Mercurial > repos > iuc > data_manager_bwameth_index_builder
diff data_manager/bwameth_index_builder.xml @ 0:a7fb84abef45 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
author | iuc |
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date | Tue, 22 Nov 2016 17:12:00 -0500 |
parents | |
children | a9aa093e2392 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/bwameth_index_builder.xml Tue Nov 22 17:12:00 2016 -0500 @@ -0,0 +1,59 @@ +<tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0"> + <description>builder</description> + <requirements> + <requirement type="package" version="0.7.12">bwa</requirement> + <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="0.2.0">bwameth</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + #if str($sequence_id).strip() != "": + #set $dbkey = $sequence_id + #else: + #set $dbkey = $all_fasta_source.fields.dbkey + #end if + + #if str($sequence_name).strip() != "": + #set $name = $sequence_name + #else: + #set $name = $all_fasta_source.fields.name + #end if + + python $__tool_directory__/bwameth_index_builder.py --output "${out_file}" + --fasta_filename "${all_fasta_source.fields.path}" + --dbkey "${dbkey}" + --name "${name}" + --data_table_name "bwameth_indexes" + ]]> + </command> + <inputs> + <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> + <options from_data_table="all_fasta" /> + </param> + <param label="ID for index" name="sequence_id" type="text" value="" help="If not specified, the value from the fasta file is used"/> + <param label="Displayed description for sequence" name="sequence_name" type="text" value="" help="If not specified, the value from the fasta file is used"/> + </inputs> + <outputs> + <data format="data_manager_json" name="out_file" /> + </outputs> + <help> +<![CDATA[ +.. 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. + +]]> + </help> + <citations> + <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}, + }</citation> + </citations> +</tool>