Mercurial > repos > dpryan79 > bwameth
changeset 5:f9c8c79b8b08 draft
Uploaded
author | dpryan79 |
---|---|
date | Tue, 13 Sep 2016 16:01:35 -0400 |
parents | 24b3fdf9c32f |
children | 8a198580ea8d |
files | bwameth.xml |
diffstat | 1 files changed, 93 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwameth.xml Tue Sep 13 16:01:35 2016 -0400 @@ -0,0 +1,93 @@ +<tool id="bwameth" name="bwameth" version="0.20"> + <description>Fast and accurate aligner of BS-Seq reads.</description> + <requirements> + <requirement type="package" version="0.20">toolshed</requirement> + <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="0.7.12">bwa</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + <regex match="Exception :" /> + </stdio> + <version_command>bwameth.py --version</version_command> + <command interpreter="python"> +<![CDATA[ + bwameth_wrapper.py + -p "\${GALAXY_SLOTS:-4}" + + #if $referenceSource.source != "indexed": + --makeIndex $referenceSource.reference + #else + --premadeIndex $referenceSource.index.fields.path + #end if + + #if str($readGroup).strip() != "": + --readGroup "${readGroup}" + #end if + + #if $single_or_paired.single_or_paired_opts == 'single': + $single_or_paired.input_singles + #else: + $single_or_paired.input_mate1 $single_or_paired.input_mate2 + #end if +]]> + </command> + <inputs> + <conditional name="referenceSource"> + <param name="source" type="select" label="Select a genome reference from your history or a built-in index?"> + <option value="history" selected="True">Use one from the history</option> + <option value="indexed">Use a built-in index</option> + </param> + <when value="history"> + <param name="reference" type="data" format="fasta" metadata_name="dbkey" label="Select a genome" help="in FASTA format" /> + </when> + <when value="indexed"> + <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin"> + <options from_data_table="bwameth_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + </conditional> + + <conditional name="single_or_paired"> + <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + </param> + <when value="single"> + <param name="input_singles" type="data" format="fastq" label="FASTQ" help="FASTQ file." /> + </when> + <when value="paired"> + <param name="input_mate1" type="data" format="fastq" label="First read in pair" help="FASTQ file." /> + <param name="input_mate2" type="data" format="fastq" label="Second read in pair" help="FASTQ file." /> + </when> + </conditional> + <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'" /> + </inputs> + <outputs> + <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="referenceSource" value="history" /> + <param name="reference" value="ref.fa" /> + <param name="single_or_paired_opts" value="paired" /> + <param name="input_mate1" value="t_R1.fastq.gz" /> + <param name="input_mate2" value="t_R2.fastq.gz" /> + <output file="alignments.bam" ftype="bam" name="output" /> + </test> + </tests> + <help> +<![CDATA[ + +**What it does** + +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> +</tool>