Mercurial > repos > eduardo > download_and_align
annotate download_align.xml @ 28:e0e38389a9cb draft default tip
Uploaded
| author | eduardo |
|---|---|
| date | Tue, 04 Aug 2015 10:59:51 -0400 |
| parents | 8f36fc727988 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="download_align" name="Download and align" version="0.0.1"> |
| 2 <description> Downloads fastq.gz, unzips, trims with cutadapt and alignes to reference</description> | |
| 3 <requirements> | |
|
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083c25559b6b
updated cutadapt dependency to 1.8 to solve env problem
Eduardo <eduardoalves@abdn.ac.uk>
parents:
19
diff
changeset
|
4 <requirement type="package" version="1.8">cutadapt</requirement> |
| 27 | 5 <requirement type="package" version="2.2.4">bowtie2</requirement> |
| 21 | 6 <requirement type="package" version="0.1.18">samtools</requirement> |
| 0 | 7 </requirements> |
| 8 <command> | |
| 9 #set index_path = '' | |
| 10 #if str($reference_genome.source) == "history": | |
|
20
083c25559b6b
updated cutadapt dependency to 1.8 to solve env problem
Eduardo <eduardoalves@abdn.ac.uk>
parents:
19
diff
changeset
|
11 bowtie2-build "$reference_genome.own_file" genome && |
| 0 | 12 ln -s "$reference_genome.own_file" genome.fa && |
| 13 #set index_path = 'genome' | |
| 14 #else: | |
| 15 #set index_path = $reference_genome.index.fields.path | |
| 16 #end if | |
| 28 | 17 wget -O - $file | gunzip -c | cutadapt -q 20 -m 20 - | bowtie2 -q |
| 0 | 18 ## index file path |
| 19 -x $index_path | |
| 28 | 20 -U - | samtools view -bS - > $output |
| 0 | 21 </command> |
| 22 <stdio> | |
| 23 <exit_code range="1:" level="fatal" description="Tool exception" /> | |
| 24 </stdio> | |
| 25 <inputs> | |
| 26 <param format="text" name="file" type="text" label="URL for fastq.gz"/> | |
| 27 <conditional name="reference_genome"> | |
| 28 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> | |
| 29 <option value="indexed">Use a built-in genome index</option> | |
| 30 <option value="history">Use a genome from the history and build index</option> | |
| 31 </param> | |
| 32 <when value="indexed"> | |
| 33 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> | |
| 34 <options from_data_table="bowtie2_indexes"> | |
| 35 <filter type="sort_by" column="2"/> | |
| 36 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | |
| 37 </options> | |
| 38 </param> | |
| 39 </when> | |
| 40 <when value="history"> | |
| 41 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" /> | |
| 42 </when> | |
| 43 </conditional> | |
| 44 </inputs> | |
| 45 <outputs> | |
| 46 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)" /> | |
| 47 </outputs> | |
| 48 <help> | |
| 49 This tool extracts reads from sra, runs cutdapt and bowtie and outputs a bam file. | |
| 50 | |
| 51 Contact Eduardo Alves at eduardoalves@abdn.ac.uk for support and bug reports. | |
| 52 </help> | |
| 53 </tool> |