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comparison tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml @ 13:623f727cdff1 draft

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Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
author peterjc
date Fri, 14 Mar 2014 07:40:46 -0400
parents 4c4a0da938ff
children 2fe07f50a41e
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12:6560192c5098 13:623f727cdff1
1 <tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.0.22"> 1 <tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.00">
2 <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo --> 2 <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo -->
3 <description>masks low complexity regions</description> 3 <description>masks low complexity regions</description>
4 <macros> 4 <macros>
5 <token name="@BINARY@">dustmasker</token> 5 <token name="@BINARY@">dustmasker</token>
6 <import>ncbi_macros.xml</import> 6 <import>ncbi_macros.xml</import>
25 <expand macro="input_conditional_nucleotide_db" /> 25 <expand macro="input_conditional_nucleotide_db" />
26 <param name="window" type="integer" value="64" label="DUST window length" /> 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" /> 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" /> 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"> 29 <param name="outformat" type="select" label="Output format">
30 <!-- acclist and maskinfo_xml are listed as possible output formats in 30 <!-- seqloc_* formats are not very useful
31 "dustmasker -help", but were not recognized by NCBI BLAST up to 31 and what BLAST+ calls 'interval' is not what Galaxy calls interval format
32 release 2.2.27+. Fixed in BLAST 2.2.28+. 32 -->
33 seqloc_* formats are not very useful -->
34 <!-- <option value="acclist">acclist</option>-->
35 <option value="fasta">FASTA</option> 33 <option value="fasta">FASTA</option>
36 <option value="interval" selected="true">interval</option>
37 <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option> 34 <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option>
38 <option value="maskinfo_asn1_text">maskinfo ASN.1 text</option> 35 <option value="maskinfo_asn1_text" selected="true">maskinfo ASN.1 text</option>
39 <!-- <option value="maskinfo_xml">maskinfo_xml</option> 36 <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> 37 </param>
44 </inputs> 38 </inputs>
45 <outputs> 39 <outputs>
46 <data name="outfile" format="interval" label="DUST Masked File"> 40 <data name="outfile" format="maskinfo-asn1" label="DUST Masked File">
47 <change_format> 41 <change_format>
48 <when input="outformat" value="fasta" format="fasta" /> 42 <when input="outformat" value="fasta" format="fasta" />
49 <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" /> 43 <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" />
44 <!--
50 <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" /> 45 <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" />
46 -->
47 <when input="outformat" value="maskinfo_xml" format="xml" />
51 </change_format> 48 </change_format>
52 </data> 49 </data>
53 </outputs> 50 </outputs>
54 <tests> 51 <tests>
55 <test> 52 <test>
81 </test> 78 </test>
82 </tests> 79 </tests>
83 <help> 80 <help>
84 **What it does** 81 **What it does**
85 82
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. 83 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 84
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. 85 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 86
90 More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_. 87 More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_.
91 88
92 .. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ 89 .. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/
90 .. _DUST: http://www.ncbi.nlm.nih.gov/pubmed/16796549
93 91
94 **References** 92 **References**
95 93
96 If you use this Galaxy tool in work leading to a scientific publication please 94 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): 95 cite the following papers (a more specific paper covering this wrapper is planned):