Mercurial > repos > eduardo > download_and_align
changeset 9:48006f05c208
Deleted selected files
author | eduardo |
---|---|
date | Mon, 03 Aug 2015 05:44:04 -0400 |
parents | a6bcb0f8f38e |
children | 8a98bfab4d56 |
files | url2bowtie/download_align.xml |
diffstat | 1 files changed, 0 insertions(+), 53 deletions(-) [+] |
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--- a/url2bowtie/download_align.xml Mon Aug 03 05:43:47 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ -<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>