Mercurial > repos > edward-kirton > blast
annotate blast/blastp.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="blastp" name="blastp" 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 protein database with protein 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 blastp |
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 -task $blast_type |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
16 -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
|
17 -out $output1 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
18 -outfmt "$out_format" |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
19 #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
|
20 $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
|
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 $adv_opts.word_size |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
29 #end if |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
30 ##Ungapped disabled for now - see comments below |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
31 ##$adv_opts.ungapped |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
32 $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
|
33 ## 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
|
34 #end if |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
35 </command> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
36 <inputs> |
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="query" type="data" format="fasta" label="Protein 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
|
38 <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
|
39 <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
|
40 <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
|
41 <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
|
42 <option value="fasta">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
|
43 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
44 <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
|
45 <param name="database" type="select" label="Precompiled Protein BLAST database"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
46 <!-- 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
|
47 column 0 is an identifier (not used), |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
48 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
|
49 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
|
50 <options from_file="blastdb_p.loc"> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
51 <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
|
52 <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
|
53 </options> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
54 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
55 <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
|
56 </when> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
57 <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
|
58 <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
|
59 <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
|
60 </when> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
61 <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
|
62 <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
|
63 <param name="subject" type="data" format="fasta" label="Protein 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
|
64 </when> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
65 </conditional> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
66 <param name="blast_type" type="select" display="radio" label="Type of BLAST"> |
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="blastp">blastp</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="blastp-short">blastp-short</option> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
69 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
70 <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
|
71 <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
|
72 <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
|
73 <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
|
74 <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
|
75 <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
|
76 <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
|
77 <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
|
78 <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
|
79 <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
|
80 <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
|
81 <!-- |
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="-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
|
83 --> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
84 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
85 <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
|
86 <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
|
87 <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
|
88 <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
|
89 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
90 <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
|
91 <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
|
92 <!-- 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
|
93 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
94 <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
|
95 <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
|
96 <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
|
97 <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
|
98 <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
|
99 <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
|
100 <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
|
101 <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
|
102 <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
|
103 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
104 <!-- 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
|
105 <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
|
106 <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
|
107 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
108 <!-- I'd like word_size to be optional, with minimum 2 for blastp --> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
109 <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
|
110 <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
|
111 </param> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
112 <!-- |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
113 Can't use '-ungapped' on its own, error back is: |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
114 Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
115 Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.' |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
116 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
117 --> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
118 <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
|
119 </when> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
120 </conditional> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
121 </inputs> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
122 <outputs> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
123 <data name="output1" format="tabular" label="${blast_type.value_label} 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
|
124 <change_format> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
125 <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
|
126 <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
|
127 <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
|
128 <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
|
129 <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
|
130 <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
|
131 <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
|
132 </change_format> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
133 </data> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
134 </outputs> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
135 <requirements> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
136 <requirement type="binary">blastp</requirement> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
137 </requirements> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
138 <tests> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
139 <test> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
140 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
141 <param name="db_opts_selector" value="file" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
142 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
143 <param name="database" value="" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
144 <param name="evalue_cutoff" value="1e-8" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
145 <param name="adv_opts_selector" value="advanced" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
146 <param name="filter_query" value="True" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
147 <param name="matrix" value="BLOSUM62" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
148 <param name="max_hits" value="0" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
149 <param name="word_size" value="0" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
150 <param name="parse_deflines" value="True" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
151 <output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
152 </test> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
153 <test> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
154 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
155 <param name="db_opts_selector" value="file" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
156 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
157 <param name="database" value="" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
158 <param name="evalue_cutoff" value="1e-8" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
159 <param name="blast_type" value="blastp" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
160 <param name="out_format" value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
161 <param name="adv_opts_selector" value="advanced" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
162 <param name="filter_query" value="True" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
163 <param name="matrix" value="BLOSUM62" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
164 <param name="max_hits" value="0" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
165 <param name="word_size" value="0" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
166 <param name="parse_deflines" value="True" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
167 <output name="output1" file="blastp_four_human_vs_rhodopsin_22c.tabular" ftype="tabular" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
168 </test> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
169 <test> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
170 <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
171 <param name="db_opts_selector" value="file" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
172 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
173 <param name="database" value="" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
174 <param name="evalue_cutoff" value="1e-8" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
175 <param name="blast_type" value="blastp" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
176 <param name="out_format" value="6" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
177 <param name="adv_opts_selector" value="basic" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
178 <output name="output1" file="blastp_rhodopsin_vs_four_human.tabular" ftype="tabular" /> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
179 </test> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
180 </tests> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
181 <help> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
182 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
183 .. class:: warningmark |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
184 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
185 **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
|
186 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
|
187 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
188 ----- |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
189 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
190 **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
|
191 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
192 Search a *protein 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
|
193 using the NCBI BLAST+ blastp 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
|
194 |
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 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
197 **Output format** |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
198 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
199 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
|
200 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
|
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 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
|
204 ------ --------- -------------------------------------------- |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
205 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
|
206 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
|
207 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
|
208 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
|
209 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
|
210 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
|
211 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
|
212 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
|
213 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
|
214 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
|
215 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
|
216 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
|
217 ====== ========= ============================================ |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
218 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
219 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
|
220 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
|
221 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
|
222 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
|
223 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
|
224 BLAST output. |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
225 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
226 ====== ============= =========================================== |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
227 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
|
228 ------ ------------- ------------------------------------------- |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
229 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
|
230 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
|
231 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
|
232 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
|
233 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
|
234 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
|
235 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
|
236 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
|
237 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
|
238 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
|
239 ====== ============= =========================================== |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
240 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
241 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
|
242 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
|
243 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
244 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
|
245 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
|
246 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
|
247 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
|
248 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
|
249 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
250 ------- |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
251 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
252 **References** |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
253 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
254 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
|
255 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
256 Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
257 |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
258 </help> |
f3ac34855f5e
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff
changeset
|
259 </tool> |