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comparison ncbi_blastx_wrapper.xml @ 0:d375502056f1 draft

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author devteam
date Fri, 17 Aug 2012 09:11:43 -0400
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1 <tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.11">
2 <description>Search protein database with translated nucleotide query sequence(s)</description>
3 <!-- If job splitting is enabled, break up the query file into four -->
4 <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
5 <version_command>blastx -version</version_command>
6 <command interpreter="python">hide_stderr.py
7 ## The command is a Cheetah template which allows some Python based syntax.
8 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
9 blastx
10 -query "$query"
11 #if $db_opts.db_opts_selector == "db":
12 -db "${db_opts.database.fields.path}"
13 #else:
14 -subject "$db_opts.subject"
15 #end if
16 -evalue $evalue_cutoff
17 -out $output1
18 ##Set the extended list here so if/when we add things, saved workflows are not affected
19 #if str($out_format)=="ext":
20 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
21 #else:
22 -outfmt $out_format
23 #end if
24 -num_threads 8
25 #if $adv_opts.adv_opts_selector=="advanced":
26 $adv_opts.filter_query
27 $adv_opts.strand
28 -matrix $adv_opts.matrix
29 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
30 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments
31 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
32 -max_target_seqs $adv_opts.max_hits
33 #end if
34 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
35 -word_size $adv_opts.word_size
36 #end if
37 $adv_opts.ungapped
38 $adv_opts.parse_deflines
39 ## End of advanced options:
40 #end if
41 </command>
42 <inputs>
43 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
44 <conditional name="db_opts">
45 <param name="db_opts_selector" type="select" label="Subject database/sequences">
46 <option value="db" selected="True">BLAST Database</option>
47 <option value="file">FASTA file</option>
48 </param>
49 <when value="db">
50 <param name="database" type="select" label="Protein BLAST database">
51 <options from_file="blastdb_p.loc">
52 <column name="value" index="0"/>
53 <column name="name" index="1"/>
54 <column name="path" index="2"/>
55 </options>
56 </param>
57 <param name="subject" type="hidden" value="" />
58 </when>
59 <when value="file">
60 <param name="database" type="hidden" value="" />
61 <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/>
62 </when>
63 </conditional>
64 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
65 <param name="out_format" type="select" label="Output format">
66 <option value="6" selected="True">Tabular (standard 12 columns)</option>
67 <option value="ext">Tabular (extended 24 columns)</option>
68 <option value="5">BLAST XML</option>
69 <option value="0">Pairwise text</option>
70 <option value="0 -html">Pairwise HTML</option>
71 <option value="2">Query-anchored text</option>
72 <option value="2 -html">Query-anchored HTML</option>
73 <option value="4">Flat query-anchored text</option>
74 <option value="4 -html">Flat query-anchored HTML</option>
75 <!--
76 <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
77 -->
78 </param>
79 <conditional name="adv_opts">
80 <param name="adv_opts_selector" type="select" label="Advanced Options">
81 <option value="basic" selected="True">Hide Advanced Options</option>
82 <option value="advanced">Show Advanced Options</option>
83 </param>
84 <when value="basic" />
85 <when value="advanced">
86 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
87 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
88 <param name="strand" type="select" label="Query strand(s) to search against database/subject">
89 <option value="-strand both">Both</option>
90 <option value="-strand plus">Plus (forward)</option>
91 <option value="-strand minus">Minus (reverse complement)</option>
92 </param>
93 <param name="matrix" type="select" label="Scoring matrix">
94 <option value="BLOSUM90">BLOSUM90</option>
95 <option value="BLOSUM80">BLOSUM80</option>
96 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
97 <option value="BLOSUM50">BLOSUM50</option>
98 <option value="BLOSUM45">BLOSUM45</option>
99 <option value="PAM250">PAM250</option>
100 <option value="PAM70">PAM70</option>
101 <option value="PAM30">PAM30</option>
102 </param>
103 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
104 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
105 <validator type="in_range" min="0" />
106 </param>
107 <!-- I'd like word_size to be optional, with minimum 2 for blastx -->
108 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
109 <validator type="in_range" min="0" />
110 </param>
111 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
112 <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"/>
113 </when>
114 </conditional>
115 </inputs>
116 <outputs>
117 <data name="output1" format="tabular" label="blastx on ${db_opts.db_opts_selector}">
118 <change_format>
119 <when input="out_format" value="0" format="txt"/>
120 <when input="out_format" value="0 -html" format="html"/>
121 <when input="out_format" value="2" format="txt"/>
122 <when input="out_format" value="2 -html" format="html"/>
123 <when input="out_format" value="4" format="txt"/>
124 <when input="out_format" value="4 -html" format="html"/>
125 <when input="out_format" value="5" format="blastxml"/>
126 </change_format>
127 </data>
128 </outputs>
129 <requirements>
130 <requirement type="package" version="2.2.26+">blast+</requirement>
131 </requirements>
132 <tests>
133 <test>
134 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
135 <param name="db_opts_selector" value="file" />
136 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
137 <param name="database" value="" />
138 <param name="evalue_cutoff" value="1e-10" />
139 <param name="out_format" value="5" />
140 <param name="adv_opts_selector" value="basic" />
141 <output name="output1" file="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
142 </test>
143 <test>
144 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
145 <param name="db_opts_selector" value="file" />
146 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
147 <param name="database" value="" />
148 <param name="evalue_cutoff" value="1e-10" />
149 <param name="out_format" value="6" />
150 <param name="adv_opts_selector" value="basic" />
151 <output name="output1" file="blastx_rhodopsin_vs_four_human.tabular" ftype="tabular" />
152 </test>
153 <test>
154 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
155 <param name="db_opts_selector" value="file" />
156 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
157 <param name="database" value="" />
158 <param name="evalue_cutoff" value="1e-10" />
159 <param name="out_format" value="ext" />
160 <param name="adv_opts_selector" value="basic" />
161 <output name="output1" file="blastx_rhodopsin_vs_four_human_ext.tabular" ftype="tabular" />
162 </test>
163 </tests>
164 <help>
165
166 .. class:: warningmark
167
168 **Note**. Database searches may take a substantial amount of time.
169 For large input datasets it is advisable to allow overnight processing.
170
171 -----
172
173 **What it does**
174
175 Search a *protein database* using a *translated nucleotide query*,
176 using the NCBI BLAST+ blastx command line tool.
177
178 -----
179
180 **Output format**
181
182 Because Galaxy focuses on processing tabular data, the default output of this
183 tool is tabular. The standard BLAST+ tabular output contains 12 columns:
184
185 ====== ========= ============================================
186 Column NCBI name Description
187 ------ --------- --------------------------------------------
188 1 qseqid Query Seq-id (ID of your sequence)
189 2 sseqid Subject Seq-id (ID of the database hit)
190 3 pident Percentage of identical matches
191 4 length Alignment length
192 5 mismatch Number of mismatches
193 6 gapopen Number of gap openings
194 7 qstart Start of alignment in query
195 8 qend End of alignment in query
196 9 sstart Start of alignment in subject (database hit)
197 10 send End of alignment in subject (database hit)
198 11 evalue Expectation value (E-value)
199 12 bitscore Bit score
200 ====== ========= ============================================
201
202 The BLAST+ tools can optionally output additional columns of information,
203 but this takes longer to calculate. Most (but not all) of these columns are
204 included by selecting the extended tabular output. The extra columns are
205 included *after* the standard 12 columns. This is so that you can write
206 workflow filtering steps that accept either the 12 or 24 column tabular
207 BLAST output.
208
209 ====== ============= ===========================================
210 Column NCBI name Description
211 ------ ------------- -------------------------------------------
212 13 sallseqid All subject Seq-id(s), separated by a ';'
213 14 score Raw score
214 15 nident Number of identical matches
215 16 positive Number of positive-scoring matches
216 17 gaps Total number of gaps
217 18 ppos Percentage of positive-scoring matches
218 19 qframe Query frame
219 20 sframe Subject frame
220 21 qseq Aligned part of query sequence
221 22 sseq Aligned part of subject sequence
222 23 qlen Query sequence length
223 24 slen Subject sequence length
224 ====== ============= ===========================================
225
226 The third option is BLAST XML output, which is designed to be parsed by
227 another program, and is understood by some Galaxy tools.
228
229 You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
230 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
231 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
232 The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
233 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
234
235 -------
236
237 **References**
238
239 Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
240
241 </help>
242 </tool>