Mercurial > repos > charles > cytosine_report_to_bedgraph
changeset 0:b3f6f58f454c draft default tip
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author | charles |
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date | Mon, 14 Nov 2016 04:53:25 -0500 |
parents | |
children | |
files | cytosine_report_to_bedgraph.xml |
diffstat | 1 files changed, 112 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cytosine_report_to_bedgraph.xml Mon Nov 14 04:53:25 2016 -0500 @@ -0,0 +1,112 @@ +<tool id="cytosine_report_to_bedgraph" name="Cytosine Report To Bedgraphs" version="0.0.0"> + + <description>Converts genome-wide cytosine methylation report to Bedgraphs</description> + + <requirements> + <requirement type="package" version="2.3.32">igvtools</requirement> + </requirements> + + <command interpreter="python"> +<![CDATA[ + cytosine_report_to_bedgraph_wrapper.py + + --tool_dir "$__tool_directory__" + + --cytosine_report "$cytosine_report" + + --coverage_bedgraph "$coverage_bedgraph" + #if $tdf['tdf_selector']: + --tdf + --igv_genome "${tdf.built_in_igv_genomes_chr_sizes.fields.path}" + --coverage_tdf "$coverage_tdf" + #end if + + #if $context: + --context + --CpG_bedgraph "$CpG_bedgraph" + --CHG_bedgraph "$CHG_bedgraph" + --CHH_bedgraph "$CHH_bedgraph" + #if $tdf['tdf_selector']: + --CpG_tdf "$CpG_tdf" + --CHG_tdf "$CHG_tdf" + --CHH_tdf "$CHH_tdf" + #end if + #else + --CXX "$CXX_bedgraph" + #if $tdf['tdf_selector']: + --CXX "$CXX_tdf" + #end if + #end if + + --log "$log_report" +]]> + </command> + <inputs> + <param name="cytosine_report" type="data" format="txt" label="Submit a genome-wide cytosine methylation report" optional="False" /> + <param name="context" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Create a bedGraph for each cytosine methylation context?" /> + <conditional name="tdf"> + <param name="tdf_selector" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a tdf file from each resulting bedGraph?" /> + <when value="true"> + <param name="built_in_igv_genomes_chr_sizes" type="select" label="Select Reference Genome (igv genomes chr.sizes)" help="If your genome of interest is not listed, contact your Galaxy admin"> + <options from_data_table="igv_genomes_chr_sizes"> + <filter type="sort_by" column="name"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="false"></when> + </conditional> + </inputs> + + <outputs> + <data name="log_report" format="txt" label="${tool.name} on ${on_string}: Log Report" /> + <data name="CpG_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CpG context"> + <filter>context is True</filter> + </data> + <data name="CHG_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CHG context"> + <filter>context is True</filter> + </data> + <data name="CHH_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CHH context"> + <filter>context is True</filter> + </data> + <data name="CXX_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CXX"> + <filter>context is False</filter> + </data> + <data name="coverage_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: Coverage" /> + <data name="CpG_tdf" format="tdf" label="${tool.name} on ${on_string}: CpG context (tdf)"> + <filter>tdf['tdf_selector'] is True and context is True</filter> + </data> + <data name="CHG_tdf" format="tdf" label="${tool.name} on ${on_string}: CHG context (tdf)"> + <filter>tdf['tdf_selector'] is True and context is True</filter> + </data> + <data name="CHH_tdf" format="tdf" label="${tool.name} on ${on_string}: CHH context (tdf)"> + <filter>tdf['tdf_selector'] is True and context is True</filter> + </data> + <data name="CXX_tdf" format="tdf" label="${tool.name} on ${on_string}: CXX (tdf)"> + <filter>context is False and tdf['tdf_selector'] is True</filter> + </data> + <data name="coverage_tdf" format="tdf" label="${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> \ No newline at end of file