Mercurial > repos > yating-l > ucsc_blat

annotate blat.xml @ 5:dede60f744f4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
author iuc
date Fri, 23 Jun 2017 23:33:09 -0400
parents 545bc7831814
children 250a7f2b1331
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"?>
5
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
2 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="35-0">
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
3 <description>BLAST-like sequence alignment tool</description>
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
4 <requirements>
5
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
5 <requirement type="package" version="35">blat</requirement>
0
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[
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
8 #if str($reference_source.reference_source_selector) == "history":
5
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
9 ## blat depends on file extension
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
10 #if $reference_source.database.is_of_type("fasta"):
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
11 #set $reference_fasta_filename = "localref.fa"
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
12 #elif $reference_source.database.is_of_type("twobit"):
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
13 #set $reference_fasta_filename = "localref.2bit"
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
14 #else
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
15 #set $reference_fasta_filename = "localref"
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
16 #end if
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
17
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
18 ln -s '${reference_source.database}' '${reference_fasta_filename}' &&
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
19 #else:
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
20 #set $reference_fasta_filename = str($reference_source.database.fields.path)
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
21 #end if
5
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
22
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
23 blat
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
24 #if $noHead == "yes"
5
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
25 -noHead
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
26 #end if
5
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
27
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
28 -q=$query_type
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
29 -t=$database_type
5
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
30
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
31 #if $mask_type.mask == "file.out":
5
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
32 -mask='${mask_type.mask_file}'
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
33 #else:
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
34 -mask=$mask_type.mask
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
35 #end if
5
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
36
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
37 '$reference_fasta_filename'
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
38 '${query}'
5
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
39
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
40 output
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
41 && sort -k 10,10 -k 12,12n output > '${output_sorted}'
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
42 ]]></command>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
43 <inputs>
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
44 <conditional name="reference_source">
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
45 <param name="reference_source_selector" type="select" label="Choose the source for the database">
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
46 <option value="cached">Locally cached</option>
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
47 <option value="history">History</option>
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
48 </param>
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
49 <when value="cached">
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
50 <param name="database" type="select" label="Select database">
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
51 <options from_data_table="all_fasta">
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
52 <filter type="sort_by" column="2" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
53 </options>
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
54 <validator type="no_options" message="A built-in database is not available" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
55 </param>
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
56 </when>
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
57 <when value="history">
5
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
58 <param name="database" type="data" format="fasta, twobit" label="Using database file, either a .fa, .nib or .2bit file" />
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
59 </when>
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
60 </conditional>
5
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
61 <param type="data" name="query" format="fasta, twobit" label="Query data, either a .fa, .nib or .2bit file"/>
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
62 <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
63 <option value="dna">dna - DNA sequence</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
64 <option value="prot">prot - protein sequence</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
65 <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
66 </param>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
67 <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
68 <option value="dna">dna - DNA sequence </option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
69 <option value="rna">rna - RNA sequence</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
70 <option value="prot">prot - protein sequence</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
71 <option value="dnax">dnax - DNA sequence translated in six frames to protein</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
72 <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
73 </param>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
74 <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
75 <option value="yes" selected="true">Yes, suppresses .psl header</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
76 <option value="no">No, do not suppresses .psl header</option>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
77 </param>
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
78 <conditional name="mask_type">
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
79 <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
80 but may extend through it in nucleotide searches. Masked areas
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
81 are ignored entirely in protein or translated searches. Default is lower" argument="-mask">
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
82 <option value="lower" selected="true">lower - mask out lower-cased sequence</option>
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
83 <option value="upper">upper - mask out upper-cased sequence</option>
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
84 <option value="out">out - mask according to database.out RepeatMasker .out file</option>
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
85 <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
86 </param>
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
87 <when value="lower" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
88 <when value="upper" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
89 <when value="out" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
90 <when value="file.out">
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
91 <param name="mask_file" type="data" format="txt" label="RepeatMasker file.out" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
92 </when>
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
93 </conditional>
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
94 </inputs>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
95 <outputs>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
96 <data format="psl" name="output_sorted" label="${tool.name} on ${on_string}"></data>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
97 </outputs>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
98 <tests>
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
99 <!-- test on query of GenBank RefSeq records for Gallus gallus and database of Amazona vittata -->
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
100 <test>
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
101 <param name="reference_source_selector" value="history" />
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
102 <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
103 <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
104 <param name="database_type" value="dnax" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
105 <param name="query_type" value="rnax" />
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
106 <param name="noHead" value="yes" />
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
107 <param name="mask" value="lower" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
108 <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
109 </test>
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
110 <!-- test on query of partial mRNA of Drosophila melanogaster and the database of Drosophila biamipes dot chromosome -->
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
111 <test>
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
112 <param name="reference_source_selector" value="history" />
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
113 <param name="database" value="dbia3/dbia3.fa" />
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
114 <param name="query" value="dbia3/dmel-transcript.fa" />
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
115 <param name="database_type" value="dnax" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
116 <param name="query_type" value="rnax" />
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
117 <param name="noHead" value="yes" />
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
118 <param name="mask" value="lower" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
119 <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
120 </test>
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
121 <!-- test on the database masked by repeat masker -->
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
122 <test>
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
123 <param name="reference_source_selector" value="history" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
124 <param name="database" value="dbia3/dbia3_masked.2bit" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
125 <param name="query" value="dbia3/dmel-transcript.fa" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
126 <param name="database_type" value="dnax" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
127 <param name="query_type" value="rnax" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
128 <param name="noHead" value="yes" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
129 <param name="mask" value="file.out" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
130 <param name="mask_file" value="dbia3/dbia3_RM.out" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
131 <output name="output_sorted" value="dbia3/dbia3_masked.sorted.psl" />
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
132 </test>
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
133
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
134 </tests>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
135 <help>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
136 <![CDATA[
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
137 BLAT
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
138 ====
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
139 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
140
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
141 blat (version: v340)- Standalone blat sequence search command line tool.
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
142 -------------------------------------------------------------------------
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
143
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
144 usage:
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
145 ++++++
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
146
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
147 $ blat database query [-ooc=11.ooc] output.psl
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
148
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
149 where:
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
150 database and query are each either a .fa, .nib or .2bit file,
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
151 or a list of these files with one file name per line.
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
152 -ooc=11.ooc tells the program to load over-occurring 11-mers from
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
153 an external file. This will increase the speed
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
154 by a factor of 40 in many cases, but is not required.
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
155 output.psl is the name of the output file.
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
156
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
157 documentation:
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
158 ++++++++++++++
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
159
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
160 See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
161
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
162 Source code:
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
163 ++++++++++++
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
164
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
165 http://hgdownload.cse.ucsc.edu/admin/exe/
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
166
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
167 ]]></help>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
168 <citations>
1
eb7fcec3fdba planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
yating-l
parents: 0
diff changeset
169 <citation type="doi">10.1101/gr.229202</citation>
0
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
170 </citations>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
171 </tool>
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
172
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
173
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
174
951076264957 planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
yating-l
parents:
diff changeset
175
5
dede60f744f4 planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
iuc
parents: 4
diff changeset
176