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1 <tool id="bsmap_meth_caller" name="BSMAP Methylation Caller">
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2 <requirements>
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3 <requirement type='package'>
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4 bsmap
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5 </requirement>
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6 </requirements>
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7 <requirements>
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8 <requirement type='package'>
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9 samtools
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10 </requirement>
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11 </requirements>
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12 <command interpreter="bash">
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13 bsmap_meth_caller.sh
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14 input=$bsmap_sam
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15 unique=$unique
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16 properly=$properly
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17 zero_meth = $zero_meth
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18 rem_dup = $rem_dup
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19 combine_cpg = $combine_cpg
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20 trimN = $trimN
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21 depth = $depth
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22 output=$output
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23 tempdir=$output.files_path
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24 #if $refGenomeSource.genomeSource == "history":
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25 ref="${refGenomeSource.myFile}"
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26 #else
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27 ref="${refGenomeSource.builtinFile.fields.path}"
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28 #end if
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29
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30 </command>
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31 <inputs>
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32 <conditional name="refGenomeSource">
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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">
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34 <option value="builtin">Use a built-in reference</option>
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35 <option value="history">Use one from the history</option>
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36 </param>
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37 <when value="builtin">
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38 <param name="builtinFile" type="select" label="Select the reference genome">
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39 <options from_data_table="bsmap_fasta">
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40 <filter type="sort_by" column="2" />
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41 <validator type="no_options" message="No reference genomes are available" />
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42 </options>
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43 </param>
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44 </when>
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45 <when value="history">
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46 <param name="myFile" type="data" format="fasta" label="Select the reference genome" />
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47 </when>
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48 </conditional>
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49
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50 <param name="bsmap_sam" format="sam" type="data" label="BSMAP mapping output file" help="Must be in SAM format" />
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51 <param name="unique" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Process only unique mappings/pairs" />
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52 <param name="properly" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Process only properly paired mappings" />
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53 <param name="zero_meth" type="boolean" truevalue="true" falsevalue="false" checked="True" label="report loci with zero methylation ratios" />
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54 <param name="rem_dup" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Remove duplicated reads" />
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55 <param name="combine_cpg" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Combine CpG methylaion ratios on both strands" />
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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" />
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57 <param name="depth" type="integer" value="1" label="Minimum sequencing depth to report loci" />
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58 </inputs>
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59 <outputs>
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60 <data name="output" format ="bed" label="BSMAP methylation output" />
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61 </outputs>
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62 <help>
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63 **What it does**
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64
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65 This methylation caller parses the BSMAP SAM output file into bed format.
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66
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67
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68 **Output format** ::
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69
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70
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71 Column Description
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72 ---------------------- --------------------------------------
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73 1 chr chromosome
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74 2 pos position
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75 3 strand strand
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76 4 context context (CHH,CHG,CpG)
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77 5 coverage totally sequenced Cs at that position
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78 6 methylated methylated Cs at that position
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79 7 percentage methylated percentage of 6
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80 </help>
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81 </tool>
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82
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