| Previous changeset 22:a55691c07823 (2012-12-03) Next changeset 24:250f29896fe0 (2012-12-03) |
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Commit message:
Deleted selected files |
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removed:
bsmap_meth_caller.xml |
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| diff -r a55691c07823 -r 75c35e2a0862 bsmap_meth_caller.xml --- a/bsmap_meth_caller.xml Mon Dec 03 02:42:04 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,75 +0,0 @@ -<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> - |