Mercurial > repos > devteam > ncbi_blast_plus
comparison tools/ncbi_blast_plus/ncbi_makeblastdb.xml @ 5:393a7a35383c draft
Uploaded v0.0.14 adding local BLAST database support.
This *requires* the matching update to the blast_datatypes repository. This adds basic wrappers for makeblastdb and blastdbinfo.
This update includes work by Edward Kirton.
author | peterjc |
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date | Fri, 09 Nov 2012 06:53:55 -0500 |
parents | |
children | 9dabbfd73c8a |
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4:9d5beacae92b | 5:393a7a35383c |
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1 <tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.1"> | |
2 <description>Make BLAST database</description> | |
3 <version_command>makeblastdb -version</version_command> | |
4 <command> | |
5 makeblastdb -out ${os.path.join($outfile.extra_files_path,'blastdb')} | |
6 $parse_seqids | |
7 $hash_index | |
8 ## Single call to -in with multiple filenames space separated with outer quotes | |
9 ## (presumably any filenames with spaces would be a problem). Note this gives | |
10 ## some extra spaces, e.g. -in " file1 file2 file3 " but BLAST seems happy: | |
11 -in " | |
12 #for $i in $in | |
13 ${i.file} #end for | |
14 " | |
15 #if $title: | |
16 -title "$title" | |
17 #else: | |
18 ##Would default to being based on the cryptic Galaxy filenames, which is unhelpful | |
19 -title "BLAST Database" | |
20 #end if | |
21 -dbtype $dbtype | |
22 ## #set $sep = '-mask_data ' | |
23 ## #for $i in $mask_data | |
24 ## $sep${i.file} | |
25 ## #set $set = ', ' | |
26 ## #end for | |
27 ## #set $sep = '-gi_mask -gi_mask_name ' | |
28 ## #for $i in $gi_mask | |
29 ## $sep${i.file} | |
30 ## #set $set = ', ' | |
31 ## #end for | |
32 ## #if $tax.select == 'id': | |
33 ## -taxid $tax.id | |
34 ## #else if $tax.select == 'map': | |
35 ## -taxid_map $tax.map | |
36 ## #end if | |
37 </command> | |
38 <stdio> | |
39 <!-- Anything other than zero is an error --> | |
40 <exit_code range="1:" /> | |
41 <exit_code range=":-1" /> | |
42 <!-- In case the return code has not been set propery check stderr too --> | |
43 <regex match="Error:" /> | |
44 <regex match="EXception:" /> | |
45 </stdio> | |
46 <inputs> | |
47 <param name="dbtype" type="select" display="radio" label="Molecule type of input"> | |
48 <option value="prot">protein</option> | |
49 <option value="nucl">nucleotide</option> | |
50 </param> | |
51 <!-- TODO Allow merging of existing BLAST databases (conditional on the database type) | |
52 <repeat name="in" title="Blast or Fasta Database" min="1"> | |
53 <param name="file" type="data" format="fasta,blastdbn,blastdbp" label="Blast or Fasta database" /> | |
54 </repeat> | |
55 --> | |
56 <repeat name="in" title="FASTA file" min="1"> | |
57 <param name="file" type="data" format="fasta" /> | |
58 </repeat> | |
59 <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" /> | |
60 <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="False" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe '|' symbols" /> | |
61 <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values." help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." /> | |
62 | |
63 <!-- SEQUENCE MASKING OPTIONS --> | |
64 <!-- TODO | |
65 <repeat name="mask_data" title="Provide one or more files containing masking data"> | |
66 <param name="file" type="data" format="asnb" label="File containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> | |
67 </repeat> | |
68 <repeat name="gi_mask" title="Create GI indexed masking data"> | |
69 <param name="file" type="data" format="asnb" label="Masking data output file" /> | |
70 </repeat> | |
71 --> | |
72 | |
73 <!-- TAXONOMY OPTIONS --> | |
74 <!-- TODO | |
75 <conditional name="tax"> | |
76 <param name="select" type="select" label="Taxonomy options"> | |
77 <option value="">Do not assign sequences to Taxonomy IDs</option> | |
78 <option value="id">Assign all sequences to one Taxonomy ID</option> | |
79 <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option> | |
80 </param> | |
81 <when value=""> | |
82 </when> | |
83 <when value="id"> | |
84 <param name="id" type="integer" value="" label="NCBI taxonomy ID" help="Integer >=0" /> | |
85 </when> | |
86 <when value="map"> | |
87 <param name="file" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" /> | |
88 </when> | |
89 </conditional> | |
90 --> | |
91 </inputs> | |
92 <outputs> | |
93 <!-- If we only accepted one FASTA file, we could use its human name here... --> | |
94 <data name="outfile" format="data" label="BLAST database from ${on_string}"> | |
95 <change_format> | |
96 <when input="dbtype" value="nucl" format="blastdbn"/> | |
97 <when input="dbtype" value="prot" format="blastdbp"/> | |
98 </change_format> | |
99 </data> | |
100 </outputs> | |
101 <requirements> | |
102 <requirement type="binary">makeblastdb</requirement> | |
103 </requirements> | |
104 <help> | |
105 **What it does** | |
106 | |
107 Make BLAST database from one or more FASTA files and/or BLAST databases. | |
108 | |
109 This is a wrapper for the NCBI BLAST+ tool 'makeblastdb', which is the | |
110 replacement for the 'formatdb' tool in the NCBI 'legacy' BLAST suite. | |
111 | |
112 <!-- | |
113 Applying masks to an existing BLAST database will not change the original database; a new database will be created. | |
114 For this reason, it's best to apply all masks at once to minimize the number of unnecessary intermediate databases. | |
115 --> | |
116 | |
117 **Documentation** | |
118 | |
119 http://www.ncbi.nlm.nih.gov/books/NBK1763/ | |
120 </help> | |
121 </tool> |