comparison samtools_rmdup.xml @ 2:3735f950b2f5 draft

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author devteam
date Tue, 21 Apr 2015 17:21:53 -0400
parents fe83e6f8e65e
children bb40e4252392
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1:fe83e6f8e65e 2:3735f950b2f5
1 <tool id="samtools_rmdup" name="rmdup" version="1.0.1"> 1 <tool id="samtools_rmdup" name="RmDup" version="2.0">
2 <requirements>
3 <requirement type="package" version="0.1.19">samtools</requirement>
4 </requirements>
5 <description>remove PCR duplicates</description> 2 <description>remove PCR duplicates</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
8 <expand macro="version_command"></expand>
6 <command>samtools rmdup 9 <command>samtools rmdup
7 #if str( $bam_paired_end_type.bam_paired_end_type_selector ) == "PE" 10 #if str( $bam_paired_end_type.bam_paired_end_type_selector ) == "PE"
8 ${bam_paired_end_type.force_se} 11 ${bam_paired_end_type.force_se}
9 #else: 12 #else:
10 -s 13 -s
11 #end if 14 #end if
12 "$input1" "$output1" 15 "$input1" "$output1"
13 2&gt;&amp;1 || echo "Error running samtools rmdup." &gt;&amp;2
14 </command> 16 </command>
15 <inputs> 17 <inputs>
16 <param name="input1" type="data" format="bam" label="BAM File" /> 18 <param name="input1" type="data" format="bam" label="BAM File" />
17 19
18 <conditional name="bam_paired_end_type"> 20 <conditional name="bam_paired_end_type">
19 <param name="bam_paired_end_type_selector" type="select" label="Is data paired-end"> 21 <param name="bam_paired_end_type_selector" type="select" label="Is this paired-end or single end data">
20 <option value="PE" selected="True">BAM is paired-end</option> 22 <option value="PE" selected="True">BAM is paired-end</option>
21 <option value="SE">BAM is single-end</option> 23 <option value="SE">BAM is single-end (-s)</option>
22 </param> 24 </param>
23 <when value="PE"> 25 <when value="PE">
24 <param name="force_se" type="boolean" label="Treat as single-end" help="(-S)" truevalue="-S" falsevalue="" checked="False"/> 26 <param name="force_se" type="boolean" label="Treat as single-end" help="-S" truevalue="-S" falsevalue="" checked="False"/>
25 </when> 27 </when>
26 <when value="SE" /> <!-- No extra parameters here --> 28 <when value="SE" /> <!-- No extra parameters here -->
27 </conditional> 29 </conditional>
28 30
29 </inputs> 31 </inputs>
30 <outputs> 32 <outputs>
31 <data name="output1" format="bam" /> 33 <data name="output1" format="bam" />
32 </outputs> 34 </outputs>
33 <tests> 35 <tests>
34 <test> 36 <test>
35 <param name="input1" value="1.bam" ftype="bam" /> 37 <param name="input1" value="samtools-rmdup-input1.bam" ftype="bam" />
36 <param name="bam_paired_end_type_selector" value="SE" />
37 <output name="output1" file="1.bam" ftype="bam" sort="True"/>
38 </test>
39 <test>
40 <param name="input1" value="1.bam" ftype="bam" />
41 <param name="bam_paired_end_type_selector" value="PE" />
42 <param name="force_se" value="True" />
43 <output name="output1" file="1.bam" ftype="bam" sort="True"/>
44 </test>
45 <test>
46 <param name="input1" value="1.bam" ftype="bam" />
47 <param name="bam_paired_end_type_selector" value="PE" /> 38 <param name="bam_paired_end_type_selector" value="PE" />
48 <param name="force_se" /> 39 <param name="force_se" />
49 <output name="output1" file="1.bam" ftype="bam" sort="True" /> 40 <output name="output1" file="samtools-rmdup-test1.bam" ftype="bam" sort="True" />
50 </test> 41 </test>
51 </tests> 42 </tests>
52 <help> 43 <help>
53 44
54 **What it does** 45 **What it does**
55 46
56 This tool uses the SAMTools_ toolkit to remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set. It does not work for unpaired reads (e.g. two ends mapped to different chromosomes or orphan reads). 47 Remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set. It does not work for unpaired reads (e.g. two ends mapped to different chromosomes or orphan reads). This tool has the following parameters::
57 48
58 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml 49 -s rmdup for SE reads
59 50 -S treat PE reads as SE in rmdup (force -s)
60 ------
61
62 **Citation**
63
64 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
65
66 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
67 51
68 </help> 52 </help>
53 <expand macro="citations"></expand>
69 </tool> 54 </tool>