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comparison bam_to_sam.xml @ 4:3bade5114f21 draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:53:40 -0400
parents 6eebf8420e31
children eac9d3319326
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3:ad3c355b8249 4:3bade5114f21
1 <tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.4"> 1 <tool id="bam_to_sam" name="BAM-to-SAM" version="2.0">
2 <requirements> 2 <macros>
3 <requirement type="package" version="0.1.19">samtools</requirement> 3 <import>macros.xml</import>
4 </requirements> 4 </macros>
5 <description>converts BAM format to SAM format</description> 5 <expand macro="requirements"></expand>
6 <command interpreter="python"> 6 <expand macro="version_command"></expand>
7 bam_to_sam.py 7 <expand macro="stdio"></expand>
8 --input1=$input1 8 <description>convert BAM to SAM</description>
9 --output1=$output1 9 <command>
10 $header 10 <![CDATA[
11 </command> 11 samtools view -o "${output1}" ${header} "${input1}"
12 <inputs> 12 ]]>
13 <param name="input1" type="data" format="bam" label="BAM File to Convert" /> 13 </command>
14 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" /> 14 <inputs>
15 </inputs> 15 <param format="bam" label="BAM File to Convert" name="input1" type="data" />
16 <outputs> 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 <data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" /> 17 <option value="-h">Include header in SAM output (-h)</option>
18 </outputs> 18 <option value="-H">Print header only (-H)</option>
19 <tests> 19 <option value="">Exclude header</option>
20 <test> 20 </param>
21 <!-- 21 </inputs>
22 Bam-to-Sam command: 22 <outputs>
23 samtools view -o bam_to_sam_out1.sam test-data/bam_to_sam_in1.bam 23 <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" />
24 bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam 24 </outputs>
25 --> 25 <tests>
26 <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" /> 26 <test>
27 <param name="header" value="" /> 27 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
28 <output name="output1" file="bam_to_sam_out1.sam" sorted="True" /> 28 <param name="header" value="-h" />
29 </test> 29 <output file="bam_to_sam_out1.sam" name="output1" sorted="True" />
30 <test> 30 </test>
31 <!-- 31 <test>
32 Bam-to-Sam command: 32 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
33 samtools view -o bam_to_sam_out2.sam test-data/bam_to_sam_in2.bam 33 <param name="header" value="-H" />
34 bam_to_sam_in2.bam can be created from bam_to_sam_in2.sam 34 <output file="bam_to_sam_out2.sam" name="output1" sorted="True" />
35 --> 35 </test>
36 <param name="input1" value="bam_to_sam_in2.bam" ftype="bam" /> 36 <test>
37 <param name="header" value="" /> 37 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
38 <output name="output1" file="bam_to_sam_out2.sam" sorted="True" /> 38 <param name="header" value="" />
39 </test> 39 <output file="bam_to_sam_out3.sam" name="output1" sorted="True" />
40 <test> 40 </test>
41 <!-- 41 </tests>
42 Bam-to-Sam command: 42 <help>
43 samtools view -h -o bam_to_sam_out3.sam test-data/bam_to_sam_in1.bam 43 <![CDATA[
44 bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
45 -->
46 <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
47 <param name="header" value="--header" />
48 <output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /><!-- header param not working in func tests so won't produce correct 6-line header (fine in browser) -->
49 </test>
50 </tests>
51 <help>
52 44
53 **What it does** 45 **What it does**
54 46
55 This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. 47 Converts BAM dataset to SAM using ``samtools view`` command::
56 48
57 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml 49 samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM]
58 50
51 ]]>
59 </help> 52 </help>
60 <citations> 53 <expand macro="citations"></expand>
61 <citation type="doi">10.1093/bioinformatics/btp352</citation>
62 </citations>
63 </tool> 54 </tool>