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comparison blast/tblastx.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="tblastx" name="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 | |
6 tblastx | |
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 $adv_opts.strand | |
21 -matrix $adv_opts.matrix | |
22 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string | |
23 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments | |
24 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): | |
25 -max_target_seqs $adv_opts.max_hits | |
26 #end if | |
27 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): | |
28 -word_size $adv_opts.word_size | |
29 #end if | |
30 $adv_opts.parse_deflines | |
31 ## End of advanced options: | |
32 #end if | |
33 </command> | |
34 <inputs> | |
35 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> | |
36 <conditional name="db_opts"> | |
37 <param name="db_opts_selector" type="select" label="Subject database/sequences"> | |
38 <option value="db" selected="True">Precompiled BLAST Database</option> | |
39 <option value="user_db">BLAST Database in your History</option> | |
40 <option value="file">FASTA file</option> | |
41 </param> | |
42 <when value="db"> | |
43 <param name="database" type="select" label="Precompiled Nucleotide BLAST database"> | |
44 <!-- The BLAST loc file has three columns: | |
45 column 0 is an identifier (not used here, see legacy megablast wrapper), | |
46 column 1 is the caption (show this to the user), | |
47 column 2 is the database path (given to BLAST+) --> | |
48 <options from_file="blastdb.loc"> | |
49 <column name="name" index="1"/> | |
50 <column name="value" index="2"/> | |
51 </options> | |
52 </param> | |
53 <param name="subject" type="hidden" value="" /> | |
54 </when> | |
55 <when value="user_db"> | |
56 <param name="database" type="hidden" value="" /> | |
57 <param name="db" type="data" format="blastdb" label="Blast DB" /> | |
58 </when> | |
59 <when value="fasta"> | |
60 <param name="database" type="hidden" value="" /> | |
61 <param name="subject" type="data" format="fasta" label="Nucleotide 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="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq">Tabular (extended 22 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 tblastx --> | |
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="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"/> | |
112 </when> | |
113 </conditional> | |
114 </inputs> | |
115 <outputs> | |
116 <data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}"> | |
117 <change_format> | |
118 <when input="out_format" value="0" format="txt"/> | |
119 <when input="out_format" value="0 -html" format="html"/> | |
120 <when input="out_format" value="2" format="txt"/> | |
121 <when input="out_format" value="2 -html" format="html"/> | |
122 <when input="out_format" value="4" format="txt"/> | |
123 <when input="out_format" value="4 -html" format="html"/> | |
124 <when input="out_format" value="5" format="blastxml"/> | |
125 </change_format> | |
126 </data> | |
127 </outputs> | |
128 <requirements> | |
129 <requirement type="binary">tblastx</requirement> | |
130 </requirements> | |
131 <tests> | |
132 </tests> | |
133 <help> | |
134 | |
135 .. class:: warningmark | |
136 | |
137 **Note**. Database searches may take a substantial amount of time. | |
138 For large input datasets it is advisable to allow overnight processing. | |
139 | |
140 ----- | |
141 | |
142 **What it does** | |
143 | |
144 Search a *translated nucleotide database* using a *protein query*, | |
145 using the NCBI BLAST+ tblastx command line tool. | |
146 | |
147 ----- | |
148 | |
149 **Output format** | |
150 | |
151 Because Galaxy focuses on processing tabular data, the default output of this | |
152 tool is tabular. The standard BLAST+ tabular output contains 12 columns: | |
153 | |
154 ====== ========= ============================================ | |
155 Column NCBI name Description | |
156 ------ --------- -------------------------------------------- | |
157 1 qseqid Query Seq-id (ID of your sequence) | |
158 2 sseqid Subject Seq-id (ID of the database hit) | |
159 3 pident Percentage of identical matches | |
160 4 length Alignment length | |
161 5 mismatch Number of mismatches | |
162 6 gapopen Number of gap openings | |
163 7 qstart Start of alignment in query | |
164 8 qend End of alignment in query | |
165 9 sstart Start of alignment in subject (database hit) | |
166 10 send End of alignment in subject (database hit) | |
167 11 evalue Expectation value (E-value) | |
168 12 bitscore Bit score | |
169 ====== ========= ============================================ | |
170 | |
171 The BLAST+ tools can optionally output additional columns of information, | |
172 but this takes longer to calculate. Most (but not all) of these columns are | |
173 included by selecting the extended tabular output. The extra columns are | |
174 included *after* the standard 12 columns. This is so that you can write | |
175 workflow filtering steps that accept either the 12 or 22 column tabular | |
176 BLAST output. | |
177 | |
178 ====== ============= =========================================== | |
179 Column NCBI name Description | |
180 ------ ------------- ------------------------------------------- | |
181 13 sallseqid All subject Seq-id(s), separated by a ';' | |
182 14 score Raw score | |
183 15 nident Number of identical matches | |
184 16 positive Number of positive-scoring matches | |
185 17 gaps Total number of gaps | |
186 18 ppos Percentage of positive-scoring matches | |
187 19 qframe Query frame | |
188 20 sframe Subject frame | |
189 21 qseq Aligned part of query sequence | |
190 22 sseq Aligned part of subject sequence | |
191 ====== ============= =========================================== | |
192 | |
193 The third option is BLAST XML output, which is designed to be parsed by | |
194 another program, and is understood by some Galaxy tools. | |
195 | |
196 You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). | |
197 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. | |
198 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. | |
199 The two query anchored outputs show a multiple sequence alignment between the query and all the matches, | |
200 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). | |
201 | |
202 ------- | |
203 | |
204 **References** | |
205 | |
206 Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. | |
207 | |
208 </help> | |
209 </tool> |