Mercurial > repos > matt-shirley > ncbi_sra_toolkit
annotate fastq_dump.xml @ 15:c71031b17e08
Avoid relative paths, and rename "ncbi" dir
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Mon, 30 Mar 2015 15:05:20 -0400 |
| parents | eb55ff614fed |
| children | 393a04ec0fa9 |
| rev | line source |
|---|---|
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eb55ff614fed
Fixed bug affecting --split-spot option.
Matt Shirley <mdshw5@gmail.com>
parents:
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diff
changeset
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1 <tool id="fastq_dump" name="Extract reads" version="1.1.2"> |
| 2 | 2 <description> from NCBI SRA.</description> |
| 3 <command> | |
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558a88cd49e4
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Matt Shirley <mdshw5@gmail.com>
parents:
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4 fastq-dump --log-level fatal |
| 2 | 5 #if $input.input_select == "file": |
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558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
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diff
changeset
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6 --accession '${input.file.name}' |
| 2 | 7 #else: |
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558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
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diff
changeset
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8 --accession $input.accession |
| 2 | 9 #end if |
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558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
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diff
changeset
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10 --defline-seq '@\$sn[_\$rn]/\$ri' |
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558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
2
diff
changeset
|
11 --stdout |
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9
eb55ff614fed
Fixed bug affecting --split-spot option.
Matt Shirley <mdshw5@gmail.com>
parents:
8
diff
changeset
|
12 #if str( $split ) == "yes": |
| 2 | 13 --split-spot |
| 14 #end if | |
| 15 #if str( $alignments ) == "aligned": | |
| 16 --aligned | |
| 17 #end if | |
| 18 #if str( $alignments ) == "unaligned": | |
| 19 --unaligned | |
| 20 #end if | |
| 21 #if str( $minID ) != "": | |
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558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
2
diff
changeset
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22 --minSpotId $minID |
| 2 | 23 #end if |
| 24 #if str( $maxID ) != "": | |
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558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
2
diff
changeset
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25 --maxSpotId $maxID |
| 2 | 26 #end if |
| 27 #if str( $minlen ) != "": | |
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558a88cd49e4
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Matt Shirley <mdshw5@gmail.com>
parents:
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diff
changeset
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28 --minReadLen $minlen |
| 2 | 29 #end if |
| 30 #if str( $readfilter ) != "": | |
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558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
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diff
changeset
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31 --read-filter $readfilter |
| 2 | 32 #end if |
| 33 #if str( $region ) != "": | |
| 34 --aligned-region $region | |
| 35 #end if | |
| 36 #if str( $spotgroups ) != "": | |
| 37 --spot-groups $spotgroups | |
| 38 #end if | |
| 39 #if str( $matepairDist ) != "": | |
| 40 --matepair-distance $matepairDist | |
| 41 #end if | |
| 42 #if $clip == "yes": | |
| 43 --clip | |
| 44 #end if | |
| 45 #if str( $outputformat ) == "fasta": | |
| 46 --fasta | |
| 47 #end if | |
| 48 #if $input.input_select=="file": | |
| 49 $input.file | |
| 50 #else: | |
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558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
2
diff
changeset
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51 $input.accession |
| 2 | 52 #end if |
| 53 > $output | |
| 54 </command> | |
| 55 <version_string>fastq-dump --version</version_string> | |
| 56 <inputs> | |
| 57 <conditional name="input"> | |
| 58 <param name="input_select" type="select" label="select input type"> | |
| 59 <option value="accession_number">SRR accession</option> | |
| 60 <option value="file">SRA archive in current history</option> | |
| 61 </param> | |
| 62 <when value="file"> | |
| 63 <param format="sra" name="file" type="data" label="sra archive"/> | |
| 64 </when> | |
| 65 <when value="accession_number"> | |
| 66 <param format="text" name="accession" type="text" label="accession"/> | |
| 67 </when> | |
| 68 </conditional> | |
| 69 <param format="text" name="minID" type="text" label="minimum spot ID"/> | |
| 70 <param format="text" name="maxID" type="text" label="maximum spot ID"/> | |
| 71 <param format="text" name="minlen" type="text" label="minimum read length"/> | |
| 72 <param format="text" name="split" type="select" value="yes"> | |
| 73 <label>split spot by read pairs</label> | |
| 74 <option value="yes">Yes</option> | |
| 75 <option value="no">No</option> | |
| 76 </param> | |
| 77 <param format="text" name="alignments" type="select" value="both"> | |
| 78 <label>aligned or unaligned reads</label> | |
| 79 <option value="both">both</option> | |
| 80 <option value="aligned">aligned only</option> | |
| 81 <option value="unaligned">unaligned only</option> | |
| 82 </param> | |
| 83 <param format="text" name="region" type="text" label="aligned region"/> | |
| 84 <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/> | |
| 85 <param format="text" name="readfilter" type="select" value=""> | |
| 86 <label>filter by value</label> | |
| 87 <option value="">None</option> | |
| 88 <option value="pass">pass</option> | |
| 89 <option value="reject">reject</option> | |
| 90 <option value="criteria">criteria</option> | |
| 91 <option value="redacted">redacted</option> | |
| 92 </param> | |
| 93 <param name="outputformat" type="select" label="select output format"> | |
| 94 <option value="fastqsanger">fastq</option> | |
| 95 <option value="fasta">fasta</option> | |
| 96 </param> | |
| 97 <param format="text" name="spotgroups" type="text" label="filter by spot-groups"/> | |
| 98 <param format="text" name="clip" type="select" value="no"> | |
| 99 <label>apply left and right clips</label> | |
| 100 <option value="no">No</option> | |
| 101 <option value="yes">Yes</option> | |
| 102 </param> | |
| 103 </inputs> | |
| 104 <outputs> | |
| 105 <data format="fastq" name="output"> | |
| 106 <change_format> | |
| 107 <when input="outputformat" value="fasta" format="fasta" /> | |
| 108 </change_format> | |
| 109 </data> | |
| 110 </outputs> | |
| 111 <stdio> | |
| 112 <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/> | |
| 113 </stdio> | |
| 114 <requirements> | |
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parents:
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115 <requirement type="package" version="2.3.4-2">sra_toolkit</requirement> |
| 2 | 116 </requirements> |
| 117 <help> | |
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Matt Shirley <mdshw5@gmail.com>
parents:
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diff
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118 This tool extracts reads from SRA archives using fastq-dump. |
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558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
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diff
changeset
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119 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. |
| 2 | 120 The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. |
| 121 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. | |
| 122 </help> | |
| 123 </tool> |