Mercurial > repos > matt-shirley > ncbi_sra_toolkit
annotate bam_dump.xml @ 29:ce2bb7841f17 default tip
Fix for https://github.com/mdshw5/sra-tools-galaxy/issues/1
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Tue, 07 Apr 2015 09:09:23 -0400 |
| parents | fdc981664a43 |
| children |
| rev | line source |
|---|---|
| 27 | 1 <tool id="bam_dump" name="Extract reads" version="1.1.2"> |
| 2 <description> in BAM format from NCBI SRA.</description> | |
| 3 <command> | |
|
28
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
4 sam-dump --log-level fatal --disable-multithreading |
| 27 | 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 | |
|
28
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
14 #if str( $header ) == "yes": |
| 27 | 15 --header |
| 16 #else: | |
| 17 --no-header | |
| 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 $input.input_select == "file": | |
| 29 $input.file | |
| 30 #elif $input.input_select == "accession_number": | |
| 31 $input.accession | |
| 32 #end if | |
|
28
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
33 | samtools view -Sb - 2> /dev/null > $output |
| 27 | 34 </command> |
| 35 <version_string>sam-dump --version</version_string> | |
| 36 <inputs> | |
| 37 <conditional name="input"> | |
| 38 <param name="input_select" type="select" label="select input type"> | |
| 39 <option value="accession_number">SRR accession</option> | |
| 40 <option value="file">SRA archive in current history</option> | |
| 41 </param> | |
| 42 <when value="file"> | |
| 43 <param format="sra" name="file" type="data" label="sra archive"/> | |
| 44 </when> | |
| 45 <when value="accession_number"> | |
| 46 <param format="text" name="accession" type="text" label="accession"/> | |
| 47 </when> | |
| 48 </conditional> | |
|
28
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
49 <param format="text" name="region" type="text" label="aligned region (chr:start-end)"/> |
|
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
50 <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to)"/> |
| 27 | 51 <param format="text" name="header" type="select" value="yes"> |
| 52 <label>output BAM header</label> | |
| 53 <option value="yes">Yes</option> | |
| 54 <option value="no">No</option> | |
| 55 </param> | |
| 56 <param format="text" name="alignments" type="select" value="both"> | |
| 57 <label>aligned or unaligned reads</label> | |
| 58 <option value="both">both</option> | |
| 59 <option value="aligned">aligned only</option> | |
| 60 <option value="unaligned">unaligned only</option> | |
| 61 </param> | |
| 62 <param format="text" name="primary" type="select" value="no"> | |
| 63 <label>only primary aligments</label> | |
| 64 <option value="no">No</option> | |
| 65 <option value="yes">Yes</option> | |
| 66 </param> | |
| 67 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> | |
| 68 </inputs> | |
| 69 <outputs> | |
| 70 <data name="output" format="bam"/> | |
| 71 </outputs> | |
|
28
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
72 <stdio> |
|
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
73 <exit_code range="127" level="fatal" description="Could not locate sam-dump and/or samtools binary"/> |
|
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
74 </stdio> |
| 27 | 75 <requirements> |
| 76 <requirement type="package" version="2.4.5">sra_toolkit</requirement> | |
| 77 <requirement type="package" version="1.2">samtools</requirement> | |
| 78 </requirements> | |
|
28
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
79 <tests> |
|
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
80 <test> |
|
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
81 <param name="input_select" value="accession_number"/> |
|
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
82 <param name="accession" value="SRR925743"/> |
|
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
83 <param name="region" value="17:41243452-41277500"/> |
|
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
84 <output name="output" file="bam_dump_result.bam" ftype="bam" /> |
|
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
85 </test> |
|
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
86 </tests> |
| 27 | 87 <help> |
|
28
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
88 This tool extracts reads from sra archives using sam-dump. |
|
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
89 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. |
|
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
90 The sam-dump program is developed at NCBI, and is available at: http://github.com/ncbi/sra-tools |
|
fdc981664a43
Update to most recent GitHub version passing tests.
Matt Shirley <mdshw5@gmail.com>
parents:
27
diff
changeset
|
91 Please submit inquiries and bug reports to http://github.com/mdshw5/sra-tools-galaxy. |
| 27 | 92 </help> |
| 93 </tool> |