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annotate fastq_dump.xml @ 2:5b83155a24f4 draft

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Using proper accession string for read deflines.
author Matthew Shirley <mdshw5@gmail.com>
date Tue, 13 Nov 2012 12:02:29 -0500
parents 4c06e5b58662
children f6bc4bdbd528
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ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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1 <tool id="fastq_dump" name="Extract fastq from SRA" version="1.0.0">
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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2 <description>Extract fastq format reads from SRA data archive.</description>
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5b83155a24f4 Using proper accession string for read deflines.
Matthew Shirley <mdshw5@gmail.com>
parents: 1
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3 <command>fastq-dump --accession ${input.name} --stdout $split $aligned $input > $output </command>
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ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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4 <version_string>fastq-dump --version</version_string>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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5 <inputs>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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6 <param format="sra" name="input" type="data" label="sra archive"/>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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7 <param format="text" name="split" type="select" value="">
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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8 <label>Split read pairs</label>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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9 <option value="">No</option>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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10 <option value="--split-spot">Yes</option>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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11 </param>
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4c06e5b58662 Fixed typo in select statement.
Matthew Shirley <mdshw5@gmail.com>
parents: 0
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12 <param format="text" name="aligned" type="select" value="">
0
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
diff changeset
13 <label>Specify alignment</label>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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14 <option value="">All</option>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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15 <option value="--aligned">Only aligned</option>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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16 <option value="--unaligned">Only unaligned</option>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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17 </param>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
diff changeset
18 </inputs>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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19 <outputs>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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20 <data format="fastqsanger" name="output"/>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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21 </outputs>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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22 <help>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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23 This tool extracts fastqsanger reads from SRA archives using fastq-dump. The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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24 </help>
ba892201bdad Wrote a wrapper for NCBI fastq-dump. Initial version.
Matthew Shirley <mdshw5@gmail.com>
parents:
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25 </tool>