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comparison ncbi_blastx_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_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.12">
2 <description>Search protein database with translated nucleotide 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>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 -query_gencode $query_gencode
17 -evalue $evalue_cutoff
18 -out $output1
19 ##Set the extended list here so if/when we add things, saved workflows are not affected
20 #if str($out_format)=="ext":
21 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
22 #else:
23 -outfmt $out_format
24 #end if
25 -num_threads 8
26 #if $adv_opts.adv_opts_selector=="advanced":
27 $adv_opts.filter_query
28 $adv_opts.strand
29 -matrix $adv_opts.matrix
30 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
31 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments
32 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
33 -max_target_seqs $adv_opts.max_hits
34 #end if
35 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
36 -word_size $adv_opts.word_size
37 #end if
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="Nucleotide 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="Protein BLAST database">
52 <options from_file="blastdb_p.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="Protein FASTA file to use as database"/>
63 </when>
64 </conditional>
65 <param name="query_gencode" type="select" label="Query genetic code">
66 <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
67 <option value="1" select="True">1. Standard</option>
68 <option value="2">2. Vertebrate Mitochondrial</option>
69 <option value="3">3. Yeast Mitochondrial</option>
70 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
71 <option value="5">5. Invertebrate Mitochondrial</option>
72 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
73 <option value="9">9. Echinoderm Mitochondrial</option>
74 <option value="10">10. Euplotid Nuclear</option>
75 <option value="11">11. Bacteria and Archaea</option>
76 <option value="12">12. Alternative Yeast Nuclear</option>
77 <option value="13">13. Ascidian Mitochondrial</option>
78 <option value="14">14. Flatworm Mitochondrial</option>
79 <option value="15">15. Blepharisma Macronuclear</option>
80 <option value="16">16. Chlorophycean Mitochondrial Code</option>
81 <option value="21">21. Trematode Mitochondrial Code</option>
82 <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>
83 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
84 <option value="24">24. Pterobranchia mitochondrial code</option>
85 </param>
86 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
87 <param name="out_format" type="select" label="Output format">
88 <option value="6" selected="True">Tabular (standard 12 columns)</option>
89 <option value="ext">Tabular (extended 24 columns)</option>
90 <option value="5">BLAST XML</option>
91 <option value="0">Pairwise text</option>
92 <option value="0 -html">Pairwise HTML</option>
93 <option value="2">Query-anchored text</option>
94 <option value="2 -html">Query-anchored HTML</option>
95 <option value="4">Flat query-anchored text</option>
96 <option value="4 -html">Flat query-anchored HTML</option>
97 <!--
98 <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
99 -->
100 </param>
101 <conditional name="adv_opts">
102 <param name="adv_opts_selector" type="select" label="Advanced Options">
103 <option value="basic" selected="True">Hide Advanced Options</option>
104 <option value="advanced">Show Advanced Options</option>
105 </param>
106 <when value="basic" />
107 <when value="advanced">
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="strand" type="select" label="Query strand(s) to search against database/subject">
111 <option value="-strand both">Both</option>
112 <option value="-strand plus">Plus (forward)</option>
113 <option value="-strand minus">Minus (reverse complement)</option>
114 </param>
115 <param name="matrix" type="select" label="Scoring matrix">
116 <option value="BLOSUM90">BLOSUM90</option>
117 <option value="BLOSUM80">BLOSUM80</option>
118 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
119 <option value="BLOSUM50">BLOSUM50</option>
120 <option value="BLOSUM45">BLOSUM45</option>
121 <option value="PAM250">PAM250</option>
122 <option value="PAM70">PAM70</option>
123 <option value="PAM30">PAM30</option>
124 </param>
125 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
126 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
127 <validator type="in_range" min="0" />
128 </param>
129 <!-- I'd like word_size to be optional, with minimum 2 for blastx -->
130 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
131 <validator type="in_range" min="0" />
132 </param>
133 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
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="blastx 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">blastx</requirement>
153 </requirements>
154 <tests>
155 <test>
156 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
157 <param name="db_opts_selector" value="file" />
158 <param name="subject" value="four_human_proteins.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="basic" />
163 <output name="output1" file="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
164 </test>
165 <test>
166 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
167 <param name="db_opts_selector" value="file" />
168 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
169 <param name="database" value="" />
170 <param name="evalue_cutoff" value="1e-10" />
171 <param name="out_format" value="6" />
172 <param name="adv_opts_selector" value="basic" />
173 <output name="output1" file="blastx_rhodopsin_vs_four_human.tabular" ftype="tabular" />
174 </test>
175 <test>
176 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
177 <param name="db_opts_selector" value="file" />
178 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
179 <param name="database" value="" />
180 <param name="evalue_cutoff" value="1e-10" />
181 <param name="out_format" value="ext" />
182 <param name="adv_opts_selector" value="basic" />
183 <output name="output1" file="blastx_rhodopsin_vs_four_human_ext.tabular" ftype="tabular" />
184 </test>
185 </tests>
186 <help>
187
188 .. class:: warningmark
189
190 **Note**. Database searches may take a substantial amount of time.
191 For large input datasets it is advisable to allow overnight processing.
192
193 -----
194
195 **What it does**
196
197 Search a *protein database* using a *translated nucleotide query*,
198 using the NCBI BLAST+ blastx command line tool.
199
200 -----
201
202 **Output format**
203
204 Because Galaxy focuses on processing tabular data, the default output of this
205 tool is tabular. The standard BLAST+ tabular output contains 12 columns:
206
207 ====== ========= ============================================
208 Column NCBI name Description
209 ------ --------- --------------------------------------------
210 1 qseqid Query Seq-id (ID of your sequence)
211 2 sseqid Subject Seq-id (ID of the database hit)
212 3 pident Percentage of identical matches
213 4 length Alignment length
214 5 mismatch Number of mismatches
215 6 gapopen Number of gap openings
216 7 qstart Start of alignment in query
217 8 qend End of alignment in query
218 9 sstart Start of alignment in subject (database hit)
219 10 send End of alignment in subject (database hit)
220 11 evalue Expectation value (E-value)
221 12 bitscore Bit score
222 ====== ========= ============================================
223
224 The BLAST+ tools can optionally output additional columns of information,
225 but this takes longer to calculate. Most (but not all) of these columns are
226 included by selecting the extended tabular output. The extra columns are
227 included *after* the standard 12 columns. This is so that you can write
228 workflow filtering steps that accept either the 12 or 24 column tabular
229 BLAST output.
230
231 ====== ============= ===========================================
232 Column NCBI name Description
233 ------ ------------- -------------------------------------------
234 13 sallseqid All subject Seq-id(s), separated by a ';'
235 14 score Raw score
236 15 nident Number of identical matches
237 16 positive Number of positive-scoring matches
238 17 gaps Total number of gaps
239 18 ppos Percentage of positive-scoring matches
240 19 qframe Query frame
241 20 sframe Subject frame
242 21 qseq Aligned part of query sequence
243 22 sseq Aligned part of subject sequence
244 23 qlen Query sequence length
245 24 slen Subject sequence length
246 ====== ============= ===========================================
247
248 The third option is BLAST XML output, which is designed to be parsed by
249 another program, and is understood by some Galaxy tools.
250
251 You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
252 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
253 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
254 The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
255 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
256
257 -------
258
259 **References**
260
261 Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
262
263 </help>
264 </tool>