Mercurial > repos > devteam > ncbi_blast_plus
comparison tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 14:2fe07f50a41e draft
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
author | peterjc |
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date | Mon, 01 Dec 2014 05:59:16 -0500 |
parents | 623f727cdff1 |
children | c16c30e9ad5b |
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13:623f727cdff1 | 14:2fe07f50a41e |
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1 <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.00"> | 1 <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.01"> |
2 <description>Search nucleotide database with nucleotide query sequence(s)</description> | 2 <description>Search nucleotide database with nucleotide query sequence(s)</description> |
3 <!-- If job splitting is enabled, break up the query file into parts --> | 3 <!-- If job splitting is enabled, break up the query file into parts --> |
4 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> | 4 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> |
5 <macros> | 5 <macros> |
6 <token name="@BINARY@">blastn</token> | 6 <token name="@BINARY@">blastn</token> |
22 @ADVANCED_OPTIONS@ | 22 @ADVANCED_OPTIONS@ |
23 #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): | 23 #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): |
24 -perc_identity $adv_opts.identity_cutoff | 24 -perc_identity $adv_opts.identity_cutoff |
25 #end if | 25 #end if |
26 $adv_opts.ungapped | 26 $adv_opts.ungapped |
27 @ADV_ID_LIST_FILTER@ | |
27 ## End of advanced options: | 28 ## End of advanced options: |
28 #end if | 29 #end if |
29 </command> | 30 </command> |
30 | 31 |
31 <expand macro="stdio" /> | 32 <expand macro="stdio" /> |
60 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."> | 61 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."> |
61 <validator type="in_range" min="0" /> | 62 <validator type="in_range" min="0" /> |
62 </param> | 63 </param> |
63 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> | 64 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> |
64 <expand macro="input_parse_deflines" /> | 65 <expand macro="input_parse_deflines" /> |
66 <expand macro="advanced_optional_id_files" /> | |
65 </expand> | 67 </expand> |
66 </inputs> | 68 </inputs> |
67 <outputs> | 69 <outputs> |
68 <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@"> | 70 <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@"> |
69 <expand macro="output_change_format" /> | 71 <expand macro="output_change_format" /> |
126 If you use this Galaxy tool in work leading to a scientific publication please | 128 If you use this Galaxy tool in work leading to a scientific publication please |
127 cite the following papers: | 129 cite the following papers: |
128 | 130 |
129 @REFERENCES@ | 131 @REFERENCES@ |
130 </help> | 132 </help> |
133 <expand macro="blast_citations" /> | |
131 </tool> | 134 </tool> |