Mercurial > repos > matt-shirley > ncbi_sra_toolkit
comparison sam_dump.xml @ 28:fdc981664a43
Update to most recent GitHub version passing tests.
author | Matt Shirley <mdshw5@gmail.com> |
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date | Wed, 01 Apr 2015 12:35:38 -0400 |
parents | 393a04ec0fa9 |
children |
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27:8be4f23d1018 | 28:fdc981664a43 |
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1 <tool id="sam_dump" name="Extract reads" version="1.1.2"> | 1 <tool id="sam_dump" name="Extract reads" version="1.1.2"> |
2 <description> in SAM format from NCBI SRA.</description> | 2 <description> in SAM format from NCBI SRA.</description> |
3 <command> | 3 <command> |
4 sam-dump --log-level fatal | 4 sam-dump --log-level fatal --disable-multithreading |
5 #if str( $region ) != "": | 5 #if str( $region ) != "": |
6 --aligned-region $region | 6 --aligned-region $region |
7 #end if | 7 #end if |
8 #if str( $matepairDist ) != "": | 8 #if str( $matepairDist ) != "": |
9 --matepair-distance $matepairDist | 9 --matepair-distance $matepairDist |
10 #end if | 10 #end if |
11 #if str( $minMapq ) != "": | 11 #if str( $minMapq ) != "": |
12 --minmapq $minMapq | 12 --minmapq $minMapq |
13 #end if | 13 #end if |
14 #if $header == "yes": | 14 #if str( $header ) == "yes": |
15 --header | 15 --header |
16 #else: | 16 #else: |
17 --no-header | 17 --no-header |
18 #end if | 18 #end if |
19 #if str( $alignments ) == "both": | 19 #if str( $alignments ) == "both": |
23 --unaligned-spots-only | 23 --unaligned-spots-only |
24 #end if | 24 #end if |
25 #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ): | 25 #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ): |
26 --primary | 26 --primary |
27 #end if | 27 #end if |
28 #if str( $fastq ) == "yes": | |
29 --fastq | |
30 #end if | |
31 #if $input.input_select == "file": | 28 #if $input.input_select == "file": |
32 $input.file | 29 $input.file |
33 #elif $input.input_select == "accession_number": | 30 #elif $input.input_select == "accession_number": |
34 $input.accession | 31 $input.accession |
35 #elif $input.input_select == "text": | |
36 `cat $input.text` | |
37 #end if | 32 #end if |
38 > $output | 33 > $output |
39 </command> | 34 </command> |
40 <version_string>sam-dump --version</version_string> | 35 <version_string>sam-dump --version</version_string> |
41 <inputs> | 36 <inputs> |
42 <conditional name="input"> | 37 <conditional name="input"> |
43 <param name="input_select" type="select" label="select input type"> | 38 <param name="input_select" type="select" label="select input type"> |
44 <option value="accession_number">SRR accession</option> | 39 <option value="accession_number">SRR accession</option> |
45 <option value="file">SRA archive in current history</option> | 40 <option value="file">SRA archive in current history</option> |
46 <option value="text">text file containing SRR accession</option> | |
47 </param> | 41 </param> |
48 <when value="file"> | 42 <when value="file"> |
49 <param format="sra" name="file" type="data" label="sra archive"/> | 43 <param format="sra" name="file" type="data" label="sra archive"/> |
50 </when> | 44 </when> |
51 <when value="accession_number"> | 45 <when value="accession_number"> |
52 <param format="text" name="accession" type="text" label="accession"/> | 46 <param format="text" name="accession" type="text" label="accession"/> |
53 </when> | 47 </when> |
54 <when value="text"> | |
55 <param format="txt" name="text" type="data" label="text file"/> | |
56 </when> | |
57 </conditional> | 48 </conditional> |
58 <param format="text" name="region" type="text" label="aligned region"/> | 49 <param format="text" name="region" type="text" label="aligned region (chr:start-end)"/> |
59 <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/> | 50 <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to)"/> |
60 <param format="text" name="header" type="select" value="yes"> | 51 <param format="text" name="header" type="select" value="yes"> |
61 <label>output SAM header</label> | 52 <label>output SAM header</label> |
62 <option value="yes">Yes</option> | 53 <option value="yes">Yes</option> |
63 <option value="no">No</option> | 54 <option value="no">No</option> |
64 </param> | 55 </param> |
72 <label>only primary aligments</label> | 63 <label>only primary aligments</label> |
73 <option value="no">No</option> | 64 <option value="no">No</option> |
74 <option value="yes">Yes</option> | 65 <option value="yes">Yes</option> |
75 </param> | 66 </param> |
76 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> | 67 <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> | 68 </inputs> |
83 <outputs> | 69 <outputs> |
84 <data name="output" format="sam"> | 70 <data name="output" format="sam"/> |
85 <change_format> | |
86 <when input="fastq" value="yes" format="fastq"/> | |
87 </change_format> | |
88 </data> | |
89 </outputs> | 71 </outputs> |
90 <requirements> | 72 <requirements> |
91 <requirement type="package" version="2.4.5">sra_toolkit</requirement> | 73 <requirement type="package" version="2.4.5">sra_toolkit</requirement> |
92 </requirements> | 74 </requirements> |
75 <tests> | |
76 <test> | |
77 <param name="input_select" value="accession_number"/> | |
78 <param name="accession" value="SRR925743"/> | |
79 <param name="region" value="17:41243452-41277500"/> | |
80 <output name="output" file="sam_dump_result.sam" ftype="sam" /> | |
81 </test> | |
82 </tests> | |
93 <help> | 83 <help> |
94 This tool extracts reads from sra archives using sam-dump. | 84 This tool extracts reads from sra archives using sam-dump. |
95 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. | 85 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. |
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. | 86 The sam-dump program is developed at NCBI, and is available at: http://github.com/ncbi/sra-tools |
97 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. | 87 Please submit inquiries and bug reports to http://github.com/mdshw5/sra-tools-galaxy. |
98 </help> | 88 </help> |
99 </tool> | 89 </tool> |