--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FilterBAMByNamesList.xml	Wed Mar 25 13:33:46 2015 -0600
@@ -0,0 +1,43 @@
+<?xml version="1.0"?>
+
+<tool id="filter_bam_by_list_1" name="Filter a BAM file">
+  <description>against a list of desired genomic regions, by name</description>
+  <version_string>echo 1.0.0</version_string>
+  <command interpreter="perl">filter_bam_by_list $bam_file $named_gene_regions_bed 
+            ## Handle reference file.
+            #if $geneNameSource.source == "file":
+                $geneNameSource.file_of_names 
+            #else:
+                "${geneNameSource.name_list}"
+            #end if
+     $filtered_bam_file $retained_regions_bed $samtools_messages</command>
+  <inputs>
+    <param format="bam" name="bam_file" type="data" label="Source BAM (mapped reads) file"/>
+    <param format="bed" name="named_gene_regions_bed" type="data" label="BED file with names for genomic regions (e.g. the UCSC hg19 refFlat gene names file available under 'Shared Data Libraries' -&gt; 'Genomic coding sequence regions')"/>
+    <conditional name="geneNameSource">
+       <param name="source" type="select" label="How would you like to specify the list of target region names?">
+            <option value="file">A file</option>
+            <option value="list">A list</option>
+       </param>
+       <when value="file">
+         <param format="text" name="file_of_names" type="data" label="Text file with target region names (usually gene names), one per line" help="Mapped reads in regions with any of these names are retained"/>
+       </when>
+       <when value="list">
+         <param name="name_list" type="text" label="Space separated list of target region names (usually gene names)" help="Mapped reads in regions with any of these names are retained"/>
+       </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data name="filtered_bam_file" format="bam" type="data" label="Reads mapped to target regions"/>
+    <data name="retained_regions_bed" format="bed" type="data" label="BED file of retained regions"/>
+    <data name="samtools_messages" format="text" type="data" label="Samtools messages"/>
+  </outputs>
+
+  <tests/>
+
+  <help>
+This tool retains sequence reads of a BAM file that map to genomics regions matching any of the labels in the "names" file. This is useful for example to 
+report only a subset of an exome run that corresponds to a set of genes of interest. The names file should have one name per line. 
+ </help>
+
+</tool>