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comparison tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.11">
2 <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description>
3 <version_command>tblastx -version</version_command>
4 <command interpreter="python">hide_stderr.py
5 ## The command is a Cheetah template which allows some Python based syntax.
6 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
7 tblastx
8 -query "$query"
9 #if $db_opts.db_opts_selector == "db":
10 -db "${db_opts.database.fields.path}"
11 #else:
12 -subject "$db_opts.subject"
13 #end if
14 -evalue $evalue_cutoff
15 -out $output1
16 ##Set the extended list here so if/when we add things, saved workflows are not affected
17 #if str($out_format)=="ext":
18 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
19 #else:
20 -outfmt $out_format
21 #end if
22 -num_threads 8
23 #if $adv_opts.adv_opts_selector=="advanced":
24 $adv_opts.filter_query
25 $adv_opts.strand
26 -matrix $adv_opts.matrix
27 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
28 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments
29 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
30 -max_target_seqs $adv_opts.max_hits
31 #end if
32 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
33 -word_size $adv_opts.word_size
34 #end if
35 $adv_opts.parse_deflines
36 ## End of advanced options:
37 #end if
38 </command>
39 <inputs>
40 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
41 <conditional name="db_opts">
42 <param name="db_opts_selector" type="select" label="Subject database/sequences">
43 <option value="db" selected="True">BLAST Database</option>
44 <option value="file">FASTA file</option>
45 </param>
46 <when value="db">
47 <param name="database" type="select" label="Nucleotide BLAST database">
48 <options from_file="blastdb.loc">
49 <column name="value" index="0"/>
50 <column name="name" index="1"/>
51 <column name="path" index="2"/>
52 </options>
53 </param>
54 <param name="subject" type="hidden" value="" />
55 </when>
56 <when value="file">
57 <param name="database" type="hidden" value="" />
58 <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/>
59 </when>
60 </conditional>
61 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
62 <param name="out_format" type="select" label="Output format">
63 <option value="6" selected="True">Tabular (standard 12 columns)</option>
64 <option value="ext">Tabular (extended 24 columns)</option>
65 <option value="5">BLAST XML</option>
66 <option value="0">Pairwise text</option>
67 <option value="0 -html">Pairwise HTML</option>
68 <option value="2">Query-anchored text</option>
69 <option value="2 -html">Query-anchored HTML</option>
70 <option value="4">Flat query-anchored text</option>
71 <option value="4 -html">Flat query-anchored HTML</option>
72 <!--
73 <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
74 -->
75 </param>
76 <conditional name="adv_opts">
77 <param name="adv_opts_selector" type="select" label="Advanced Options">
78 <option value="basic" selected="True">Hide Advanced Options</option>
79 <option value="advanced">Show Advanced Options</option>
80 </param>
81 <when value="basic" />
82 <when value="advanced">
83 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
84 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
85 <param name="strand" type="select" label="Query strand(s) to search against database/subject">
86 <option value="-strand both">Both</option>
87 <option value="-strand plus">Plus (forward)</option>
88 <option value="-strand minus">Minus (reverse complement)</option>
89 </param>
90 <param name="matrix" type="select" label="Scoring matrix">
91 <option value="BLOSUM90">BLOSUM90</option>
92 <option value="BLOSUM80">BLOSUM80</option>
93 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
94 <option value="BLOSUM50">BLOSUM50</option>
95 <option value="BLOSUM45">BLOSUM45</option>
96 <option value="PAM250">PAM250</option>
97 <option value="PAM70">PAM70</option>
98 <option value="PAM30">PAM30</option>
99 </param>
100 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
101 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
102 <validator type="in_range" min="0" />
103 </param>
104 <!-- I'd like word_size to be optional, with minimum 2 for tblastx -->
105 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
106 <validator type="in_range" min="0" />
107 </param>
108 <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
109 </when>
110 </conditional>
111 </inputs>
112 <outputs>
113 <data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}">
114 <change_format>
115 <when input="out_format" value="0" format="txt"/>
116 <when input="out_format" value="0 -html" format="html"/>
117 <when input="out_format" value="2" format="txt"/>
118 <when input="out_format" value="2 -html" format="html"/>
119 <when input="out_format" value="4" format="txt"/>
120 <when input="out_format" value="4 -html" format="html"/>
121 <when input="out_format" value="5" format="blastxml"/>
122 </change_format>
123 </data>
124 </outputs>
125 <requirements>
126 <requirement type="binary">tblastx</requirement>
127 </requirements>
128 <help>
129
130 .. class:: warningmark
131
132 **Note**. Database searches may take a substantial amount of time.
133 For large input datasets it is advisable to allow overnight processing.
134
135 -----
136
137 **What it does**
138
139 Search a *translated nucleotide database* using a *protein query*,
140 using the NCBI BLAST+ tblastx command line tool.
141
142 -----
143
144 **Output format**
145
146 Because Galaxy focuses on processing tabular data, the default output of this
147 tool is tabular. The standard BLAST+ tabular output contains 12 columns:
148
149 ====== ========= ============================================
150 Column NCBI name Description
151 ------ --------- --------------------------------------------
152 1 qseqid Query Seq-id (ID of your sequence)
153 2 sseqid Subject Seq-id (ID of the database hit)
154 3 pident Percentage of identical matches
155 4 length Alignment length
156 5 mismatch Number of mismatches
157 6 gapopen Number of gap openings
158 7 qstart Start of alignment in query
159 8 qend End of alignment in query
160 9 sstart Start of alignment in subject (database hit)
161 10 send End of alignment in subject (database hit)
162 11 evalue Expectation value (E-value)
163 12 bitscore Bit score
164 ====== ========= ============================================
165
166 The BLAST+ tools can optionally output additional columns of information,
167 but this takes longer to calculate. Most (but not all) of these columns are
168 included by selecting the extended tabular output. The extra columns are
169 included *after* the standard 12 columns. This is so that you can write
170 workflow filtering steps that accept either the 12 or 24 column tabular
171 BLAST output.
172
173 ====== ============= ===========================================
174 Column NCBI name Description
175 ------ ------------- -------------------------------------------
176 13 sallseqid All subject Seq-id(s), separated by a ';'
177 14 score Raw score
178 15 nident Number of identical matches
179 16 positive Number of positive-scoring matches
180 17 gaps Total number of gaps
181 18 ppos Percentage of positive-scoring matches
182 19 qframe Query frame
183 20 sframe Subject frame
184 21 qseq Aligned part of query sequence
185 22 sseq Aligned part of subject sequence
186 23 qlen Query sequence length
187 24 slen Subject sequence length
188 ====== ============= ===========================================
189
190 The third option is BLAST XML output, which is designed to be parsed by
191 another program, and is understood by some Galaxy tools.
192
193 You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
194 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
195 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
196 The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
197 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
198
199 -------
200
201 **References**
202
203 Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
204
205 </help>
206 </tool>