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comparison bsmap_meth_caller.xml @ 14:2fb3be685c17 draft

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author eiriche
date Fri, 30 Nov 2012 09:15:06 -0500
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13:c01ef10d055c 14:2fb3be685c17
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 #if $refGenomeSource.genomeSource == "history":
25 ref="${refGenomeSource.myFile}"
26 #else
27 ref="${refGenomeSource.builtinFile.fields.path}"
28 #end if
29
30 </command>
31 <inputs>
32 <conditional name="refGenomeSource">
33 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in reference?" help="Must be the same reference as used for the mapping">
34 <option value="builtin">Use a built-in reference</option>
35 <option value="history">Use one from the history</option>
36 </param>
37 <when value="builtin">
38 <param name="builtinFile" type="select" label="Select the reference genome">
39 <options from_data_table="bsmap_fasta">
40 <filter type="sort_by" column="2" />
41 <validator type="no_options" message="No reference genomes are available" />
42 </options>
43 </param>
44 </when>
45 <when value="history">
46 <param name="myFile" type="data" format="fasta" label="Select the reference genome" />
47 </when>
48 </conditional>
49
50 <param name="bsmap_sam" format="sam" type="data" label="BSMAP mapping output file" help="Must be in SAM format" />
51 <param name="unique" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Process only unique mappings/pairs" />
52 <param name="properly" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Process only properly paired mappings" />
53 <param name="zero_meth" type="boolean" truevalue="true" falsevalue="false" checked="True" label="report loci with zero methylation ratios" />
54 <param name="rem_dup" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Remove duplicated reads" />
55 <param name="combine_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Combine CpG methylaion ratios on both strands" />
56 <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" />
57 <param name="depth" type="integer" value="1" label="Minimum sequencing depth to report loci" />
58 </inputs>
59 <outputs>
60 <data name="output" format ="bed" label="BSMAP methylation output" />
61 </outputs>
62 <help>
63 **What it does**
64
65 This methylation caller parses the BSMAP SAM output file into bed format.
66
67
68 **Output format** ::
69
70
71 Column Description
72 ---------------------- --------------------------------------
73 1 chr chromosome
74 2 pos position
75 3 strand strand
76 4 context context (CHH,CHG,CpG)
77 5 coverage totally sequenced Cs at that position
78 6 methylated methylated Cs at that position
79 7 percentage methylated percentage of 6
80 </help>
81 </tool>
82