depth" type="integer" optional="true" value="100000" help="max per-file depth" />
+    <param name="MappingQuality" type="integer" optional="true" value="0" help="skip alignments with mapQ smaller than INT" />
+    <param name="BaseQuality" type="integer" optional="true" value="0" help="skip bases with baseQ/BAQ smaller than INT" />
+    <expand macro="reference_loc"/>
+  </inputs>
+  <outputs>
+    <data format="pileup" name="output" label="mpileup on ${on_string}"/>
+    <data format="txt" name="log" label="mpileup on ${on_string}:log"/>
+  </outputs>
+  <help>
+**more information** at http://www.htslib.org/doc/samtools-1.2.html
+
+**Implemented options** samtools mpileup
+  -B, --no-BAQ            disable BAQ (per-Base Alignment Quality)
+  -C, --adjust-MQ INT     adjust mapping quality; recommended:50, disable:0 [0]
+  -d, --max-depth INT     max per-file depth; avoids excessive memory usage [8000]
+  -f, --fasta-ref FILE    faidx indexed reference sequence file
+  -l, --positions FILE    skip unlisted positions (chr pos) or regions (BED)
+  -q, --min-MQ INT        skip alignments with mapQ smaller than INT [0]
+  -Q, --min-BQ INT        skip bases with baseQ/BAQ smaller than INT [13]
+**fixed option**
+  -A, --count-orphans     do not discard anomalous read pairs
+
+  </help>
+  <citations>
+        <citation type="doi">10.1186/s12864-018-4508-1</citation>
+  </citations>
+</tool>
+