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comparison blat.xml @ 1:eb7fcec3fdba draft

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planemo upload commit 78ad97a2be3ed2c75777ec97ef9489f819cbc471
author yating-l
date Thu, 01 Jun 2017 14:17:51 -0400
parents 951076264957
children a1b3d24b55a1
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0:951076264957 1:eb7fcec3fdba
3 <description>Standalone blat sequence search command line tool</description> 3 <description>Standalone blat sequence search command line tool</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement> 5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 blat 8 #if str($reference_source.reference_source_selector) == "history":
9 #if $noHead == "yes" 9 #set $reference_fasta_filename = "localref.fa"
10 -noHead 10 ln -s '${reference_source.database}' '${reference_fasta_filename}' &&
11 #end if 11 #else:
12 -q=$query_type 12 #set $reference_fasta_filename = str($reference_source.database.fields.path)
13 -t=$database_type 13 #end if
14 -mask=$mask 14 blat
15 '${database}' 15 #if $noHead == "yes"
16 '${query}' 16 -noHead
17 output 17 #end if
18 && sort -k 10,10 -k 12,12n output > '${output_sorted}' 18 -q=$query_type
19 -t=$database_type
20 #if $mask_type.mask == "file.out":
21 -mask=$mask_type.mask_file
22 #else:
23 -mask=$mask_type.mask
24 #end if
25 '$reference_fasta_filename'
26 '${query}'
27 output
28 && sort -k 10,10 -k 12,12n output > '${output_sorted}'
19 ]]></command> 29 ]]></command>
20 <inputs> 30 <inputs>
21 <param type="data" name="database" format="fasta" /> 31 <conditional name="reference_source">
22 <param type="data" name="query" format="fasta" /> 32 <param name="reference_source_selector" type="select" label="Choose the source for the database">
33 <option value="cached">Locally cached</option>
34 <option value="history">History</option>
35 </param>
36 <when value="cached">
37 <param name="database" type="select" label="Select database">
38 <options from_data_table="all_fasta">
39 <filter type="sort_by" column="2" />
40 </options>
41 <validator type="no_options" message="A built-in database is not available" />
42 </param>
43 </when>
44 <when value="history">
45 <param name="database" type="data" format="fasta, twobit" label="Using database file, either a .fa, .nib or .2bit file" />
46 </when>
47 </conditional>
48 <param type="data" name="query" format="fasta, twobit" label="Query data, either a .fa, .nib or .2bit file"/>
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"> 49 <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> 50 <option value="dna">dna - DNA sequence</option>
25 <option value="prot">prot - protein sequence</option> 51 <option value="prot">prot - protein sequence</option>
26 <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option> 52 <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option>
27 </param> 53 </param>
34 </param> 60 </param>
35 <param type="select" name="noHead" format="text" label="Suppresses .psl header (so it's just a tab-separated file)." > 61 <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> 62 <option value="yes" selected="true">Yes, suppresses .psl header</option>
37 <option value="no">No, do not suppresses .psl header</option> 63 <option value="no">No, do not suppresses .psl header</option>
38 </param> 64 </param>
39 <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region 65 <conditional name="mask_type">
66 <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 67 but may extend through it in nucleotide searches. Masked areas
41 are ignored entirely in protein or translated searches. Default is lower" argument="-mask"> 68 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> 69 <option value="lower" selected="true">lower - mask out lower-cased sequence</option>
43 <option value="upper">upper - mask out upper-cased sequence</option> 70 <option value="upper">upper - mask out upper-cased sequence</option>
44 <option value="out">out - mask according to database.out RepeatMasker .out file</option> 71 <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> 72 <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
46 </param> 73 </param>
74 <when value="lower" />
75 <when value="upper" />
76 <when value="out" />
77 <when value="file.out">
78 <param name="mask_file" type="data" format="txt" label="RepeatMasker file.out" />
79 </when>
80 </conditional>
47 </inputs> 81 </inputs>
48 <outputs> 82 <outputs>
49 <data format="psl" name="output_sorted" label="${tool.name} on ${on_string}"></data> 83 <data format="psl" name="output_sorted" label="${tool.name} on ${on_string}"></data>
50 </outputs> 84 </outputs>
51 <tests> 85 <tests>
86 <!-- test on query of GenBank RefSeq records for Gallus gallus and database of Amazona vittata -->
52 <test> 87 <test>
88 <param name="reference_source_selector" value="history" />
53 <param name="database" value="amaVit1_Gallus/amaVit1.fa" /> 89 <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
54 <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" /> 90 <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
55 <param name="database_type" value="dnax" /> 91 <param name="database_type" value="dnax" />
56 <param name="query_type" value="rnax" /> 92 <param name="query_type" value="rnax" />
57 <param name="noHead" value="true" /> 93 <param name="noHead" value="yes" />
58 <param name="mask" value="lower" /> 94 <param name="mask" value="lower" />
59 <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" /> 95 <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" />
60 </test> 96 </test>
97 <!-- test on query of partial mRNA of Drosophila melanogaster and the database of Drosophila biamipes dot chromosome -->
61 <test> 98 <test>
99 <param name="reference_source_selector" value="history" />
62 <param name="database" value="dbia3/dbia3.fa" /> 100 <param name="database" value="dbia3/dbia3.fa" />
63 <param name="query" value="dbia3/dmel-all-transcript-r6.13.fasta" /> 101 <param name="query" value="dbia3/dmel-transcript.fa" />
64 <param name="database_type" value="dnax" /> 102 <param name="database_type" value="dnax" />
65 <param name="query_type" value="rnax" /> 103 <param name="query_type" value="rnax" />
66 <param name="noHead" value="true" /> 104 <param name="noHead" value="yes" />
67 <param name="mask" value="lower" /> 105 <param name="mask" value="lower" />
68 <output name="output_sorted" value="dbia3/dbia3.sorted.psl" /> 106 <output name="output_sorted" value="dbia3/dbia3.sorted.psl" />
107 </test>
108 <!-- test on the database masked by repeat masker -->
109 <test>
110 <param name="reference_source_selector" value="history" />
111 <param name="database" value="dbia3/dbia3_masked.2bit" />
112 <param name="query" value="dbia3/dmel-transcript.fa" />
113 <param name="database_type" value="dnax" />
114 <param name="query_type" value="rnax" />
115 <param name="noHead" value="yes" />
116 <param name="mask" value="file.out" />
117 <param name="mask_file" value="dbia3/dbia3_RM.out" />
118 <output name="output_sorted" value="dbia3/dbia3_masked.sorted.psl" />
69 </test> 119 </test>
70 120
71 </tests> 121 </tests>
72 <help> 122 <help>
73 <![CDATA[ 123 <![CDATA[
101 151
102 http://hgdownload.cse.ucsc.edu/admin/exe/ 152 http://hgdownload.cse.ucsc.edu/admin/exe/
103 153
104 ]]></help> 154 ]]></help>
105 <citations> 155 <citations>
106 <citation type="bibtex">@article{kent2002blat, 156 <citation type="doi">10.1101/gr.229202</citation>
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> 157 </citations>
117 </tool> 158 </tool>
118 159
119 160
120 161