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comparison ncbi_tblastn_wrapper.xml @ 2:ab1a8640f817 draft

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Uploaded v0.0.12 again, without extra path
author peterjc
date Thu, 23 Aug 2012 07:32:06 -0400
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1:27d7e1deada4 2:ab1a8640f817
1 <tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.12">
2 <description>Search translated nucleotide database with protein query sequence(s)</description>
3 <!-- If job splitting is enabled, break up the query file into parts -->
4 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism>
5 <version_command>tblastn -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 tblastn
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 -db_gencode $adv_opts.db_gencode
27 $adv_opts.filter_query
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 $adv_opts.word_size
36 #end if
37 ##Ungapped disabled for now - see comments below
38 ##$adv_opts.ungapped
39 $adv_opts.parse_deflines
40 ## End of advanced options:
41 #end if
42 </command>
43 <inputs>
44 <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/>
45 <conditional name="db_opts">
46 <param name="db_opts_selector" type="select" label="Subject database/sequences">
47 <option value="db" selected="True">BLAST Database</option>
48 <option value="file">FASTA file (pairwise e-values)</option>
49 </param>
50 <when value="db">
51 <param name="database" type="select" label="Nucleotide BLAST database">
52 <options from_file="blastdb.loc">
53 <column name="value" index="0"/>
54 <column name="name" index="1"/>
55 <column name="path" index="2"/>
56 </options>
57 </param>
58 <param name="subject" type="hidden" value="" />
59 </when>
60 <when value="file">
61 <param name="database" type="hidden" value="" />
62 <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/>
63 </when>
64 </conditional>
65 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
66 <param name="out_format" type="select" label="Output format">
67 <option value="6" selected="True">Tabular (standard 12 columns)</option>
68 <option value="ext">Tabular (extended 24 columns)</option>
69 <option value="5">BLAST XML</option>
70 <option value="0">Pairwise text</option>
71 <option value="0 -html">Pairwise HTML</option>
72 <option value="2">Query-anchored text</option>
73 <option value="2 -html">Query-anchored HTML</option>
74 <option value="4">Flat query-anchored text</option>
75 <option value="4 -html">Flat query-anchored HTML</option>
76 <!--
77 <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
78 -->
79 </param>
80 <conditional name="adv_opts">
81 <param name="adv_opts_selector" type="select" label="Advanced Options">
82 <option value="basic" selected="True">Hide Advanced Options</option>
83 <option value="advanced">Show Advanced Options</option>
84 </param>
85 <when value="basic" />
86 <when value="advanced">
87 <param name="db_gencode" type="select" label="Database/subject genetic code">
88 <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
89 <option value="1" select="True">1. Standard</option>
90 <option value="2">2. Vertebrate Mitochondrial</option>
91 <option value="3">3. Yeast Mitochondrial</option>
92 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
93 <option value="5">5. Invertebrate Mitochondrial</option>
94 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
95 <option value="9">9. Echinoderm Mitochondrial</option>
96 <option value="10">10. Euplotid Nuclear</option>
97 <option value="11">11. Bacteria and Archaea</option>
98 <option value="12">12. Alternative Yeast Nuclear</option>
99 <option value="13">13. Ascidian Mitochondrial</option>
100 <option value="14">14. Flatworm Mitochondrial</option>
101 <option value="15">15. Blepharisma Macronuclear</option>
102 <option value="16">16. Chlorophycean Mitochondrial Code</option>
103 <option value="21">21. Trematode Mitochondrial Code</option>
104 <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>
105 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
106 <option value="24">24. Pterobranchia mitochondrial code</option>
107 </param>
108 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
109 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
110 <param name="matrix" type="select" label="Scoring matrix">
111 <option value="BLOSUM90">BLOSUM90</option>
112 <option value="BLOSUM80">BLOSUM80</option>
113 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
114 <option value="BLOSUM50">BLOSUM50</option>
115 <option value="BLOSUM45">BLOSUM45</option>
116 <option value="PAM250">PAM250</option>
117 <option value="PAM70">PAM70</option>
118 <option value="PAM30">PAM30</option>
119 </param>
120 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
121 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
122 <validator type="in_range" min="0" />
123 </param>
124 <!-- I'd like word_size to be optional, with minimum 2 for blastp -->
125 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
126 <validator type="in_range" min="0" />
127 </param>
128 <!--
129 Can't use '-ungapped' on its own, error back is:
130 Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
131 Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.'
132 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
133 -->
134 <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"/>
135 </when>
136 </conditional>
137 </inputs>
138 <outputs>
139 <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}">
140 <change_format>
141 <when input="out_format" value="0" format="txt"/>
142 <when input="out_format" value="0 -html" format="html"/>
143 <when input="out_format" value="2" format="txt"/>
144 <when input="out_format" value="2 -html" format="html"/>
145 <when input="out_format" value="4" format="txt"/>
146 <when input="out_format" value="4 -html" format="html"/>
147 <when input="out_format" value="5" format="blastxml"/>
148 </change_format>
149 </data>
150 </outputs>
151 <requirements>
152 <requirement type="binary">tblastn</requirement>
153 </requirements>
154 <tests>
155 <test>
156 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
157 <param name="db_opts_selector" value="file" />
158 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
159 <param name="database" value="" />
160 <param name="evalue_cutoff" value="1e-10" />
161 <param name="out_format" value="5" />
162 <param name="adv_opts_selector" value="advanced" />
163 <param name="filter_query" value="false" />
164 <param name="matrix" value="BLOSUM80" />
165 <param name="max_hits" value="0" />
166 <param name="word_size" value="0" />
167 <param name="parse_deflines" value="false" />
168 <output name="output1" file="tblastn_four_human_vs_rhodopsin.xml" ftype="blastxml" />
169 </test>
170 <test>
171 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
172 <param name="db_opts_selector" value="file" />
173 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
174 <param name="database" value="" />
175 <param name="evalue_cutoff" value="1e-10" />
176 <param name="out_format" value="ext" />
177 <param name="adv_opts_selector" value="advanced" />
178 <param name="filter_query" value="false" />
179 <param name="matrix" value="BLOSUM80" />
180 <param name="max_hits" value="0" />
181 <param name="word_size" value="0" />
182 <param name="parse_deflines" value="false" />
183 <output name="output1" file="tblastn_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" />
184 </test>
185 <test>
186 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
187 <param name="db_opts_selector" value="file" />
188 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
189 <param name="database" value="" />
190 <param name="evalue_cutoff" value="1e-10" />
191 <param name="out_format" value="6" />
192 <param name="adv_opts_selector" value="advanced" />
193 <param name="filter_query" value="false" />
194 <param name="matrix" value="BLOSUM80" />
195 <param name="max_hits" value="0" />
196 <param name="word_size" value="0" />
197 <param name="parse_deflines" value="false" />
198 <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" />
199 </test>
200 <test>
201 <!-- Same as above, but parse deflines - on BLAST 2.2.25+ makes no difference -->
202 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
203 <param name="db_opts_selector" value="file" />
204 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
205 <param name="database" value="" />
206 <param name="evalue_cutoff" value="1e-10" />
207 <param name="out_format" value="6" />
208 <param name="adv_opts_selector" value="advanced" />
209 <param name="filter_query" value="false" />
210 <param name="matrix" value="BLOSUM80" />
211 <param name="max_hits" value="0" />
212 <param name="word_size" value="0" />
213 <param name="parse_deflines" value="true" />
214 <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" />
215 </test>
216 <test>
217 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
218 <param name="db_opts_selector" value="file" />
219 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
220 <param name="database" value="" />
221 <param name="evalue_cutoff" value="1e-10" />
222 <param name="out_format" value="0 -html" />
223 <param name="adv_opts_selector" value="advanced" />
224 <param name="filter_query" value="false" />
225 <param name="matrix" value="BLOSUM80" />
226 <param name="max_hits" value="0" />
227 <param name="word_size" value="0" />
228 <param name="parse_deflines" value="false" />
229 <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" />
230 </test>
231 </tests>
232 <help>
233
234 .. class:: warningmark
235
236 **Note**. Database searches may take a substantial amount of time.
237 For large input datasets it is advisable to allow overnight processing.
238
239 -----
240
241 **What it does**
242
243 Search a *translated nucleotide database* using a *protein query*,
244 using the NCBI BLAST+ tblastn command line tool.
245
246 -----
247
248 **Output format**
249
250 Because Galaxy focuses on processing tabular data, the default output of this
251 tool is tabular. The standard BLAST+ tabular output contains 12 columns:
252
253 ====== ========= ============================================
254 Column NCBI name Description
255 ------ --------- --------------------------------------------
256 1 qseqid Query Seq-id (ID of your sequence)
257 2 sseqid Subject Seq-id (ID of the database hit)
258 3 pident Percentage of identical matches
259 4 length Alignment length
260 5 mismatch Number of mismatches
261 6 gapopen Number of gap openings
262 7 qstart Start of alignment in query
263 8 qend End of alignment in query
264 9 sstart Start of alignment in subject (database hit)
265 10 send End of alignment in subject (database hit)
266 11 evalue Expectation value (E-value)
267 12 bitscore Bit score
268 ====== ========= ============================================
269
270 The BLAST+ tools can optionally output additional columns of information,
271 but this takes longer to calculate. Most (but not all) of these columns are
272 included by selecting the extended tabular output. The extra columns are
273 included *after* the standard 12 columns. This is so that you can write
274 workflow filtering steps that accept either the 12 or 24 column tabular
275 BLAST output.
276
277 ====== ============= ===========================================
278 Column NCBI name Description
279 ------ ------------- -------------------------------------------
280 13 sallseqid All subject Seq-id(s), separated by a ';'
281 14 score Raw score
282 15 nident Number of identical matches
283 16 positive Number of positive-scoring matches
284 17 gaps Total number of gaps
285 18 ppos Percentage of positive-scoring matches
286 19 qframe Query frame
287 20 sframe Subject frame
288 21 qseq Aligned part of query sequence
289 22 sseq Aligned part of subject sequence
290 23 qlen Query sequence length
291 24 slen Subject sequence length
292 ====== ============= ===========================================
293
294 The third option is BLAST XML output, which is designed to be parsed by
295 another program, and is understood by some Galaxy tools.
296
297 You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
298 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
299 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
300 The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
301 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
302
303 -------
304
305 **References**
306
307 Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
308
309 </help>
310 </tool>