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