Mercurial > repos > yating-l > ucsc_blat

annotate blat.xml @ 0:951076264957 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
author yating-l
date Wed, 12 Apr 2017 17:47:43 -0400
parents
children eb7fcec3fdba
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
1 <?xml version="1.0"?>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
2 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.0">
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
3 <description>Standalone blat sequence search command line tool</description>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
4 <requirements>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
6 </requirements>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
8 blat
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
9 #if $noHead == "yes"
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
10 -noHead
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
11 #end if
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
12 -q=$query_type
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
13 -t=$database_type
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
14 -mask=$mask
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
15 '${database}'
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
16 '${query}'
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
17 output
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
18 && sort -k 10,10 -k 12,12n output > '${output_sorted}'
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
19 ]]></command>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
20 <inputs>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
21 <param type="data" name="database" format="fasta" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
22 <param type="data" name="query" format="fasta" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
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">
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
24 <option value="dna">dna - DNA sequence</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
25 <option value="prot">prot - protein sequence</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
26 <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
27 </param>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
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">
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
29 <option value="dna">dna - DNA sequence </option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
30 <option value="rna">rna - RNA sequence</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
31 <option value="prot">prot - protein sequence</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
32 <option value="dnax">dnax - DNA sequence translated in six frames to protein</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
33 <option value="rnax" selected="true">rnax - DNA sequence translated in three frames to protein</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
34 </param>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
35 <param type="select" name="noHead" format="text" label="Suppresses .psl header (so it's just a tab-separated file)." >
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
36 <option value="yes" selected="true">Yes, suppresses .psl header</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
37 <option value="no">No, do not suppresses .psl header</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
38 </param>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
39 <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
40 but may extend through it in nucleotide searches. Masked areas
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
41 are ignored entirely in protein or translated searches. Default is lower" argument="-mask">
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
42 <option value="lower" selected="true">lower - mask out lower-cased sequence</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
43 <option value="upper">upper - mask out upper-cased sequence</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
44 <option value="out">out - mask according to database.out RepeatMasker .out file</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
45 <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
46 </param>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
47 </inputs>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
48 <outputs>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
49 <data format="psl" name="output_sorted" label="${tool.name} on ${on_string}"></data>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
50 </outputs>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
51 <tests>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
52 <test>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
53 <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
54 <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
55 <param name="database_type" value="dnax" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
56 <param name="query_type" value="rnax" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
57 <param name="noHead" value="true" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
58 <param name="mask" value="lower" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
59 <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
60 </test>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
61 <test>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
62 <param name="database" value="dbia3/dbia3.fa" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
63 <param name="query" value="dbia3/dmel-all-transcript-r6.13.fasta" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
64 <param name="database_type" value="dnax" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
65 <param name="query_type" value="rnax" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
66 <param name="noHead" value="true" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
67 <param name="mask" value="lower" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
68 <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
69 </test>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
70
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
71 </tests>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
72 <help>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
73 <![CDATA[
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
74 BLAT
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
75 ====
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
76 BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments.
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
77
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
78 blat (version: v340)- Standalone blat sequence search command line tool.
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
79 -------------------------------------------------------------------------
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
80
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
81 usage:
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
82 ++++++
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
83
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
84 $ blat database query [-ooc=11.ooc] output.psl
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
85
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
86 where:
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
87 database and query are each either a .fa, .nib or .2bit file,
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
88 or a list of these files with one file name per line.
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
89 -ooc=11.ooc tells the program to load over-occurring 11-mers from
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
90 an external file. This will increase the speed
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
91 by a factor of 40 in many cases, but is not required.
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
92 output.psl is the name of the output file.
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
93
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
94 documentation:
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
95 ++++++++++++++
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
96
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
97 See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
98
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
99 Source code:
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
100 ++++++++++++
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
101
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
102 http://hgdownload.cse.ucsc.edu/admin/exe/
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
103
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
104 ]]></help>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
105 <citations>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
106 <citation type="bibtex">@article{kent2002blat,
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
107 title={BLAT—the BLAST-like alignment tool},
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
108 author={Kent, W James},
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
109 journal={Genome research},
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
110 volume={12},
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
111 number={4},
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
112 pages={656--664},
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
113 year={2002},
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
114 publisher={Cold Spring Harbor Lab}
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
115 }</citation>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
116 </citations>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
117 </tool>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
118
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
119
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
120
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
121
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
122