/tools/samtools/sam2interval.xml

 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
37Converts 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
43Converting 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
52into 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 
61Setting  *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>