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1 <tool id="cpgFilter" name="Mask CpG/non-CpG sites" version="1.0.0">
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2 <description> from MAF file</description>
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3 <requirements>
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4 <requirement type="package" version="0.7.1">bx-python</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 maf_cpg_filter.py
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8 $input
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9 $out_file1
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10 $masksite.type
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11 #if $masksite.type == "CpG":
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12 $masksite.definition
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13 #else:
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14 "NA"
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15 #end if
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16 -m $mask_char
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17 </command>
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18 <inputs>
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19 <page>
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20 <param format="maf" name="input" type="data" label="Select data"/>
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21 <param name="mask_char" size="5" type="select" label="Mask character">
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22 <option value="0" selected="true">#</option>
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23 <option value="1">$</option>
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24 <option value="2">^</option>
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25 <option value="3">*</option>
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26 <option value="4">?</option>
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27 <option value="5">N</option>
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28 </param>
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29 <conditional name="masksite">
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30 <param name="type" size="5" type="select" label="Sites to be masked">
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31 <option value="CpG" selected="true">CpG sites</option>
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32 <option value="nonCpG">non-CpG sites</option>
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33 </param>
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34 <when value="CpG">
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35 <param name="definition" size="5" type="select" label="Definition">
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36 <option value="0" selected="true">Inclusive</option>
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37 <option value="1">Restricted</option>
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38 </param>
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39 </when>
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40 <when value="nonCpG" />
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41 </conditional>
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42 </page>
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43 </inputs>
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44 <outputs>
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45 <data format="maf" name="out_file1" metadata_source="input"/>
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46 </outputs>
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47 <requirements>
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48 <requirement type="python-module">numpy</requirement>
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49 </requirements>
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50 <tests>
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51 <test>
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52 <param name="input" value="6.maf"/>
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53 <param name="mask_char" value="0"/>
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54 <param name="type" value="CpG" />
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55 <param name="definition" value="0" />
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56 <output name="out_file1" file="6_mask_cpg.maf"/>
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57 </test>
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58 <test>
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59 <param name="input" value="6.maf"/>
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60 <param name="mask_char" value="0"/>
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61 <param name="type" value="nonCpG" />
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62 <output name="out_file1" file="6_mask_noncpg.maf"/>
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63 </test>
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64 </tests>
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65 <help>
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66
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67 .. class:: infomark
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68
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69 **What it does**
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70
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71 This tool takes a MAF file as input and masks CpG sites in every alignment block of the MAF file.
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72
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73 -----
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74
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75 .. class:: warningmark
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76
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77 **Note**
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78
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79 *Inclusive definition* defines CpG sites as those sites that are CG in at least one of the species.
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80
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81 *Restricted definition* considers sites to be CpG if they are CG in at least one of the species, however, sites that are part of overlapping CpGs are excluded.
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82
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83 For more information on CpG site definitions, please refer this article_.
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84
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85 .. _article: http://mbe.oxfordjournals.org/cgi/content/full/23/3/565
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86
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87 </help>
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88
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89
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90 </tool>
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