Mercurial > repos > devteam > ncbi_blast_plus
comparison tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml @ 11:4c4a0da938ff draft
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
Supports $GALAXY_SLOTS.
Includes more tests and heavy use of macros.
author | peterjc |
---|---|
date | Thu, 05 Dec 2013 06:55:59 -0500 |
parents | |
children | 623f727cdff1 |
comparison
equal
deleted
inserted
replaced
10:70e7dcbf6573 | 11:4c4a0da938ff |
---|---|
1 <tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.0.22"> | |
2 <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo --> | |
3 <description>masks low complexity regions</description> | |
4 <macros> | |
5 <token name="@BINARY@">dustmasker</token> | |
6 <import>ncbi_macros.xml</import> | |
7 </macros> | |
8 <expand macro="requirements" /> | |
9 <command> | |
10 ## The command is a Cheetah template which allows some Python based syntax. | |
11 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces | |
12 dustmasker | |
13 #if $db_opts.db_opts_selector == "db": | |
14 -in "${db_opts.database.fields.path}" -infmt blastdb | |
15 #elif $db_opts.db_opts_selector == "histdb": | |
16 -in "${os.path.join($db_opts.histdb.extra_files_path, 'blastdb')}" -infmt blastdb | |
17 #else: | |
18 -in "$subject" -infmt fasta | |
19 #end if | |
20 -out "$outfile" | |
21 -window $window -level $level -linker $linker -outfmt $outformat | |
22 </command> | |
23 <expand macro="stdio" /> | |
24 <inputs> | |
25 <expand macro="input_conditional_nucleotide_db" /> | |
26 <param name="window" type="integer" value="64" label="DUST window length" /> | |
27 <param name="level" type="integer" value="20" label="DUST level" help="Score threshold for subwindows" /> | |
28 <param name="linker" type="integer" value="1" label="DUST linker" help="How close masked intervals should be to get merged together" /> | |
29 <param name="outformat" type="select" label="Output format"> | |
30 <!-- acclist and maskinfo_xml are listed as possible output formats in | |
31 "dustmasker -help", but were not recognized by NCBI BLAST up to | |
32 release 2.2.27+. Fixed in BLAST 2.2.28+. | |
33 seqloc_* formats are not very useful --> | |
34 <!-- <option value="acclist">acclist</option>--> | |
35 <option value="fasta">FASTA</option> | |
36 <option value="interval" selected="true">interval</option> | |
37 <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option> | |
38 <option value="maskinfo_asn1_text">maskinfo ASN.1 text</option> | |
39 <!-- <option value="maskinfo_xml">maskinfo_xml</option> | |
40 <option value="seqloc_asn1_bin">seqloc_asn1_bin</option> | |
41 <option value="seqloc_asn1_text">seqloc_asn1_text</option> | |
42 <option value="seqloc_xml">seqloc_xml</option>--> | |
43 </param> | |
44 </inputs> | |
45 <outputs> | |
46 <data name="outfile" format="interval" label="DUST Masked File"> | |
47 <change_format> | |
48 <when input="outformat" value="fasta" format="fasta" /> | |
49 <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" /> | |
50 <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" /> | |
51 </change_format> | |
52 </data> | |
53 </outputs> | |
54 <tests> | |
55 <test> | |
56 <param name="db_opts_selector" value="file" /> | |
57 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> | |
58 <param name="window" value="64" /> | |
59 <param name="level" value="20" /> | |
60 <param name="linker" value="1" /> | |
61 <param name="outformat" value="fasta" /> | |
62 <output name="outfile" file="dustmasker_three_human.fasta" /> | |
63 </test> | |
64 <test> | |
65 <param name="db_opts_selector" value="file" /> | |
66 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> | |
67 <param name="window" value="64" /> | |
68 <param name="level" value="20" /> | |
69 <param name="linker" value="1" /> | |
70 <param name="outformat" value="maskinfo_asn1_bin" /> | |
71 <output name="outfile" file="dustmasker_three_human.maskinfo-asn1-binary" /> | |
72 </test> | |
73 <test> | |
74 <param name="db_opts_selector" value="file" /> | |
75 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> | |
76 <param name="window" value="64" /> | |
77 <param name="level" value="20" /> | |
78 <param name="linker" value="1" /> | |
79 <param name="outformat" value="maskinfo_asn1_text" /> | |
80 <output name="outfile" file="dustmasker_three_human.maskinfo-asn1" /> | |
81 </test> | |
82 </tests> | |
83 <help> | |
84 **What it does** | |
85 | |
86 This tool identifies and masks out low complexity regions of a nucleotide database (or sequences in FASTA format) by using the symmetric DUST algorithm. | |
87 | |
88 If you select *maskinfo ASN.1* (binary or text) as output format, the output file can be used as masking data for NCBI BLAST+ makeblastdb tool. | |
89 | |
90 More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_. | |
91 | |
92 .. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ | |
93 | |
94 **References** | |
95 | |
96 If you use this Galaxy tool in work leading to a scientific publication please | |
97 cite the following papers (a more specific paper covering this wrapper is planned): | |
98 | |
99 @REFERENCES@ | |
100 </help> | |
101 </tool> |