comparison cytosine_report_to_bedgraph/cytosine_report_to_bedgraph.xml @ 5:ee5badb527cd draft default tip

Uploaded

4:e989fc4b1b76

    <data name="coverage_tdf" format="tdf" label="${tool.name} on ${on_string}: Coverage (tdf)" >
      <filter>tdf['tdf_selector'] is True</filter>
    </data>
  </outputs>

  <tests></tests>

  <help>
<![CDATA[

**What it does**

  | 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). 
  | These bedGraphs display, for a given context, the ratio of methylation of each covered cytosine in the genome.
  |
  | It also produces a bedGraph displaying the coverage count of each cytosine in the genome (non-covered cytosine are ignored).
  | 

  .. class:: infomark

  | The tool outputs offer the possibility to vizualise the methylation signal of covered cytosines thanks to softwares like IGV (*Integrative Genomics Viewer*).
  | 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.
]]>
  </help>
</tool>

5:ee5badb527cd

    <data name="coverage_tdf" format="tdf" label="${tool.name} on ${on_string}: Coverage (tdf)" >
      <filter>tdf['tdf_selector'] is True</filter>
    </data>
  </outputs>

  <tests><!--TO DO --></tests>

  <help>
<![CDATA[

**What it does**

  | 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). 
  | These bedGraphs display, for any given context, the ratio of methylation of each covered cytosine in the genome.
  |
  | It also produces a bedGraph displaying the coverage count of each cytosine in the genome (non-covered cytosine are ignored).
  | 

  .. class:: infomark

  | The tool outputs offer the possibility to vizualise the methylation signal of covered cytosines thanks to softwares like IGV (*Integrative Genomics Viewer*).
  | 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.
]]>
  </help>
</tool>