Mercurial > repos > matt-shirley > sra_tools
comparison sam_dump.xml @ 37:4da2d7f0128e draft
Exposed more options for fastq_dump and sam_dump
author | Matt Shirley <mdshw5@gmail.com> |
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date | Thu, 01 Aug 2013 13:57:27 -0400 |
parents | 423f3eb06428 |
children | a0925f507352 |
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36:b5274b0e61bc | 37:4da2d7f0128e |
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1 <tool id="sam_dump" name="Extract SAM" version="1.0.2"> | 1 <tool id="sam_dump" name="Extract reads" version="1.1.0"> |
2 <description> format reads from NCBI sra.</description> | 2 <description> in SAM format from NCBI SRA.</description> |
3 <command>sam-dump $header $aligned $primary '$input' > $output</command> | 3 <command> |
4 sam-dump --log-level fatal | |
5 #if str( $region ) != "": | |
6 --aligned-region $region | |
7 #end if | |
8 #if str( $matepairDist ) != "": | |
9 --matepair-distance $matepairDist | |
10 #end if | |
11 #if $header == "yes": | |
12 --header | |
13 #else: | |
14 --no-header | |
15 #end if | |
16 #if str( $alignments ) == "both": | |
17 --unaligned | |
18 #end if | |
19 #if str( $alignments ) == "unaligned": | |
20 --unaligned-spots-only | |
21 #end if | |
22 #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ): | |
23 --primary | |
24 #end if | |
25 #if $input.input_select == "file": | |
26 $input.file | |
27 #else: | |
28 $input.accession | |
29 #end if | |
30 > $output | |
31 </command> | |
4 <version_string>sam-dump --version</version_string> | 32 <version_string>sam-dump --version</version_string> |
5 <inputs> | 33 <inputs> |
6 <param format="SRA" name="input" type="data" label="sra archive"/> | 34 <conditional name="input"> |
7 <param format="text" name="header" type="select" value=""> | 35 <param name="input_select" type="select" label="select input type"> |
8 <label>Output SAM header</label> | 36 <option value="accession_number">SRR accession</option> |
9 <option value="--header">Yes</option> | 37 <option value="file">SRA archive in current history</option> |
10 <option value="--no-header">No</option> | 38 </param> |
39 <when value="file"> | |
40 <param format="sra" name="file" type="data" label="sra archive"/> | |
41 </when> | |
42 <when value="accession_number"> | |
43 <param format="text" name="accession" type="text" label="accession"/> | |
44 </when> | |
45 </conditional> | |
46 <param format="text" name="region" type="text" label="aligned region"/> | |
47 <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/> | |
48 <param format="text" name="header" type="select" value="yes"> | |
49 <label>output SAM header</label> | |
50 <option value="yes">Yes</option> | |
51 <option value="no">No</option> | |
11 </param> | 52 </param> |
12 <param format="text" name="aligned" type="select" value=""> | 53 <param format="text" name="alignments" type="select" value="both"> |
13 <label>Output unaligned reads as well as aligned reads</label> | 54 <label>aligned or unaligned reads</label> |
14 <option value="">No</option> | 55 <option value="both">both</option> |
15 <option value="--unaligned">Yes</option> | 56 <option value="aligned">aligned only</option> |
57 <option value="unaligned">unaligned only</option> | |
16 </param> | 58 </param> |
17 <param format="text" name="primary" type="select" value=""> | 59 <param format="text" name="primary" type="select" value="no"> |
18 <label>Output only primary aligments</label> | 60 <label>only primary aligments</label> |
19 <option value="">No</option> | 61 <option value="no">No</option> |
20 <option value="--primary">Yes</option> | 62 <option value="yes">Yes</option> |
21 </param> | 63 </param> |
64 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> | |
22 </inputs> | 65 </inputs> |
23 <outputs> | 66 <outputs> |
24 <data format="sam" name="output"/> | 67 <data format="sam" name="output"/> |
25 </outputs> | 68 </outputs> |
26 <requirements> | 69 <requirements> |
27 <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> | 70 <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> |
28 </requirements> | 71 </requirements> |
29 <help> | 72 <help> |
30 This tool extracts sam format reads from sra archives using sam-dump. | 73 This tool extracts reads from sra archives using sam-dump. |
31 The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. | 74 The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. |
32 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. | 75 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. |
33 </help> | 76 </help> |
34 </tool> | 77 </tool> |