Mercurial > repos > eiriche > bsmap
view bsmap_meth_caller.xml @ 21:b9a31a60c708 draft
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author | eiriche |
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date | Mon, 03 Dec 2012 02:41:55 -0500 |
parents | e3e36b45c1da |
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<tool id="bsmap_meth_caller" name="BSMAP Methylation Caller"> <requirements> <requirement type='package' version="2.6">bsmap</requirement> <requirement type='package'>samtools</requirement> <command interpreter="bash"> bsmap_meth_caller.sh input=$bsmap_sam unique=$unique properly=$properly zero_meth = $zero_meth rem_dup = $rem_dup combine_cpg = $combine_cpg trimN = $trimN depth = $depth output=$output tempdir=$output.files_path #if $refGenomeSource.genomeSource == "history": ref="${refGenomeSource.myFile}" #else ref="${refGenomeSource.builtinFile.fields.path}" #end if </command> <inputs> <conditional name="refGenomeSource"> <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"> <option value="builtin">Use a built-in reference</option> <option value="history">Use one from the history</option> </param> <when value="builtin"> <param name="builtinFile" type="select" label="Select the reference genome"> <options from_data_table="bsmap_fasta"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No reference genomes are available" /> </options> </param> </when> <when value="history"> <param name="myFile" type="data" format="fasta" label="Select the reference genome" /> </when> </conditional> <param name="bsmap_sam" format="sam" type="data" label="BSMAP mapping output file" help="Must be in SAM format" /> <param name="unique" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Process only unique mappings/pairs" /> <param name="properly" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Process only properly paired mappings" /> <param name="zero_meth" type="boolean" truevalue="true" falsevalue="false" checked="True" label="report loci with zero methylation ratios" /> <param name="rem_dup" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Remove duplicated reads" /> <param name="combine_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Combine CpG methylaion ratios on both strands" /> <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" /> <param name="depth" type="integer" value="1" label="Minimum sequencing depth to report loci" /> </inputs> <outputs> <data name="output" format ="bed" label="BSMAP methylation output" /> </outputs> <help> **What it does** This methylation caller parses the BSMAP SAM output file into bed format. **Output format** :: Column Description ---------------------- -------------------------------------- 1 chr chromosome 2 pos position 3 strand strand 4 context context (CHH,CHG,CpG) 5 coverage totally sequenced Cs at that position 6 methylated methylated Cs at that position 7 percentage methylated percentage of 6 </help> </tool>