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1 <tool id="cytosine_report_to_bedgraph" name="Cytosine Report To Bedgraphs" version="0.0.0">
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2
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3 <description>Converts genome-wide cytosine methylation report to Bedgraphs</description>
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4
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5 <requirements>
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6 <requirement type="package" version="2.3.32">igvtools</requirement>
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7 </requirements>
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8
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9 <command interpreter="python">
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10 <![CDATA[
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11 cytosine_report_to_bedgraph_wrapper.py
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12
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13 --tool_dir "$__tool_directory__"
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14
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15 --cytosine_report "$cytosine_report"
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16
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17 --coverage_bedgraph "$coverage_bedgraph"
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18 #if $tdf['tdf_selector']:
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19 --tdf
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20 --igv_genome "${tdf.built_in_igv_genomes_chr_sizes.fields.path}"
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21 --coverage_tdf "$coverage_tdf"
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22 #end if
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23
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24 #if $context:
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25 --context
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26 --CpG_bedgraph "$CpG_bedgraph"
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27 --CHG_bedgraph "$CHG_bedgraph"
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28 --CHH_bedgraph "$CHH_bedgraph"
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29 #if $tdf['tdf_selector']:
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30 --CpG_tdf "$CpG_tdf"
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31 --CHG_tdf "$CHG_tdf"
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32 --CHH_tdf "$CHH_tdf"
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33 #end if
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34 #else
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35 --CXX "$CXX_bedgraph"
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36 #if $tdf['tdf_selector']:
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37 --CXX "$CXX_tdf"
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38 #end if
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39 #end if
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40
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41 --log "$log_report"
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42 ]]>
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43 </command>
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44 <inputs>
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45 <param name="cytosine_report" type="data" format="txt" label="Submit a genome-wide cytosine methylation report" optional="False" />
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46 <param name="context" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Create a bedGraph for each cytosine methylation context?" />
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47 <conditional name="tdf">
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48 <param name="tdf_selector" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a tdf file from each resulting bedGraph?" />
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49 <when value="true">
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50 <param name="built_in_igv_genomes_chr_sizes" type="select" label="Select Reference Genome (igv genomes chr.sizes)" help="If your genome of interest is not listed, contact your Galaxy admin">
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51 <options from_data_table="igv_genomes_chr_sizes">
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52 <filter type="sort_by" column="name"/>
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53 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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54 </options>
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55 </param>
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56 </when>
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57 <when value="false"></when>
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58 </conditional>
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59 </inputs>
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60
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61 <outputs>
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62 <data name="log_report" format="txt" label="${tool.name} on ${on_string}: Log Report" />
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63 <data name="CpG_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CpG context">
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64 <filter>context is True</filter>
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65 </data>
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66 <data name="CHG_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CHG context">
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67 <filter>context is True</filter>
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68 </data>
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69 <data name="CHH_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CHH context">
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70 <filter>context is True</filter>
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71 </data>
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72 <data name="CXX_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CXX">
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73 <filter>context is False</filter>
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74 </data>
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75 <data name="coverage_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: Coverage" />
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76 <data name="CpG_tdf" format="tdf" label="${tool.name} on ${on_string}: CpG context (tdf)">
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77 <filter>tdf['tdf_selector'] is True and context is True</filter>
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78 </data>
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79 <data name="CHG_tdf" format="tdf" label="${tool.name} on ${on_string}: CHG context (tdf)">
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80 <filter>tdf['tdf_selector'] is True and context is True</filter>
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81 </data>
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82 <data name="CHH_tdf" format="tdf" label="${tool.name} on ${on_string}: CHH context (tdf)">
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83 <filter>tdf['tdf_selector'] is True and context is True</filter>
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84 </data>
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85 <data name="CXX_tdf" format="tdf" label="${tool.name} on ${on_string}: CXX (tdf)">
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86 <filter>context is False and tdf['tdf_selector'] is True</filter>
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87 </data>
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88 <data name="coverage_tdf" format="tdf" label="${tool.name} on ${on_string}: Coverage (tdf)" >
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89 <filter>tdf['tdf_selector'] is True</filter>
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90 </data>
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91 </outputs>
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92
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93 <tests></tests>
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94
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95 <help>
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96 <![CDATA[
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97
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98 **What it does**
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99
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100 | This tool takes as input a genome-wide cytosine methylation report (generated by the tool *Bismark Meth. Extractor*) and converts it into a bedGraph for each cytosine context (CpG, CHG and CHH).
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101 | These bedGraphs display, for a given context, the ratio of methylation of each covered cytosine in the genome.
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102 |
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103 | It also produces a bedGraph displaying the coverage count of each cytosine in the genome (non-covered cytosine are ignored).
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104 |
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105
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106 .. class:: infomark
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107
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108 | The tool outputs offer the possibility to vizualise the methylation signal of covered cytosines thanks to softwares like IGV (*Integrative Genomics Viewer*).
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109 | In this respect, the tool can optionally generate a tdf binary file (*Tiled Data Format*) from each converted bedGraph. Tdf format is indeed better handled by IGV than bedGraph.
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110 ]]>
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111 </help>
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112 </tool> |
