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

リビジョン 2, 8.7 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.1">
2    <description>Search translated nucleotide database with translated nucleotide 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
6tblastx
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$adv_opts.strand
16$adv_opts.matrix
17-out $output1
18$out_format
19-num_threads 8
20## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
21## Note -max_target_seqs overrides -num_descriptions and -num_alignments
22#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
23-max_target_seqs $adv_opts.max_hits
24#end if
25#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
26-word_size $adv_opts.word_size
27#end if
28    </command>
29    <inputs>
30        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
31        <conditional name="db_opts">
32            <param name="db_opts_selector" type="select" label="Subject database/sequences">
33              <option value="db" selected="True">BLAST Database</option>
34              <option value="file">FASTA file</option>
35            </param>
36            <when value="db">
37                <param name="database" type="select" label="Nucleotide BLAST database">
38                    <options from_file="blastdb.loc">
39                      <column name="name" index="0"/>
40                      <column name="value" index="1"/>
41                    </options>
42                </param>
43                <param name="subject" type="hidden" value="" />
44            </when>
45            <when value="file">
46                <param name="database" type="hidden" value="" />
47                <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/>
48            </when>
49        </conditional>
50        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" />
51        <param name="out_format" type="select" label="Output format">
52            <option value="-outfmt 6" selected="True">Tabular</option>
53            <option value="-outfmt 5">BLAST XML</option>
54            <option value="-outfmt 0">Pairwise text</option>
55            <option value="-outfmt 0 -html">Pairwise HTML</option>
56            <option value="-outfmt 2">Query-anchored text</option>
57            <option value="-outfmt 2 -html">Query-anchored HTML</option>
58            <option value="-outfmt 4">Flat query-anchored text</option>
59            <option value="-outfmt 4 -html">Flat query-anchored HTML</option>
60            <!--
61            <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
62            -->
63        </param>
64        <conditional name="adv_opts">
65            <param name="adv_opts_selector" type="select" label="Advanced Options">
66              <option value="basic" selected="True">Hide Advanced Options</option>
67              <option value="advanced">Show Advanced Options</option>
68            </param>
69            <when value="basic">
70                <param name="filter_query" type="hidden" value="" />
71                <param name="strand" 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            </when>
76            <when value="advanced">
77                <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
78                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
79                <param name="strand" type="select" label="Query strand(s) to search against database/subject">
80                    <option value="-strand both">Both</option>
81                    <option value="-strand plus">Plus (forward)</option>
82                    <option value="-strand minus">Minus (reverse complement)</option>
83                </param>
84                <param name="matrix" type="select" label="Scoring matrix">
85                    <option value="-matrix BLOSUM90">BLOSUM90</option>
86                    <option value="-matrix BLOSUM80">BLOSUM80</option>
87                    <option value="-matrix BLOSUM62" selected="true">BLOSUM62 (default)</option>
88                    <option value="-matrix BLOSUM50">BLOSUM50</option>
89                    <option value="-matrix BLOSUM45">BLOSUM45</option>
90                    <option value="-matrix PAM250">PAM250</option>
91                    <option value="-matrix PAM70">PAM70</option>
92                    <option value="-matrix PAM30">PAM30</option>
93                </param>
94                <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
95                <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
96                    <validator type="in_range" min="0" />
97                </param>
98                <!-- I'd like word_size to be optional, with minimum 2 for tblastx -->
99                <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
100                    <validator type="in_range" min="0" />
101                </param>
102            </when>
103        </conditional>
104    </inputs>
105    <outputs>
106        <data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}">
107            <change_format>
108                <when input="out_format" value="-outfmt 0" format="txt"/>
109                <when input="out_format" value="-outfmt 0 -html" format="html"/>
110                <when input="out_format" value="-outfmt 2" format="txt"/>
111                <when input="out_format" value="-outfmt 2 -html" format="html"/>
112                <when input="out_format" value="-outfmt 4" format="txt"/>
113                <when input="out_format" value="-outfmt 4 -html" format="html"/>
114                <when input="out_format" value="-outfmt 5" format="blastxml"/>
115            </change_format>
116        </data>
117    </outputs>
118    <requirements>
119        <requirement type="binary">blastn</requirement>
120    </requirements>
121    <tests>
122        <test>
123            <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/>
124            <!-- database needs to match the entry in the blastdb.loc file (first column), which includes the last update date if appropriate -->
125            <param name="database" value="phiX" />
126            <param name="blast_type" value="megablast" />
127            <!--
128            <param name="word_size" value="28" />
129            <param name="iden_cutoff" value="99.0" />
130            -->
131            <param name="evalue_cutoff" value="10.0" />
132            <param name="filter_query" value="yes" />
133            <param name="out_format" value="-outfmt 6" />
134            <output name="output1" file="megablast_wrapper_test1.out"/>
135        </test>
136    </tests>
137    <help>
138   
139.. class:: warningmark
140
141**Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. 
142
143-----
144
145**What it does**
146
147Search a *translated nucleotide database* using a *protein query*,
148using the NCBI BLAST+ tblastx command line tool.
149
150-----
151
152**Output format**
153
154Because Galaxy focuses on processing tabular data, the default output of this tool is tabular. This contains 12 columns:
155
1561. Id of your sequence
1572. GI of the database hit
1583. % identity
1594. Alignment length
1605. # mismatches
1616. # gaps
1627. Start position in your sequence
1638. End position in your sequence
1649. Start position in database hit
16510. End position in database hit
16611. E-value
16712. Bit score
168
169The second option is BLAST XML output, which is designed to be parsed by another program, and is understood by other Galaxy tools.
170
171You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
172The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
173The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
174The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
175and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
176
177-------
178
179**References**
180
181Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
182
183    </help>
184</tool>
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