--- a/samtool_filter2.xml	Fri Oct 09 17:24:03 2015 -0400
+++ b/samtool_filter2.xml	Thu Mar 17 11:39:47 2016 -0400
@@ -1,7 +1,7 @@
-<tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.1">
+<tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.2">
   <description>files on FLAG MAPQ RG LN or by region</description>
   <requirements>
-    <requirement type="package" version="0.1.18">samtools</requirement>
+    <requirement type="package" version="1.2">samtools</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" />
@@ -17,7 +17,7 @@
   #set $input = 'input.sam'
   ln -s "$input1" $input &&
 #end if
-samtools view -o "$output1" $header
+samtools view $possibly_select_inverse "$output1" $header
 
   #if $input1.datatype.file_ext == 'sam':
    -S
@@ -115,6 +115,7 @@
     <param name="read_group" type="text" value="" label="Select alignments from Read Group"
            help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>
     <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE" help="(-L)"/>
+    <param name="possibly_select_inverse" checked="false" label="Use inverse selection" type="boolean" truevalue="-U" falsevalue="-o" help="Select the opposite of the listed chromosomes" />
     <param name="regions" type="text" value="" label="Select regions (only used when the input is in BAM format)"
            help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/>
     <param name="outputtype" type="select" label="Select the output format">