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comparison tools/samtools/sam2interval.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="sam2interval" name="Convert SAM" version="1.0.1">
2 <description>to interval</description>
3 <command interpreter="python">sam2interval.py --input_sam_file=$input1 $print_all > $out_file1
4 </command>
5 <inputs>
6 <param format="sam" name="input1" type="data" label="Select dataset to convert"/>
7 <param name="print_all" type="select" label="Print all?" help="Do you want to retain original SAM fields? See example below.">
8 <option value="-p">Yes</option>
9 <option value="">No</option>
10 </param>
11 </inputs>
12 <outputs>
13 <data format="interval" name="out_file1" label="Converted Interval" />
14 </outputs>
15 <tests>
16 <test>
17 <param name="input1" value="sam_bioinf_example.sam" ftype="sam"/>
18 <param name="print_all" value="Yes"/>
19 <output name="out_file1" file="sam2interval_printAll.dat" ftype="interval"/>
20 </test>
21 <test>
22 <param name="input1" value="sam_bioinf_example.sam" ftype="sam"/>
23 <param name="print_all" value="No"/>
24 <output name="out_file1" file="sam2interval_noprintAll.dat" ftype="interval"/>
25 </test>
26 <test>
27 <param name="input1" value="sam2interval-test3.sam" ftype="sam"/>
28 <param name="print_all" value="No"/>
29 <output name="out_file1" file="sam2interval_with_unmapped_reads_noprintAll.dat" ftype="interval"/>
30 </test>
31
32 </tests>
33 <help>
34
35 **What it does**
36
37 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.
38
39 -----
40
41 **Example**
42
43 Converting the following dataset::
44
45 r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA *
46 r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA *
47 r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1
48 r004 0 ref 16 30 6M14N5M * 0 0 ATAGCTTCAGC *
49 r003 16 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0
50 r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT *
51
52 into Interval format will produce the following if *Print all?* is set to **Yes**::
53
54 ref 6 22 + r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA *
55 ref 8 19 + r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA *
56 ref 8 14 + r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1
57 ref 15 40 + r004 0 ref 16 30 6M14N5M * 0 0 ATAGCTTCAGC *
58 ref 28 33 - r003 16 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0
59 ref 36 45 - r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT *
60
61 Setting *Print all?* to **No** will generate the following::
62
63 ref 6 22 + r001
64 ref 8 19 + r002
65 ref 8 14 + r003
66 ref 15 40 + r004
67 ref 28 33 - r003
68 ref 36 45 - r001
69
70
71 </help>
72 </tool>