Mercurial > repos > eduardo > download_and_align
view download_align.xml @ 19:d839829f8494
package_bowtie version 2.2.4
author | Eduardo <eduardoalves@abdn.ac.uk> |
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date | Mon, 03 Aug 2015 17:32:31 +0100 |
parents | dd22ac8fc5cf |
children | 083c25559b6b |
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<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>