Mercurial > repos > eugen > bs_seq_test_1
changeset 10:35df90c1f4aa draft
Uploaded
author | eugen |
---|---|
date | Wed, 15 Aug 2012 08:26:45 -0400 |
parents | 5eaa87eeca9a |
children | 7ad77d2e23d0 |
files | bismark_meth_caller.xml |
diffstat | 1 files changed, 57 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bismark_meth_caller.xml Wed Aug 15 08:26:45 2012 -0400 @@ -0,0 +1,57 @@ +<tool id="bismark_meth_caller" name="Bismark Methylation Caller"> + <requirements> + <requirement type="package"> + Bismark + </requirement> + </requirements> + <command interpreter="bash"> + bismark_meth_caller.sh + input=$bismark_sam + method=$single_paired + output=$output + tempdir=$output.files_path + + </command> + <inputs> + <param name="single_paired" type="select" label="Please select whether Reads are single-end or paired-end"> + <option value="s">Single-end</option> + <option value="p">Paired-end</option> + </param> + <param format="sam" name="bismark_sam" type="data" label="Bismark mapping output file" help="Must be in SAM format"/> + </inputs> + <outputs> + <data name="output" format ="bed" label="Bismark methylation output" /> + </outputs> + <tests> + <test> + <param name="bismark_sam" value="bismark_mapped_reads_single.sam" ftype="sam"/> + <param name="single_paired" value="s"/> + <output name="output" file="bismark_methylation_output_single.bed"/> + </test> + <test> + <param name="bismark_sam" value="bismark_mapped_reads_single.sam" ftype="sam"/> + <param name="single_paired" value="p"/> + <output name="output" file="bismark_methylation_output_paired.bed"/> + </test> + </tests> + <help> +**What it does** + +This methylation caller parses the Bismark SAM output file into bed format. You only need to specify whether the reads are single-end or paired-end + + +**Output format** :: + + + Column Description + ---------------------- -------------------------------------- + 1 chr chromosome + 2 pos position + 3 strand strand + 4 context context (CHH,CHG,CpG) + 5 coverage totally sequenced Cs at that position + 6 methylated methylated Cs at that position + 7 percentage methylated percentage of 6 + </help> +</tool> +