Mercurial > repos > bgruening > bismark
diff bismark_methylation_extractor.xml @ 21:507901240749 draft
Uploaded
author | bgruening |
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date | Wed, 11 Feb 2015 16:21:27 -0500 |
parents | 0895fe70075d |
children | 047eb877b6f0 |
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--- a/bismark_methylation_extractor.xml Mon Jan 26 14:46:05 2015 -0500 +++ b/bismark_methylation_extractor.xml Wed Feb 11 16:21:27 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.10.1"> +<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.10.2"> <!-- Wrapper compatible with Bismark version 0.10 --> <description>Reports on methylation status of reads mapped by Bismark</description> <!--<version_command>bismark_methylation_extractor version</version_command>--> @@ -9,6 +9,7 @@ </requirements> <parallelism method="basic"></parallelism> <command interpreter="python"> +<![CDATA[ bismark_methylation_extractor.py --infile $input @@ -78,6 +79,7 @@ ## end compress #end if +]]> </command> <inputs> <!-- Input Parameters --> @@ -187,11 +189,12 @@ </tests> <help> +<![CDATA[ **What it does** The following is a brief description of all options to control the Bismark_ -methylation extractor. The script reads in a bisulfite read alignment results file +methylation extractor. The script reads in a bisulfite read alignment results file produced by the Bismark bisulfite mapper and extracts the methylation information for individual cytosines. This information is found in the methylation call field which can contain the following characters: @@ -285,8 +288,8 @@ Output:: - --comprehensive Specifying this option will merge all four possible strand-specific - methylation info into context-dependent output files. The default + --comprehensive Specifying this option will merge all four possible strand-specific + methylation info into context-dependent output files. The default contexts are: - CpG context - CHG context @@ -301,5 +304,6 @@ this script. +]]> </help> </tool>