Mercurial > repos > yating-l > ucsc_blat

annotate blat.xml @ 19:355af6f61974 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
author yating-l
date Fri, 12 May 2017 17:22:07 -0400
parents 275949b792a4
children 181a8b8ac4da
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
1 <?xml version="1.0"?>
0
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
2 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.0">
5
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
3 <description>Standalone blat sequence search command line tool</description>
0
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
4 <requirements>
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
6 </requirements>
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
19
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
8 #if str($reference_source.reference_source_selector) == "history":
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
9 #set $reference_fasta_filename = "localref.fa"
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
10 ln -s '${reference_source.database}' '${reference_fasta_filename}' &&
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
11 #else:
18
275949b792a4 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 13
diff changeset
12 #set $reference_fasta_filename = str($reference_source.database.fields.path)
19
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
13 #end if
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
14 blat
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
15 #if $noHead == "yes"
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
16 -noHead
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
17 #end if
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
18 -q=$query_type
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
19 -t=$database_type
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
20 -mask=$mask
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
21 '$reference_fasta_filename'
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
22 '${query}'
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
23 output
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
24 && sort -k 10,10 -k 12,12n output > '${output_sorted}'
0
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
25 ]]></command>
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
26 <inputs>
12
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
27 <conditional name="reference_source">
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
28 <param name="reference_source_selector" type="select" label="Choose the source for the database">
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
29 <option value="cached">Locally cached</option>
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
30 <option value="history">History</option>
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
31 </param>
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
32 <when value="cached">
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
33 <param name="database" type="select" label="Select database">
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
34 <options from_data_table="all_fasta">
19
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
35 <filter type="sort_by" column="2" />
12
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
36 </options>
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
37 <validator type="no_options" message="A built-in database is not available" />
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
38 </param>
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
39 </when>
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
40 <when value="history">
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
41 <param name="database" type="data" format="fasta" label="Using database file" />
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
42 </when>
61e2768506c1 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 11
diff changeset
43 </conditional>
0
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
44 <param type="data" name="query" format="fasta" />
11
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
45 <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t">
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
46 <option value="dna">dna - DNA sequence</option>
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
47 <option value="prot">prot - protein sequence</option>
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
48 <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option>
0
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
49 </param>
11
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
50 <param type="select" name="query_type" format="text" multiple="false" label="query type" help="Choose your query type, the default is rnax" argument="-q">
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
51 <option value="dna">dna - DNA sequence </option>
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
52 <option value="rna">rna - RNA sequence</option>
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
53 <option value="prot">prot - protein sequence</option>
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
54 <option value="dnax">dnax - DNA sequence translated in six frames to protein</option>
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
55 <option value="rnax" selected="true">rnax - DNA sequence translated in three frames to protein</option>
0
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
56 </param>
11
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
57 <param type="select" name="noHead" format="text" label="Suppresses .psl header (so it's just a tab-separated file)." >
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
58 <option value="yes" selected="true">Yes, suppresses .psl header</option>
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
59 <option value="no">No, do not suppresses .psl header</option>
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
60 </param>
0
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
61 <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
62 but may extend through it in nucleotide searches. Masked areas
11
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
63 are ignored entirely in protein or translated searches. Default is lower" argument="-mask">
9aad7a2258e5 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents: 10
diff changeset
64 <option value="lower" selected="true">lower - mask out lower-cased sequence</option>
0
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
65 <option value="upper">upper - mask out upper-cased sequence</option>
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
66 <option value="out">out - mask according to database.out RepeatMasker .out file</option>
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
67 <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
68 </param>
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
69 </inputs>
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
70 <outputs>
6
6f06b6d68c0b planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 5
diff changeset
71 <data format="psl" name="output_sorted" label="${tool.name} on ${on_string}"></data>
0
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
72 </outputs>
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
73 <tests>
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
74 <test>
13
42f1509f3d5a planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 12
diff changeset
75 <param name="reference_source_selector" value="history" />
9
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf
yating-l
parents: 8
diff changeset
76 <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf
yating-l
parents: 8
diff changeset
77 <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
0
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
78 <param name="database_type" value="dnax" />
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
79 <param name="query_type" value="rnax" />
13
42f1509f3d5a planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 12
diff changeset
80 <param name="noHead" value="yes" />
0
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
81 <param name="mask" value="lower" />
9
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf
yating-l
parents: 8
diff changeset
82 <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" />
0
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
83 </test>
9
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf
yating-l
parents: 8
diff changeset
84 <test>
13
42f1509f3d5a planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 12
diff changeset
85 <param name="reference_source_selector" value="history" />
9
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf
yating-l
parents: 8
diff changeset
86 <param name="database" value="dbia3/dbia3.fa" />
10
3511cb739854 planemo upload commit 98f55adc515e51ba5c71a0135a620f3e1fcca9b9
yating-l
parents: 9
diff changeset
87 <param name="query" value="dbia3/dmel-all-transcript-r6.13.fasta" />
9
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf
yating-l
parents: 8
diff changeset
88 <param name="database_type" value="dnax" />
10
3511cb739854 planemo upload commit 98f55adc515e51ba5c71a0135a620f3e1fcca9b9
yating-l
parents: 9
diff changeset
89 <param name="query_type" value="rnax" />
13
42f1509f3d5a planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 12
diff changeset
90 <param name="noHead" value="yes" />
9
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf
yating-l
parents: 8
diff changeset
91 <param name="mask" value="lower" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf
yating-l
parents: 8
diff changeset
92 <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf
yating-l
parents: 8
diff changeset
93 </test>
19
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
94 <test>
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
95 <param name="reference_source_selector" value="cached" />
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
96 <param name="database" value="dbia3" />
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
97 <param name="query" value="dbia3/dmel-all-transcript-r6.13.fasta" />
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
98 <param name="database_type" value="dnax" />
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
99 <param name="query_type" value="rnax" />
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
100 <param name="noHead" value="yes" />
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
101 <param name="mask" value="lower" />
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
102 <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />
355af6f61974 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
yating-l
parents: 18
diff changeset
103 </test>
9
c4f0808a68ad planemo upload commit e948e26e96631447718ac125a92dd5fef0cecdcf
yating-l
parents: 8
diff changeset
104
5
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
105 </tests>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
106 <help>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
107 <![CDATA[
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
108 BLAT
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
109 ====
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
110 BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments.
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
111
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
112 blat (version: v340)- Standalone blat sequence search command line tool.
7
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
113 -------------------------------------------------------------------------
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
114
5
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
115 usage:
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
116 ++++++
7
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
117
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
118 $ blat database query [-ooc=11.ooc] output.psl
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
119
5
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
120 where:
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
121 database and query are each either a .fa, .nib or .2bit file,
7
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
122 or a list of these files with one file name per line.
5
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
123 -ooc=11.ooc tells the program to load over-occurring 11-mers from
7
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
124 an external file. This will increase the speed
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
125 by a factor of 40 in many cases, but is not required.
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
126 output.psl is the name of the output file.
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
127
5
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
128 documentation:
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
129 ++++++++++++++
7
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
130
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
131 See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
132
5
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
133 Source code:
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
134 ++++++++++++
7
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
135
5
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
136 http://hgdownload.cse.ucsc.edu/admin/exe/
7
bd3352c46beb planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 6
diff changeset
137
10
3511cb739854 planemo upload commit 98f55adc515e51ba5c71a0135a620f3e1fcca9b9
yating-l
parents: 9
diff changeset
138 ]]></help>
5
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
139 <citations>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
140 <citation type="bibtex">@article{kent2002blat,
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
141 title={BLAT—the BLAST-like alignment tool},
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
142 author={Kent, W James},
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
143 journal={Genome research},
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
144 volume={12},
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
145 number={4},
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
146 pages={656--664},
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
147 year={2002},
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
148 publisher={Cold Spring Harbor Lab}
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
149 }</citation>
70d7377d5e24 planemo upload commit 7856c637db5bd4ea0b8b4db63e242618421a9cc6-dirty
yating-l
parents: 0
diff changeset
150 </citations>
0
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
151 </tool>
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
152
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
153
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
154
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
155
9e56efe1c371 planemo upload
yating-l
parents:
diff changeset
156