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comparison blast/tblastn.xml @ 0:f3ac34855f5e default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | edward-kirton |
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date | Tue, 07 Jun 2011 17:30:11 -0400 |
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1 <tool id="tblastn" name="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 | |
6 tblastn | |
7 -query "$query" | |
8 #if $db_opts.db_opts_selector == "db": | |
9 -db "$db_opts.database" | |
10 #elif $db_opts.db_opts_selector == "user_db": | |
11 -db "$db_opts.db" | |
12 #else: | |
13 -subject "$db_opts.subject" | |
14 #end if | |
15 -evalue $evalue_cutoff | |
16 -out $output1 | |
17 -outfmt "$out_format" | |
18 #if $adv_opts.adv_opts_selector=="advanced": | |
19 $adv_opts.filter_query | |
20 -matrix $adv_opts.matrix | |
21 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string | |
22 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments | |
23 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): | |
24 -max_target_seqs $adv_opts.max_hits | |
25 #end if | |
26 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): | |
27 -word_size $adv_opts.word_size | |
28 #end if | |
29 ##Ungapped disabled for now - see comments below | |
30 ##$adv_opts.ungapped | |
31 $adv_opts.parse_deflines | |
32 ## End of advanced options: | |
33 #end if | |
34 </command> | |
35 <inputs> | |
36 <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> | |
37 <conditional name="db_opts"> | |
38 <param name="db_opts_selector" type="select" label="Subject database/sequences"> | |
39 <option value="db" selected="True">Precompiled BLAST Database</option> | |
40 <option value="user_db">BLAST Database in your History</option> | |
41 <option value="fasta">FASTA file</option> | |
42 </param> | |
43 <when value="db"> | |
44 <param name="database" type="select" label="Precompiled Nucleotide BLAST database"> | |
45 <!-- The BLAST loc file has three columns: | |
46 column 0 is an identifier (not used here, see legacy megablast wrapper), | |
47 column 1 is the caption (show this to the user), | |
48 column 2 is the database path (given to BLAST+) --> | |
49 <options from_file="blastdb.loc"> | |
50 <column name="name" index="1"/> | |
51 <column name="value" index="2"/> | |
52 </options> | |
53 </param> | |
54 <param name="subject" type="hidden" value="" /> | |
55 </when> | |
56 <when value="user_db"> | |
57 <param name="database" type="hidden" value="" /> | |
58 <param name="db" type="data" format="blastdb" label="Blast DB" /> | |
59 </when> | |
60 <when value="fasta"> | |
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="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq">Tabular (extended 22 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 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> | |
88 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> | |
89 <param name="matrix" type="select" label="Scoring matrix"> | |
90 <option value="BLOSUM90">BLOSUM90</option> | |
91 <option value="BLOSUM80">BLOSUM80</option> | |
92 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> | |
93 <option value="BLOSUM50">BLOSUM50</option> | |
94 <option value="BLOSUM45">BLOSUM45</option> | |
95 <option value="PAM250">PAM250</option> | |
96 <option value="PAM70">PAM70</option> | |
97 <option value="PAM30">PAM30</option> | |
98 </param> | |
99 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> | |
100 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> | |
101 <validator type="in_range" min="0" /> | |
102 </param> | |
103 <!-- I'd like word_size to be optional, with minimum 2 for blastp --> | |
104 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> | |
105 <validator type="in_range" min="0" /> | |
106 </param> | |
107 <!-- | |
108 Can't use '-ungapped' on its own, error back is: | |
109 Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search | |
110 Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.' | |
111 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> | |
112 --> | |
113 <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"/> | |
114 </when> | |
115 </conditional> | |
116 </inputs> | |
117 <outputs> | |
118 <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}"> | |
119 <change_format> | |
120 <when input="out_format" value="0" format="txt"/> | |
121 <when input="out_format" value="0 -html" format="html"/> | |
122 <when input="out_format" value="2" format="txt"/> | |
123 <when input="out_format" value="2 -html" format="html"/> | |
124 <when input="out_format" value="4" format="txt"/> | |
125 <when input="out_format" value="4 -html" format="html"/> | |
126 <when input="out_format" value="5" format="blastxml"/> | |
127 </change_format> | |
128 </data> | |
129 </outputs> | |
130 <requirements> | |
131 <requirement type="binary">tblastn</requirement> | |
132 </requirements> | |
133 <tests> | |
134 <test> | |
135 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> | |
136 <param name="db_opts_selector" value="file" /> | |
137 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> | |
138 <param name="database" value="" /> | |
139 <param name="evalue_cutoff" value="1e-10" /> | |
140 <param name="out_format" value="6" /> | |
141 <param name="adv_opts_selector" value="advanced" /> | |
142 <param name="filter_query" value="false" /> | |
143 <param name="matrix" value="BLOSUM80" /> | |
144 <param name="max_hits" value="0" /> | |
145 <param name="word_size" value="0" /> | |
146 <param name="parse_deflines" value="false" /> | |
147 <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /> | |
148 </test> | |
149 <test> | |
150 <!-- Same as above, but parse deflines --> | |
151 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> | |
152 <param name="db_opts_selector" value="file" /> | |
153 <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> | |
154 <param name="database" value="" /> | |
155 <param name="evalue_cutoff" value="1e-10" /> | |
156 <param name="out_format" value="6" /> | |
157 <param name="adv_opts_selector" value="advanced" /> | |
158 <param name="filter_query" value="false" /> | |
159 <param name="matrix" value="BLOSUM80" /> | |
160 <param name="max_hits" value="0" /> | |
161 <param name="word_size" value="0" /> | |
162 <param name="parse_deflines" value="true" /> | |
163 <output name="output1" file="tblastn_four_human_vs_rhodopsin_parse_deflines.tabular" ftype="tabular" /> | |
164 </test> | |
165 </tests> | |
166 <help> | |
167 | |
168 .. class:: warningmark | |
169 | |
170 **Note**. Database searches may take a substantial amount of time. | |
171 For large input datasets it is advisable to allow overnight processing. | |
172 | |
173 ----- | |
174 | |
175 **What it does** | |
176 | |
177 Search a *translated nucleotide database* using a *protein query*, | |
178 using the NCBI BLAST+ tblastn command line tool. | |
179 | |
180 ----- | |
181 | |
182 **Output format** | |
183 | |
184 Because Galaxy focuses on processing tabular data, the default output of this | |
185 tool is tabular. The standard BLAST+ tabular output contains 12 columns: | |
186 | |
187 ====== ========= ============================================ | |
188 Column NCBI name Description | |
189 ------ --------- -------------------------------------------- | |
190 1 qseqid Query Seq-id (ID of your sequence) | |
191 2 sseqid Subject Seq-id (ID of the database hit) | |
192 3 pident Percentage of identical matches | |
193 4 length Alignment length | |
194 5 mismatch Number of mismatches | |
195 6 gapopen Number of gap openings | |
196 7 qstart Start of alignment in query | |
197 8 qend End of alignment in query | |
198 9 sstart Start of alignment in subject (database hit) | |
199 10 send End of alignment in subject (database hit) | |
200 11 evalue Expectation value (E-value) | |
201 12 bitscore Bit score | |
202 ====== ========= ============================================ | |
203 | |
204 The BLAST+ tools can optionally output additional columns of information, | |
205 but this takes longer to calculate. Most (but not all) of these columns are | |
206 included by selecting the extended tabular output. The extra columns are | |
207 included *after* the standard 12 columns. This is so that you can write | |
208 workflow filtering steps that accept either the 12 or 22 column tabular | |
209 BLAST output. | |
210 | |
211 ====== ============= =========================================== | |
212 Column NCBI name Description | |
213 ------ ------------- ------------------------------------------- | |
214 13 sallseqid All subject Seq-id(s), separated by a ';' | |
215 14 score Raw score | |
216 15 nident Number of identical matches | |
217 16 positive Number of positive-scoring matches | |
218 17 gaps Total number of gaps | |
219 18 ppos Percentage of positive-scoring matches | |
220 19 qframe Query frame | |
221 20 sframe Subject frame | |
222 21 qseq Aligned part of query sequence | |
223 22 sseq Aligned part of subject sequence | |
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> |