4
|
1 <tool id="bam_to_sam" name="BAM-to-SAM" version="2.0">
|
3
|
2 <macros>
|
|
3 <import>macros.xml</import>
|
|
4 </macros>
|
|
5 <expand macro="requirements"></expand>
|
|
6 <expand macro="version_command"></expand>
|
|
7 <expand macro="stdio"></expand>
|
4
|
8 <description>convert BAM to SAM</description>
|
3
|
9 <command>
|
|
10 <![CDATA[
|
4
|
11 samtools view -o "${output1}" ${header} "${input1}"
|
3
|
12 ]]>
|
|
13 </command>
|
|
14 <inputs>
|
|
15 <param format="bam" label="BAM File to Convert" name="input1" type="data" />
|
4
|
16 <param name="header" label="Header options" type="select" help="Allows to choose between seeing the entire dataset with the header, header only, or data only.">
|
|
17 <option value="-h">Include header in SAM output (-h)</option>
|
|
18 <option value="-H">Print header only (-H)</option>
|
|
19 <option value="">Exclude header</option>
|
|
20 </param>
|
3
|
21 </inputs>
|
|
22 <outputs>
|
|
23 <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" />
|
|
24 </outputs>
|
|
25 <tests>
|
|
26 <test>
|
|
27 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
|
4
|
28 <param name="header" value="-h" />
|
3
|
29 <output file="bam_to_sam_out1.sam" name="output1" sorted="True" />
|
|
30 </test>
|
|
31 <test>
|
4
|
32 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
|
|
33 <param name="header" value="-H" />
|
3
|
34 <output file="bam_to_sam_out2.sam" name="output1" sorted="True" />
|
|
35 </test>
|
|
36 <test>
|
|
37 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
|
4
|
38 <param name="header" value="" />
|
3
|
39 <output file="bam_to_sam_out3.sam" name="output1" sorted="True" />
|
|
40 </test>
|
|
41 </tests>
|
|
42 <help>
|
|
43 <![CDATA[
|
0
|
44
|
|
45 **What it does**
|
|
46
|
4
|
47 Converts BAM dataset to SAM using ``samtools view`` command::
|
0
|
48
|
4
|
49 samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM]
|
|
50
|
3
|
51 ]]>
|
0
|
52 </help>
|
3
|
53 <expand macro="citations"></expand>
|
0
|
54 </tool>
|