|
0
|
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>
|
