--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_CollectHsMetrics.xml	Fri May 31 03:21:52 2019 -0400
@@ -0,0 +1,92 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool name="CollectHsMetrics" id="picard_CollectHsMetrics" version="@TOOL_VERSION@">
+    <description>compute metrics about datasets generated through hybrid-selection (e.g. exome)</description>
+    <macros>
+        <import>picard_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@java_options@
+@symlink_element_identifier@
+
+picard
+CollectHsMetrics
+INPUT='$escaped_element_identifier'
+OUTPUT='${outFile}'
+MINIMUM_MAPPING_QUALITY=${minimum_mapping_quality}
+MINIMUM_BASE_QUALITY=${minimum_base_quality}
+COVERAGE_CAP=${coverage_cap}
+CLIP_OVERLAPPING_READS=${clip_overlapping_reads}
+BAIT_INTERVALS='${baitFile}'
+TARGET_INTERVALS='${targetFile}'
+VALIDATION_STRINGENCY=${validation_stringency}
+QUIET=true
+VERBOSITY=ERROR
+@TMPDIR_OPTION@
+    ]]></command>
+    <inputs>
+        <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
+        <param name="baitFile" type="data" format="picard_interval_list" label="An interval list file that contains the locations of the baits used" help="If empty, upload or convert from BED" />
+        <param name="targetFile" type="data" format="picard_interval_list" label="An interval list file that contains the locations of the targets" help="If empty, upload or convert from BED" />
+        <param name="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for a read to contribute coverage" help="MINIMUM_MAPPING_QUALITY; default=20" />
+        <param name="minimum_base_quality" type="integer" value="20" label="Minimum base quality for a base to contribute coverage" help="MINIMUM_BASE_QUALITY; default=20" />
+        <param name="coverage_cap" type="integer" value="200" label="Treat bases with coverage exceeding this value as if they had coverage at this value" help="COVERAGE_CAP; default=200" />
+        <param name="clip_overlapping_reads" type="boolean" label="Clip overlapping reads" checked="true" truevalue="true" falsevalue="false" help="CLIP_OVERLAPPING_READS; default=true" />
+        <expand macro="VS" />
+    </inputs>
+    <outputs>
+        <data name="outFile" format="txt" label="${tool.name} on ${on_string}: Summary data" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputFile" value="picard_CollectHsMetrics.bam" ftype="bam" />
+            <param name="baitFile" value="picard_CollectHsMetrics.baits" ftype="picard_interval_list" />
+            <param name="targetFile" value="picard_CollectHsMetrics.target" ftype="picard_interval_list" />
+            <param name="minimum_mapping_quality" value="20" />
+            <param name="minimum_base_quality" value="20" />
+            <param name="coverage_cap" value="200" />
+            <param name="clip_overlapping_reads" value="true" />
+            <output name="outFile" file="picard_CollectHsMetrics_test1.tab" lines_diff="6" />
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**Purpose**
+
+Computes a number of metrics that are useful for evaluating coverage and performance of datasets generated through hybrid-selection. 
+Hybrid-selection (HS) is the most commonly used technique to capture exon-specific sequences for targeted sequencing experiments 
+such as exome sequencing.
+
+@dataset_collections@
+
+-----
+
+.. class:: warningmark
+
+**Obtaining bait and target interval files in Picard interval_list format**
+
+This tool requires an aligned SAM or BAM file as well as bait and target interval files in Picard interval_list format. 
+You should use the bait and interval files that correspond to the capture kit that was used to generate the capture libraries
+for sequencing, which can generally be obtained from the kit manufacturer.
+If the baits and target intervals are provided in BED format, you can convert them to the Picard interval_list format 
+using Picard's **BedToIntervalList** tool, which will also add the required SAM style header.
+
+@description@
+
+  MINIMUM_MAPPING_QUALITY=Integer
+  MQ=Integer                    Minimum mapping quality for a read to contribute coverage.  Default value: 20.
+
+  MINIMUM_BASE_QUALITY=Integer
+  Q=Integer                     Minimum base quality for a base to contribute coverage.  Default value: 20.
+
+  COVERAGE_CAP=Integer
+  CAP=Integer                   Treat bases with coverage exceeding this value as if they had coverage at this value.
+                                Default value: 200.
+  CLIP_OVERLAPPING_READS=Boolean
+                                If true, clip overlapping reads, false otherwise. Default value: true.
+
+@more_info@
+    ]]></help>
+    <expand macro="citations" />
+</tool>