Mercurial > repos > eiriche > bsmap
comparison bsmap_meth_caller.xml @ 19:e3e36b45c1da draft
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| author | eiriche |
|---|---|
| date | Mon, 03 Dec 2012 02:38:26 -0500 |
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| 18:765fe3947e2a | 19:e3e36b45c1da |
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| 1 <tool id="bsmap_meth_caller" name="BSMAP Methylation Caller"> | |
| 2 <requirements> | |
| 3 <requirement type='package' version="2.6">bsmap</requirement> | |
| 4 <requirement type='package'>samtools</requirement> | |
| 5 <command interpreter="bash"> | |
| 6 bsmap_meth_caller.sh | |
| 7 input=$bsmap_sam | |
| 8 unique=$unique | |
| 9 properly=$properly | |
| 10 zero_meth = $zero_meth | |
| 11 rem_dup = $rem_dup | |
| 12 combine_cpg = $combine_cpg | |
| 13 trimN = $trimN | |
| 14 depth = $depth | |
| 15 output=$output | |
| 16 tempdir=$output.files_path | |
| 17 #if $refGenomeSource.genomeSource == "history": | |
| 18 ref="${refGenomeSource.myFile}" | |
| 19 #else | |
| 20 ref="${refGenomeSource.builtinFile.fields.path}" | |
| 21 #end if | |
| 22 | |
| 23 </command> | |
| 24 <inputs> | |
| 25 <conditional name="refGenomeSource"> | |
| 26 <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"> | |
| 27 <option value="builtin">Use a built-in reference</option> | |
| 28 <option value="history">Use one from the history</option> | |
| 29 </param> | |
| 30 <when value="builtin"> | |
| 31 <param name="builtinFile" type="select" label="Select the reference genome"> | |
| 32 <options from_data_table="bsmap_fasta"> | |
| 33 <filter type="sort_by" column="2" /> | |
| 34 <validator type="no_options" message="No reference genomes are available" /> | |
| 35 </options> | |
| 36 </param> | |
| 37 </when> | |
| 38 <when value="history"> | |
| 39 <param name="myFile" type="data" format="fasta" label="Select the reference genome" /> | |
| 40 </when> | |
| 41 </conditional> | |
| 42 | |
| 43 <param name="bsmap_sam" format="sam" type="data" label="BSMAP mapping output file" help="Must be in SAM format" /> | |
| 44 <param name="unique" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Process only unique mappings/pairs" /> | |
| 45 <param name="properly" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Process only properly paired mappings" /> | |
| 46 <param name="zero_meth" type="boolean" truevalue="true" falsevalue="false" checked="True" label="report loci with zero methylation ratios" /> | |
| 47 <param name="rem_dup" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Remove duplicated reads" /> | |
| 48 <param name="combine_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Combine CpG methylaion ratios on both strands" /> | |
| 49 <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" /> | |
| 50 <param name="depth" type="integer" value="1" label="Minimum sequencing depth to report loci" /> | |
| 51 </inputs> | |
| 52 <outputs> | |
| 53 <data name="output" format ="bed" label="BSMAP methylation output" /> | |
| 54 </outputs> | |
| 55 <help> | |
| 56 **What it does** | |
| 57 | |
| 58 This methylation caller parses the BSMAP SAM output file into bed format. | |
| 59 | |
| 60 | |
| 61 **Output format** :: | |
| 62 | |
| 63 | |
| 64 Column Description | |
| 65 ---------------------- -------------------------------------- | |
| 66 1 chr chromosome | |
| 67 2 pos position | |
| 68 3 strand strand | |
| 69 4 context context (CHH,CHG,CpG) | |
| 70 5 coverage totally sequenced Cs at that position | |
| 71 6 methylated methylated Cs at that position | |
| 72 7 percentage methylated percentage of 6 | |
| 73 </help> | |
| 74 </tool> | |
| 75 |