Mercurial > repos > matt-shirley > ncbi_sra_toolkit
annotate sam_dump.xml @ 18:3da3d1a4deae
Back to shell commands. Maybe change_directory directive does not support reading env variables?
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Mon, 30 Mar 2015 20:31:50 -0400 |
| parents | 558a88cd49e4 |
| children | 393a04ec0fa9 |
| rev | line source |
|---|---|
| 4 | 1 <tool id="sam_dump" name="Extract reads" version="1.1.2"> |
| 2 | 2 <description> in SAM format from NCBI SRA.</description> |
| 3 <command> | |
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parents:
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4 sam-dump --log-level fatal |
| 2 | 5 #if str( $region ) != "": |
| 6 --aligned-region $region | |
| 7 #end if | |
| 8 #if str( $matepairDist ) != "": | |
| 9 --matepair-distance $matepairDist | |
| 10 #end if | |
| 11 #if str( $minMapq ) != "": | |
| 12 --minmapq $minMapq | |
| 13 #end if | |
| 14 #if $header == "yes": | |
| 15 --header | |
| 16 #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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17 --no-header |
| 2 | 18 #end if |
| 19 #if str( $alignments ) == "both": | |
| 20 --unaligned | |
| 21 #end if | |
| 22 #if str( $alignments ) == "unaligned": | |
| 23 --unaligned-spots-only | |
| 24 #end if | |
| 25 #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ): | |
| 26 --primary | |
| 27 #end if | |
| 28 #if str( $fastq ) == "yes": | |
| 29 --fastq | |
| 30 #end if | |
| 31 #if $input.input_select == "file": | |
| 32 $input.file | |
| 33 #elif $input.input_select == "accession_number": | |
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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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34 $input.accession |
| 2 | 35 #elif $input.input_select == "text": |
| 36 `cat $input.text` | |
| 37 #end if | |
| 38 > $output | |
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558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
4
diff
changeset
|
39 </command> |
| 2 | 40 <version_string>sam-dump --version</version_string> |
| 41 <inputs> | |
| 42 <conditional name="input"> | |
| 43 <param name="input_select" type="select" label="select input type"> | |
| 44 <option value="accession_number">SRR accession</option> | |
| 45 <option value="file">SRA archive in current history</option> | |
| 46 <option value="text">text file containing SRR accession</option> | |
| 47 </param> | |
| 48 <when value="file"> | |
| 49 <param format="sra" name="file" type="data" label="sra archive"/> | |
| 50 </when> | |
| 51 <when value="accession_number"> | |
| 52 <param format="text" name="accession" type="text" label="accession"/> | |
| 53 </when> | |
| 54 <when value="text"> | |
| 55 <param format="txt" name="text" type="data" label="text file"/> | |
| 56 </when> | |
| 57 </conditional> | |
| 58 <param format="text" name="region" type="text" label="aligned region"/> | |
| 59 <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/> | |
| 60 <param format="text" name="header" type="select" value="yes"> | |
| 61 <label>output SAM header</label> | |
| 62 <option value="yes">Yes</option> | |
| 63 <option value="no">No</option> | |
| 64 </param> | |
| 65 <param format="text" name="alignments" type="select" value="both"> | |
| 66 <label>aligned or unaligned reads</label> | |
| 67 <option value="both">both</option> | |
| 68 <option value="aligned">aligned only</option> | |
| 69 <option value="unaligned">unaligned only</option> | |
| 70 </param> | |
| 71 <param format="text" name="primary" type="select" value="no"> | |
| 72 <label>only primary aligments</label> | |
| 73 <option value="no">No</option> | |
| 74 <option value="yes">Yes</option> | |
| 75 </param> | |
| 76 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> | |
| 77 <param format="text" name="fastq" type="select" value="no"> | |
| 78 <label>output fastq</label> | |
| 79 <option value="no">No</option> | |
| 80 <option value="yes">Yes</option> | |
| 81 </param> | |
| 82 </inputs> | |
| 83 <outputs> | |
| 84 <data name="output" format="sam"> | |
| 85 <change_format> | |
| 86 <when input="fastq" value="yes" format="fastq"/> | |
| 87 </change_format> | |
| 88 </data> | |
| 89 </outputs> | |
| 90 <requirements> | |
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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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91 <requirement type="package" version="2.3.4-2">sra_toolkit</requirement> |
| 2 | 92 </requirements> |
| 93 <help> | |
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558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
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94 This tool extracts reads from sra archives using sam-dump. |
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558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
4
diff
changeset
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95 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. |
| 2 | 96 The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. |
| 97 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. | |
| 98 </help> | |
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558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
4
diff
changeset
|
99 </tool> |