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bsmap_meth_caller.xml |
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| diff -r b5a8c2ecef59 -r b9a31a60c708 bsmap_meth_caller.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bsmap_meth_caller.xml Mon Dec 03 02:41:55 2012 -0500 |
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| @@ -0,0 +1,75 @@ +<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> + |