root/galaxy-central/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml

リビジョン 2, 8.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.1">
2    <description>Search translated nucleotide database with protein query sequence(s)</description>
3    <command>
4## The command is a Cheetah template which allows some Python based syntax.
5## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
6tblastn
7-query "$query"
8#if $db_opts.db_opts_selector == "db":
9  -db "$db_opts.database"
10#else:
11  -subject "$db_opts.subject"
12#end if
13-evalue $evalue_cutoff
14$adv_opts.filter_query
15$adv_opts.matrix
16-out $output1
17$out_format
18-num_threads 8
19## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
20## Note -max_target_seqs overrides -num_descriptions and -num_alignments
21#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
22-max_target_seqs $adv_opts.max_hits
23#end if
24#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
25-word_size $adv_opts.word_size
26#end if
27##Ungapped disabled for now - see comments below
28##$adv_opts.ungapped
29    </command>
30    <inputs>
31        <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/>
32        <conditional name="db_opts">
33            <param name="db_opts_selector" type="select" label="Subject database/sequences">
34              <option value="db" selected="True">BLAST Database</option>
35              <option value="file">FASTA file</option>
36            </param>
37            <when value="db">
38                <param name="database" type="select" label="Nucleotide BLAST database">
39                    <options from_file="blastdb.loc">
40                      <column name="name" index="0"/>
41                      <column name="value" index="1"/>
42                    </options>
43                </param>
44                <param name="subject" type="hidden" value="" />
45            </when>
46            <when value="file">
47                <param name="database" type="hidden" value="" />
48                <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/>
49            </when>
50        </conditional>
51        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" />
52        <param name="out_format" type="select" label="Output format">
53            <option value="-outfmt 6" selected="True">Tabular</option>
54            <option value="-outfmt 5">BLAST XML</option>
55            <option value="-outfmt 0">Pairwise text</option>
56            <option value="-outfmt 0 -html">Pairwise HTML</option>
57            <option value="-outfmt 2">Query-anchored text</option>
58            <option value="-outfmt 2 -html">Query-anchored HTML</option>
59            <option value="-outfmt 4">Flat query-anchored text</option>
60            <option value="-outfmt 4 -html">Flat query-anchored HTML</option>
61            <!--
62            <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
63            -->
64        </param>
65        <conditional name="adv_opts">
66            <param name="adv_opts_selector" type="select" label="Advanced Options">
67              <option value="basic" selected="True">Hide Advanced Options</option>
68              <option value="advanced">Show Advanced Options</option>
69            </param>
70            <when value="basic">
71                <param name="filter_query" type="hidden" value="" />
72                <param name="matrix" type="hidden" value="" />
73                <param name="max_hits" type="hidden" value="" />
74                <param name="word_size" type="hidden" value="" />
75                <!--
76                Ungapped disabled for now, see comments below
77                <param name="ungapped" type="hidden" value="" />
78                -->
79            </when>
80            <when value="advanced">
81                <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
82                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
83                <param name="matrix" type="select" label="Scoring matrix">
84                    <option value="-matrix BLOSUM90">BLOSUM90</option>
85                    <option value="-matrix BLOSUM80">BLOSUM80</option>
86                    <option value="-matrix BLOSUM62" selected="true">BLOSUM62 (default)</option>
87                    <option value="-matrix BLOSUM50">BLOSUM50</option>
88                    <option value="-matrix BLOSUM45">BLOSUM45</option>
89                    <option value="-matrix PAM250">PAM250</option>
90                    <option value="-matrix PAM70">PAM70</option>
91                    <option value="-matrix PAM30">PAM30</option>
92                </param>
93                <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
94                <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
95                    <validator type="in_range" min="0" />
96                </param>
97                <!-- I'd like word_size to be optional, with minimum 2 for blastp -->
98                <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
99                    <validator type="in_range" min="0" />
100                </param>
101                <!--
102                Can't use '-ungapped' on its own, error back is:
103                Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
104                Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.'
105                <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
106                -->
107            </when>
108        </conditional>
109    </inputs>
110    <outputs>
111        <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}">
112            <change_format>
113                <when input="out_format" value="-outfmt 0" format="txt"/>
114                <when input="out_format" value="-outfmt 0 -html" format="html"/>
115                <when input="out_format" value="-outfmt 2" format="txt"/>
116                <when input="out_format" value="-outfmt 2 -html" format="html"/>
117                <when input="out_format" value="-outfmt 4" format="txt"/>
118                <when input="out_format" value="-outfmt 4 -html" format="html"/>
119                <when input="out_format" value="-outfmt 5" format="blastxml"/>
120            </change_format>
121        </data>
122    </outputs>
123    <requirements>
124        <requirement type="binary">blastn</requirement>
125    </requirements>
126    <tests>
127    </tests>
128    <help>
129   
130.. class:: warningmark
131
132**Note**. Database searches may take substantial amount of time.
133For large input datasets it is advisable to allow overnight processing. 
134
135-----
136
137**What it does**
138
139Search a *translated nucleotide database* using a *protein query*,
140using the NCBI BLAST+ tblastn command line tool.
141
142-----
143
144**Output format**
145
146Because Galaxy focuses on processing tabular data, the default output of this tool is tabular. This contains 12 columns:
147
1481. Id of your sequence
1492. GI of the database hit
1503. % identity
1514. Alignment length
1525. # mismatches
1536. # gaps
1547. Start position in your sequence
1558. End position in your sequence
1569. Start position in database hit
15710. End position in database hit
15811. E-value
15912. Bit score
160
161The second option is BLAST XML output, which is designed to be parsed by another program, and is understood by other Galaxy tools.
162
163You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
164The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
165The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
166The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
167and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
168
169-------
170
171**References**
172
173Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
174
175    </help>
176</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。