Mercurial > repos > eduardo > download_and_align
changeset 13:1a837f49fdc9
cleanup
author | Eduardo <eduardoalves@abdn.ac.uk> |
---|---|
date | Mon, 03 Aug 2015 11:31:51 +0100 |
parents | 65f85eae1776 |
children | d4d02c4b2756 |
files | download_align.xml |
diffstat | 1 files changed, 53 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/download_align.xml Mon Aug 03 11:31:51 2015 +0100 @@ -0,0 +1,53 @@ +<tool id="download_align" name="Download and align" version="0.0.1"> + <description> Downloads fastq.gz, unzips, trims with cutadapt and alignes to reference</description> + <requirements> + <requirement type="package" version="1.6">cutadapt</requirement> + <requirement type="package" version="2.2.4">bowtie2</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> + </requirements> + <command> + #set index_path = '' + #if str($reference_genome.source) == "history": + echo \${PATH} && bowtie2-build "$reference_genome.own_file" genome && + ln -s "$reference_genome.own_file" genome.fa && + #set index_path = 'genome' + #else: + #set index_path = $reference_genome.index.fields.path + #end if + wget -O - $file | gunzip -c | cutadapt -q 20 - | bowtie2 -q + ## index file path + -x $index_path + -U - | samtools view -b - > $output + </command> + <stdio> + <exit_code range="1:" level="fatal" description="Tool exception" /> + </stdio> + <inputs> + <param format="text" name="file" type="text" label="URL for fastq.gz"/> + <conditional name="reference_genome"> + <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> + <option value="indexed">Use a built-in genome index</option> + <option value="history">Use a genome from the history and build index</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> + <options from_data_table="bowtie2_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="history"> + <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)" /> + </outputs> + <help> + This tool extracts reads from sra, runs cutdapt and bowtie and outputs a bam file. + + Contact Eduardo Alves at eduardoalves@abdn.ac.uk for support and bug reports. + </help> +</tool>