view data_manager/bwameth_index_builder.xml @ 4:a9aa093e2392 draft

"planemo upload for repository commit 823259bba9405d22dc2add24746057122c819ad3"
author iuc
date Tue, 01 Oct 2019 17:53:16 -0400
parents a7fb84abef45
children 5ab25caa7b7d
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<tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="">
        <token name="@TOOL_VERSION@">0.2.2</token>
        <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement>
    <command detect_errors="aggressive"><![CDATA[
#if str($sequence_id).strip():
    #set $dbkey = $sequence_id
    #set $dbkey = $all_fasta_source.fields.dbkey
#end if

#if str($sequence_name).strip():
    #set $name = $sequence_name
    #set $name = $
#end if

python '$__tool_directory__/' --output '${out_file}'
--fasta_filename '${all_fasta_source.fields.path}'
--dbkey '${dbkey}'
--name '${name}'
--data_table_name bwameth_indexes
        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
            <options from_data_table="all_fasta" />
        <param name="sequence_id" type="text" value="" label="ID for index" help="If not specified, the value from the fasta file is used"/>
        <param name="sequence_name" type="text" value="" label="Displayed description for sequence" help="If not specified, the value from the fasta file is used"/>
        <data name="out_file" format="data_manager_json" />
.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically.

What is BWA-meth?

BWA-meth performs alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. The methodology employed for this is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool.

        <citation type="bibtex">@misc{1401.1129,
        Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
        Title = {Fast and accurate alignment of long bisulfite-seq reads},
        Year = {2014},
        Eprint = {arXiv:1401.1129},