Mercurial > repos > edward-kirton > blast
annotate 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 |
---|---|
date | Tue, 07 Jun 2011 17:30:11 -0400 |
parents | |
children |
rev | line source |
---|---|
0
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
1 <tool id="tblastx" name="tblastx" version="0.0.1"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
2 <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
3 <command> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
4 ## The command is a Cheetah template which allows some Python based syntax. |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
5 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
6 tblastx |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
7 -query "$query" |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
8 #if $db_opts.db_opts_selector == "db": |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
9 -db "$db_opts.database" |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
10 #elif $db_opts.db_opts_selector == "user_db": |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
11 -db "$db_opts.db" |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
12 #else: |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
13 -subject "$db_opts.subject" |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
14 #end if |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
15 -evalue $evalue_cutoff |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
16 -out $output1 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
17 -outfmt "$out_format" |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
18 #if $adv_opts.adv_opts_selector=="advanced": |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
19 $adv_opts.filter_query |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
20 $adv_opts.strand |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
21 -matrix $adv_opts.matrix |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
22 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
23 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
24 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
25 -max_target_seqs $adv_opts.max_hits |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
26 #end if |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
27 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
28 -word_size $adv_opts.word_size |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
29 #end if |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
30 $adv_opts.parse_deflines |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
31 ## End of advanced options: |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
32 #end if |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
33 </command> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
34 <inputs> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
35 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
36 <conditional name="db_opts"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
37 <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
38 <option value="db" selected="True">Precompiled BLAST Database</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
39 <option value="user_db">BLAST Database in your History</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
40 <option value="file">FASTA file</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
41 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
42 <when value="db"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
43 <param name="database" type="select" label="Precompiled Nucleotide BLAST database"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
44 <!-- The BLAST loc file has three columns: |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
45 column 0 is an identifier (not used here, see legacy megablast wrapper), |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
46 column 1 is the caption (show this to the user), |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
47 column 2 is the database path (given to BLAST+) --> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
48 <options from_file="blastdb.loc"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
49 <column name="name" index="1"/> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
50 <column name="value" index="2"/> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
51 </options> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
52 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
53 <param name="subject" type="hidden" value="" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
54 </when> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
55 <when value="user_db"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
56 <param name="database" type="hidden" value="" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
57 <param name="db" type="data" format="blastdb" label="Blast DB" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
58 </when> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
59 <when value="fasta"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
60 <param name="database" type="hidden" value="" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
61 <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
62 </when> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
63 </conditional> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
64 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
65 <param name="out_format" type="select" label="Output format"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
66 <option value="6" selected="True">Tabular (standard 12 columns)</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
67 <option value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq">Tabular (extended 22 columns)</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
68 <option value="5">BLAST XML</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
69 <option value="0">Pairwise text</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
70 <option value="0 -html">Pairwise HTML</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
71 <option value="2">Query-anchored text</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
72 <option value="2 -html">Query-anchored HTML</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
73 <option value="4">Flat query-anchored text</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
74 <option value="4 -html">Flat query-anchored HTML</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
75 <!-- |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
76 <option value="-outfmt 11">BLAST archive format (ASN.1)</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
77 --> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
78 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
79 <conditional name="adv_opts"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
80 <param name="adv_opts_selector" type="select" label="Advanced Options"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
81 <option value="basic" selected="True">Hide Advanced Options</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
82 <option value="advanced">Show Advanced Options</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
83 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
84 <when value="basic" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
85 <when value="advanced"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
86 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
87 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
88 <param name="strand" type="select" label="Query strand(s) to search against database/subject"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
89 <option value="-strand both">Both</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
90 <option value="-strand plus">Plus (forward)</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
91 <option value="-strand minus">Minus (reverse complement)</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
92 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
93 <param name="matrix" type="select" label="Scoring matrix"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
94 <option value="BLOSUM90">BLOSUM90</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
95 <option value="BLOSUM80">BLOSUM80</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
96 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
97 <option value="BLOSUM50">BLOSUM50</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
98 <option value="BLOSUM45">BLOSUM45</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
99 <option value="PAM250">PAM250</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
100 <option value="PAM70">PAM70</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
101 <option value="PAM30">PAM30</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
102 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
103 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
104 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
105 <validator type="in_range" min="0" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
106 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
107 <!-- I'd like word_size to be optional, with minimum 2 for tblastx --> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
108 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
109 <validator type="in_range" min="0" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
110 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
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"/> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
112 </when> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
113 </conditional> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
114 </inputs> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
115 <outputs> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
116 <data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
117 <change_format> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
118 <when input="out_format" value="0" format="txt"/> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
119 <when input="out_format" value="0 -html" format="html"/> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
120 <when input="out_format" value="2" format="txt"/> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
121 <when input="out_format" value="2 -html" format="html"/> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
122 <when input="out_format" value="4" format="txt"/> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
123 <when input="out_format" value="4 -html" format="html"/> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
124 <when input="out_format" value="5" format="blastxml"/> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
125 </change_format> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
126 </data> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
127 </outputs> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
128 <requirements> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
129 <requirement type="binary">tblastx</requirement> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
130 </requirements> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
131 <tests> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
132 </tests> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
133 <help> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
134 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
135 .. class:: warningmark |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
136 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
137 **Note**. Database searches may take a substantial amount of time. |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
138 For large input datasets it is advisable to allow overnight processing. |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
139 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
140 ----- |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
141 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
142 **What it does** |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
143 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
144 Search a *translated nucleotide database* using a *protein query*, |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
145 using the NCBI BLAST+ tblastx command line tool. |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
146 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
147 ----- |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
148 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
149 **Output format** |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
150 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
151 Because Galaxy focuses on processing tabular data, the default output of this |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
152 tool is tabular. The standard BLAST+ tabular output contains 12 columns: |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
153 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
154 ====== ========= ============================================ |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
155 Column NCBI name Description |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
156 ------ --------- -------------------------------------------- |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
157 1 qseqid Query Seq-id (ID of your sequence) |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
158 2 sseqid Subject Seq-id (ID of the database hit) |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
159 3 pident Percentage of identical matches |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
160 4 length Alignment length |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
161 5 mismatch Number of mismatches |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
162 6 gapopen Number of gap openings |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
163 7 qstart Start of alignment in query |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
164 8 qend End of alignment in query |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
165 9 sstart Start of alignment in subject (database hit) |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
166 10 send End of alignment in subject (database hit) |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
167 11 evalue Expectation value (E-value) |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
168 12 bitscore Bit score |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
169 ====== ========= ============================================ |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
170 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
171 The BLAST+ tools can optionally output additional columns of information, |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
172 but this takes longer to calculate. Most (but not all) of these columns are |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
173 included by selecting the extended tabular output. The extra columns are |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
174 included *after* the standard 12 columns. This is so that you can write |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
175 workflow filtering steps that accept either the 12 or 22 column tabular |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
176 BLAST output. |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
177 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
178 ====== ============= =========================================== |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
179 Column NCBI name Description |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
180 ------ ------------- ------------------------------------------- |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
181 13 sallseqid All subject Seq-id(s), separated by a ';' |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
182 14 score Raw score |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
183 15 nident Number of identical matches |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
184 16 positive Number of positive-scoring matches |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
185 17 gaps Total number of gaps |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
186 18 ppos Percentage of positive-scoring matches |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
187 19 qframe Query frame |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
188 20 sframe Subject frame |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
189 21 qseq Aligned part of query sequence |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
190 22 sseq Aligned part of subject sequence |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
191 ====== ============= =========================================== |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
192 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
193 The third option is BLAST XML output, which is designed to be parsed by |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
194 another program, and is understood by some Galaxy tools. |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
195 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
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). |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
197 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
198 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
199 The two query anchored outputs show a multiple sequence alignment between the query and all the matches, |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
200 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
201 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
202 ------- |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
203 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
204 **References** |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
205 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
206 Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
207 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
208 </help> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
209 </tool> |