Mercurial > repos > devteam > ncbi_blast_plus

annotate tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 4:9d5beacae92b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.13 which uses the recently added error handling. No longer bundles the hide_stderr.py script which is now redundant.
author peterjc
date Wed, 19 Sep 2012 13:08:31 -0400
parents 643338ac83c0
children 393a7a35383c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
9d5beacae92b Uploaded v0.0.13 which uses the recently added error handling. No longer bundles the hide_stderr.py script which is now redundant.
peterjc
parents: 3
diff changeset
1 <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.13">
3
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
2 <description>Search nucleotide database with nucleotide query sequence(s)</description>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
3 <!-- If job splitting is enabled, break up the query file into parts -->
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
4 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
5 <version_command>blastn -version</version_command>
4
9d5beacae92b Uploaded v0.0.13 which uses the recently added error handling. No longer bundles the hide_stderr.py script which is now redundant.
peterjc
parents: 3
diff changeset
6 <command>
3
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
7 ## The command is a Cheetah template which allows some Python based syntax.
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
8 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
9 blastn
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
10 -query "$query"
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
11 #if $db_opts.db_opts_selector == "db":
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
12 -db "${db_opts.database.fields.path}"
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
13 #else:
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
14 -subject "$db_opts.subject"
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
15 #end if
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
16 -task $blast_type
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
17 -evalue $evalue_cutoff
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
18 -out $output1
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
19 ##Set the extended list here so if/when we add things, saved workflows are not affected
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
20 #if str($out_format)=="ext":
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
21 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
22 #else:
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
23 -outfmt $out_format
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
24 #end if
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
25 -num_threads 8
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
26 #if $adv_opts.adv_opts_selector=="advanced":
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
27 $adv_opts.filter_query
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
28 $adv_opts.strand
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
29 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
30 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
31 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
32 -max_target_seqs $adv_opts.max_hits
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
33 #end if
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
34 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
35 -word_size $adv_opts.word_size
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
36 #end if
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
37 $adv_opts.ungapped
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
38 $adv_opts.parse_deflines
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
39 ## End of advanced options:
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
40 #end if
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
41 </command>
4
9d5beacae92b Uploaded v0.0.13 which uses the recently added error handling. No longer bundles the hide_stderr.py script which is now redundant.
peterjc
parents: 3
diff changeset
42 <stdio>
9d5beacae92b Uploaded v0.0.13 which uses the recently added error handling. No longer bundles the hide_stderr.py script which is now redundant.
peterjc
parents: 3
diff changeset
43 <exit_code range="1:" />
9d5beacae92b Uploaded v0.0.13 which uses the recently added error handling. No longer bundles the hide_stderr.py script which is now redundant.
peterjc
parents: 3
diff changeset
44 <exit_code range="://0" />
9d5beacae92b Uploaded v0.0.13 which uses the recently added error handling. No longer bundles the hide_stderr.py script which is now redundant.
peterjc
parents: 3
diff changeset
45 </stdio>
3
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
46 <inputs>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
47 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
48 <conditional name="db_opts">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
49 <param name="db_opts_selector" type="select" label="Subject database/sequences">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
50 <option value="db" selected="True">BLAST Database</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
51 <option value="file">FASTA file (pairwise e-values)</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
52 </param>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
53 <when value="db">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
54 <param name="database" type="select" label="Nucleotide BLAST database">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
55 <options from_file="blastdb.loc">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
56 <column name="value" index="0"/>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
57 <column name="name" index="1"/>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
58 <column name="path" index="2"/>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
59 </options>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
60 </param>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
61 <param name="subject" type="hidden" value="" />
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
62 </when>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
63 <when value="file">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
64 <param name="database" type="hidden" value="" />
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
65 <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
66 </when>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
67 </conditional>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
68 <param name="blast_type" type="select" display="radio" label="Type of BLAST">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
69 <option value="megablast">megablast</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
70 <option value="blastn">blastn</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
71 <option value="blastn-short">blastn-short</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
72 <option value="dc-megablast">dc-megablast</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
73 <!-- Using BLAST 2.2.24+ this gives an error:
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
74 BLAST engine error: Program type 'vecscreen' not supported
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
75 <option value="vecscreen">vecscreen</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
76 -->
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
77 </param>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
78 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
79 <param name="out_format" type="select" label="Output format">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
80 <option value="6" selected="True">Tabular (standard 12 columns)</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
81 <option value="ext">Tabular (extended 24 columns)</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
82 <option value="5">BLAST XML</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
83 <option value="0">Pairwise text</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
84 <option value="0 -html">Pairwise HTML</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
85 <option value="2">Query-anchored text</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
86 <option value="2 -html">Query-anchored HTML</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
87 <option value="4">Flat query-anchored text</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
88 <option value="4 -html">Flat query-anchored HTML</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
89 <!--
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
90 <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
91 -->
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
92 </param>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
93 <conditional name="adv_opts">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
94 <param name="adv_opts_selector" type="select" label="Advanced Options">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
95 <option value="basic" selected="True">Hide Advanced Options</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
96 <option value="advanced">Show Advanced Options</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
97 </param>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
98 <when value="basic" />
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
99 <when value="advanced">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
100 <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' -->
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
101 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" />
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
102 <param name="strand" type="select" label="Query strand(s) to search against database/subject">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
103 <option value="-strand both">Both</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
104 <option value="-strand plus">Plus (forward)</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
105 <option value="-strand minus">Minus (reverse complement)</option>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
106 </param>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
107 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
108 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
109 <validator type="in_range" min="0" />
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
110 </param>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
111 <!-- I'd like word_size to be optional, with minimum 4 for blastn -->
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
112 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4.">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
113 <validator type="in_range" min="0" />
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
114 </param>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
115 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
116 <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"/>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
117 </when>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
118 </conditional>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
119 </inputs>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
120 <outputs>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
121 <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}">
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
122 <change_format>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
123 <when input="out_format" value="0" format="txt"/>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
124 <when input="out_format" value="0 -html" format="html"/>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
125 <when input="out_format" value="2" format="txt"/>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
126 <when input="out_format" value="2 -html" format="html"/>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
127 <when input="out_format" value="4" format="txt"/>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
128 <when input="out_format" value="4 -html" format="html"/>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
129 <when input="out_format" value="5" format="blastxml"/>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
130 </change_format>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
131 </data>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
132 </outputs>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
133 <requirements>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
134 <requirement type="binary">blastn</requirement>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
135 </requirements>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
136 <help>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
137
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
138 .. class:: warningmark
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
139
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
140 **Note**. Database searches may take a substantial amount of time.
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
141 For large input datasets it is advisable to allow overnight processing.
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
142
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
143 -----
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
144
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
145 **What it does**
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
146
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
147 Search a *nucleotide database* using a *nucleotide query*,
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
148 using the NCBI BLAST+ blastn command line tool.
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
149 Algorithms include blastn, megablast, and discontiguous megablast.
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
150
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
151 -----
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
152
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
153 **Output format**
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
154
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
155 Because Galaxy focuses on processing tabular data, the default output of this
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
156 tool is tabular. The standard BLAST+ tabular output contains 12 columns:
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
157
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
158 ====== ========= ============================================
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
159 Column NCBI name Description
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
160 ------ --------- --------------------------------------------
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
161 1 qseqid Query Seq-id (ID of your sequence)
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
162 2 sseqid Subject Seq-id (ID of the database hit)
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
163 3 pident Percentage of identical matches
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
164 4 length Alignment length
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
165 5 mismatch Number of mismatches
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
166 6 gapopen Number of gap openings
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
167 7 qstart Start of alignment in query
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
168 8 qend End of alignment in query
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
169 9 sstart Start of alignment in subject (database hit)
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
170 10 send End of alignment in subject (database hit)
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
171 11 evalue Expectation value (E-value)
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
172 12 bitscore Bit score
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
173 ====== ========= ============================================
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
174
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
175 The BLAST+ tools can optionally output additional columns of information,
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
176 but this takes longer to calculate. Most (but not all) of these columns are
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
177 included by selecting the extended tabular output. The extra columns are
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
178 included *after* the standard 12 columns. This is so that you can write
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
179 workflow filtering steps that accept either the 12 or 24 column tabular
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
180 BLAST output.
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
181
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
182 ====== ============= ===========================================
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
183 Column NCBI name Description
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
184 ------ ------------- -------------------------------------------
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
185 13 sallseqid All subject Seq-id(s), separated by a ';'
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
186 14 score Raw score
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
187 15 nident Number of identical matches
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
188 16 positive Number of positive-scoring matches
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
189 17 gaps Total number of gaps
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
190 18 ppos Percentage of positive-scoring matches
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
191 19 qframe Query frame
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
192 20 sframe Subject frame
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
193 21 qseq Aligned part of query sequence
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
194 22 sseq Aligned part of subject sequence
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
195 23 qlen Query sequence length
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
196 24 slen Subject sequence length
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
197 ====== ============= ===========================================
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
198
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
199 The third option is BLAST XML output, which is designed to be parsed by
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
200 another program, and is understood by some Galaxy tools.
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
201
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
202 You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
203 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
204 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
205 The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
206 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
207
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
208 -------
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
209
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
210 **References**
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
211
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
212 Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
213
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
214 </help>
643338ac83c0 Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff changeset
215 </tool>