--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam2interval.xml	Mon Aug 26 15:12:38 2013 -0400
@@ -0,0 +1,72 @@
+<tool id="sam2interval" name="Convert SAM" version="1.0.1">
+  <description>to interval</description>
+  <command interpreter="python">sam2interval.py --input_sam_file=$input1 $print_all > $out_file1
+  </command>
+  <inputs>
+    <param format="sam" name="input1" type="data" label="Select dataset to convert"/>
+    <param name="print_all" type="select" label="Print all?" help="Do you want to retain original SAM fields? See example below.">
+        <option value="-p">Yes</option>
+        <option value="">No</option>
+    </param>
+  </inputs>
+ <outputs>
+    <data format="interval" name="out_file1" label="Converted Interval" />
+  </outputs>
+<tests>
+    <test>          
+        <param name="input1" value="sam_bioinf_example.sam" ftype="sam"/>
+        <param name="print_all" value="Yes"/>
+        <output name="out_file1" file="sam2interval_printAll.dat" ftype="interval"/>
+    </test>
+    <test>          
+        <param name="input1" value="sam_bioinf_example.sam" ftype="sam"/>
+        <param name="print_all" value="No"/>
+        <output name="out_file1" file="sam2interval_noprintAll.dat" ftype="interval"/>
+    </test>
+    <test>
+        <param name="input1" value="sam2interval-test3.sam" ftype="sam"/>
+        <param name="print_all" value="No"/>
+        <output name="out_file1" file="sam2interval_with_unmapped_reads_noprintAll.dat" ftype="interval"/>
+    </test>
+
+</tests>
+  <help>
+
+**What it does**
+
+Converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.
+
+-----
+
+**Example**
+
+Converting the following dataset::
+
+ r001 163 ref  7 30 8M2I4M1D3M = 37  39 TTAGATAAAGGATACTA *
+ r002   0 ref  9 30 3S6M1P1I4M *  0   0 AAAAGATAAGGATA    *
+ r003   0 ref  9 30       5H6M *  0   0 AGCTAA            * NM:i:1
+ r004   0 ref 16 30    6M14N5M *  0   0 ATAGCTTCAGC       *
+ r003  16 ref 29 30       6H5M *  0   0 TAGGC             * NM:i:0
+ r001  83 ref 37 30         9M =  7 -39 CAGCGCCAT         *
+
+into Interval format will produce the following if *Print all?* is set to **Yes**::
+
+ ref  6 22 + r001 163 ref  7 30 8M2I4M1D3M = 37  39 TTAGATAAAGGATACTA *
+ ref  8 19 + r002   0 ref  9 30 3S6M1P1I4M *  0   0 AAAAGATAAGGATA    *
+ ref  8 14 + r003   0 ref  9 30 5H6M       *  0   0 AGCTAA            * NM:i:1
+ ref 15 40 + r004   0 ref 16 30 6M14N5M    *  0   0 ATAGCTTCAGC       *
+ ref 28 33 - r003  16 ref 29 30 6H5M       *  0   0 TAGGC             * NM:i:0
+ ref 36 45 - r001  83 ref 37 30 9M         =  7 -39 CAGCGCCAT         *
+ 
+Setting  *Print all?* to **No** will generate the following::
+
+ ref  6 22 + r001
+ ref  8 19 + r002
+ ref  8 14 + r003
+ ref 15 40 + r004
+ ref 28 33 - r003
+ ref 36 45 - r001
+
+
+  </help>
+</tool>