Mercurial > repos > eiriche > bsmap

comparison bsmap_meth_caller.xml @ 4:e5025e0378d0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author eiriche
date Thu, 29 Nov 2012 10:10:39 -0500
parents
children
comparison
equal deleted inserted replaced
3:91e88de226a3 4:e5025e0378d0
1 <tool id="bsmap_meth_caller" name="BSMAP Methylation Caller">
2 <requirements>
3 <requirement type='package'>
4 bsmap
5 </requirement>
6 </requirements>
7 <requirements>
8 <requirement type='package'>
9 samtools
10 </requirement>
11 </requirements>
12 <command interpreter="bash">
13 bsmap_meth_caller.sh
14 input=$bsmap_sam
15 unique=$unique
16 properly=$properly
17 zero_meth = $zero_meth
18 rem_dup = $rem_dup
19 combine_cpg = $combine_cpg
20 trimN = $trimN
21 depth = $depth
22 output=$output
23 tempdir=$output.files_path
24 ref="${ filter( lambda x: str( x[1] ) == str( $bsmap_sam.metadata.dbkey ), $__app__.tool_data_tables['bsmap_fasta'].get_fields() )[0][3] }"
25 </command>
26 <inputs>
27 <param name="bsmap_sam" format="sam" type="data" label="BSMAP mapping output file" help="Must be in SAM format" />
28 <param name="unique" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Process only unique mappings/pairs" />
29 <param name="properly" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Process only properly paired mappings" />
30 <param name="zero_meth" type="boolean" truevalue="true" falsevalue="false" checked="True" label="report loci with zero methylation ratios" />
31 <param name="rem_dup" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Remove duplicated reads" />
32 <param name="combine_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Combine CpG methylaion ratios on both strands" />
33 <param name="trimN" type="integer" value="2" label="Trim N fill-in nucleotides in DNA fragment end-repairing" help="This option is only for pair-end mapping. For RRBS, N could be detetmined by the distance between cuttings sites on forward and reverse strands. For WGBS, N is usually between 0~3" />
34 <param name="depth" type="integer" value="1" label="Minimum sequencing depth to report loci" />
35 </inputs>
36 <outputs>
37 <data name="output" format ="bed" label="BSMAP methylation output" />
38 </outputs>
39 <help>
40 **What it does**
41
42 This methylation caller parses the BSMAP SAM output file into bed format.
43
44
45 **Output format** ::
46
47
48 Column Description
49 ---------------------- --------------------------------------
50 1 chr chromosome
51 2 pos position
52 3 strand strand
53 4 context context (CHH,CHG,CpG)
54 5 coverage totally sequenced Cs at that position
55 6 methylated methylated Cs at that position
56 7 percentage methylated percentage of 6
57 </help>
58 </tool>
59