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comparison blat.xml @ 0:951076264957 draft

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planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
author yating-l
date Wed, 12 Apr 2017 17:47:43 -0400
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1 <?xml version="1.0"?>
2 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.0">
3 <description>Standalone blat sequence search command line tool</description>
4 <requirements>
5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 blat
9 #if $noHead == "yes"
10 -noHead
11 #end if
12 -q=$query_type
13 -t=$database_type
14 -mask=$mask
15 '${database}'
16 '${query}'
17 output
18 && sort -k 10,10 -k 12,12n output > '${output_sorted}'
19 ]]></command>
20 <inputs>
21 <param type="data" name="database" format="fasta" />
22 <param type="data" name="query" format="fasta" />
23 <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t">
24 <option value="dna">dna - DNA sequence</option>
25 <option value="prot">prot - protein sequence</option>
26 <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option>
27 </param>
28 <param type="select" name="query_type" format="text" multiple="false" label="query type" help="Choose your query type, the default is rnax" argument="-q">
29 <option value="dna">dna - DNA sequence </option>
30 <option value="rna">rna - RNA sequence</option>
31 <option value="prot">prot - protein sequence</option>
32 <option value="dnax">dnax - DNA sequence translated in six frames to protein</option>
33 <option value="rnax" selected="true">rnax - DNA sequence translated in three frames to protein</option>
34 </param>
35 <param type="select" name="noHead" format="text" label="Suppresses .psl header (so it's just a tab-separated file)." >
36 <option value="yes" selected="true">Yes, suppresses .psl header</option>
37 <option value="no">No, do not suppresses .psl header</option>
38 </param>
39 <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region
40 but may extend through it in nucleotide searches. Masked areas
41 are ignored entirely in protein or translated searches. Default is lower" argument="-mask">
42 <option value="lower" selected="true">lower - mask out lower-cased sequence</option>
43 <option value="upper">upper - mask out upper-cased sequence</option>
44 <option value="out">out - mask according to database.out RepeatMasker .out file</option>
45 <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
46 </param>
47 </inputs>
48 <outputs>
49 <data format="psl" name="output_sorted" label="${tool.name} on ${on_string}"></data>
50 </outputs>
51 <tests>
52 <test>
53 <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
54 <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
55 <param name="database_type" value="dnax" />
56 <param name="query_type" value="rnax" />
57 <param name="noHead" value="true" />
58 <param name="mask" value="lower" />
59 <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" />
60 </test>
61 <test>
62 <param name="database" value="dbia3/dbia3.fa" />
63 <param name="query" value="dbia3/dmel-all-transcript-r6.13.fasta" />
64 <param name="database_type" value="dnax" />
65 <param name="query_type" value="rnax" />
66 <param name="noHead" value="true" />
67 <param name="mask" value="lower" />
68 <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />
69 </test>
70
71 </tests>
72 <help>
73 <![CDATA[
74 BLAT
75 ====
76 BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments.
77
78 blat (version: v340)- Standalone blat sequence search command line tool.
79 -------------------------------------------------------------------------
80
81 usage:
82 ++++++
83
84 $ blat database query [-ooc=11.ooc] output.psl
85
86 where:
87 database and query are each either a .fa, .nib or .2bit file,
88 or a list of these files with one file name per line.
89 -ooc=11.ooc tells the program to load over-occurring 11-mers from
90 an external file. This will increase the speed
91 by a factor of 40 in many cases, but is not required.
92 output.psl is the name of the output file.
93
94 documentation:
95 ++++++++++++++
96
97 See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)
98
99 Source code:
100 ++++++++++++
101
102 http://hgdownload.cse.ucsc.edu/admin/exe/
103
104 ]]></help>
105 <citations>
106 <citation type="bibtex">@article{kent2002blat,
107 title={BLAT—the BLAST-like alignment tool},
108 author={Kent, W James},
109 journal={Genome research},
110 volume={12},
111 number={4},
112 pages={656--664},
113 year={2002},
114 publisher={Cold Spring Harbor Lab}
115 }</citation>
116 </citations>
117 </tool>
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