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author | charles-bernard |
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date | Mon, 14 Nov 2016 05:01:41 -0500 |
parents | b03e31cab4a6 |
children | ee5badb527cd |
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<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>