--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_FilterSamReads.xml	Tue Dec 16 19:03:21 2014 -0500
@@ -0,0 +1,134 @@
+<tool name="FilterSamReads" id="picard_FilterSamReads" version="1.126.0">
+  <description>include or exclude aligned and unaligned reads and read lists</description>
+  <requirements>
+    <requirement type="package" version="1.126.0">picard</requirement>
+  </requirements>
+  
+  <macros>
+    <import>picard_macros.xml</import>
+  </macros>
+  
+  <command>
+    @java_options@
+    
+    ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order
+    
+    java -jar \$JAVA_JAR_PATH/picard.jar
+    SortSam
+    INPUT="${inputFile}"
+    OUTPUT=query_sorted_bam.bam
+    SORT_ORDER=queryname
+    VALIDATION_STRINGENCY=LENIENT
+    QUIET=true
+    VERBOSITY=ERROR
+    
+    &amp;&amp;
+    
+    java -jar \$JAVA_JAR_PATH/picard.jar
+    FilterSamReads
+    INPUT=query_sorted_bam.bam
+    FILTER="${filter_type.filter}"
+    
+    #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ):
+      READ_LIST_FILE="${filter_type.read_list_file}"
+    #end if
+    
+    OUTPUT="${outFile}"
+    SORT_ORDER=coordinate
+    VALIDATION_STRINGENCY="${validation_stringency}"
+    QUIET=true
+    VERBOSITY=ERROR
+  
+  </command>
+  <inputs>
+    <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
+    <conditional name="filter_type">
+      <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info">
+        <option value="includeAligned">Include aligned</option>
+        <option value="excludeAligned">Exclude aligned</option>
+        <option value="includeReadList">Include read list</option>
+        <option value="excludeReadList">Exclude read list</option>
+      </param>
+      <when value="includeAligned"/> <!-- do nothing -->
+      <when value="excludeAligned"/> <!-- do nothing -->
+      <when value="includeReadList">
+        <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be INCLUDED in the output" help="READ_LIST_FILE"/>
+      </when>
+      <when value="excludeReadList">
+        <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be EXCLUDED in the output" help="READ_LIST_FILE"/>
+      </when>
+    </conditional>
+    
+    <expand macro="VS" />
+    
+  </inputs> 
+  
+  <outputs>
+    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
+      <param name="filter" value="includeReadList"/>
+      <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
+      <param name="validation_stringency" value="LENIENT"/>
+      <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="2"/>
+    </test>
+    <test>
+      <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
+      <param name="filter" value="excludeReadList"/>
+      <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
+      <param name="validation_stringency" value="LENIENT"/>
+      <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="2"/>
+    </test>
+  </tests>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  <help>
+
+**Purpose**
+
+Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
+
+------
+
+.. class:: warningmark
+
+**Warning on using this tool on BWA-MEM output**
+
+This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts. 
+
+@dataset_collections@
+
+@description@
+
+  FILTER=Filter                 Filter.  Required. Possible values:
+                                includeAligned [OUTPUT SAM/BAM will contain aligned 
+                                reads only. (Note that *both* first and 
+                                second of paired reads must be aligned to be included
+                                in the OUTPUT SAM or BAM)], 
+                                
+                                excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only.
+                                (Note that *both* first and second of pair must be aligned to be 
+                                excluded from the OUTPUT SAM or BAM)]
+                                
+                                includeReadList [OUTPUT SAM/BAM will contain reads 
+                                that are supplied in the READ_LIST_FILE file]
+                                
+                                excludeReadList [OUTPUT bam will contain 
+                                reads that are *not* supplied in the READ_LIST_FILE file]} 
+
+  READ_LIST_FILE=File
+  RLF=File                      Read List File containing reads that will be included or excluded from the OUTPUT SAM or 
+                                BAM file.  Default value: null. 
+  
+@more_info@
+
+  </help>
+</tool>
+
+