Mercurial > repos > devteam > ncbi_blast_plus
comparison tools/ncbi_blast_plus/ncbi_blastx_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 |
---|---|
date | Mon, 01 Dec 2014 05:59:16 -0500 |
parents | 623f727cdff1 |
children | c16c30e9ad5b |
comparison
equal
deleted
inserted
replaced
13:623f727cdff1 | 14:2fe07f50a41e |
---|---|
1 <tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.1.00"> | 1 <tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.1.01"> |
2 <description>Search protein database with translated nucleotide query sequence(s)</description> | 2 <description>Search protein database with translated 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@">blastx</token> | 6 <token name="@BINARY@">blastx</token> |
20 #if $adv_opts.adv_opts_selector=="advanced": | 20 #if $adv_opts.adv_opts_selector=="advanced": |
21 $adv_opts.strand | 21 $adv_opts.strand |
22 -matrix $adv_opts.matrix | 22 -matrix $adv_opts.matrix |
23 @ADVANCED_OPTIONS@ | 23 @ADVANCED_OPTIONS@ |
24 $adv_opts.ungapped | 24 $adv_opts.ungapped |
25 @ADV_ID_LIST_FILTER@ | |
25 ## End of advanced options: | 26 ## End of advanced options: |
26 #end if | 27 #end if |
27 </command> | 28 </command> |
28 | 29 |
29 <expand macro="stdio" /> | 30 <expand macro="stdio" /> |
43 <expand macro="input_scoring_matrix" /> | 44 <expand macro="input_scoring_matrix" /> |
44 <expand macro="input_max_hits" /> | 45 <expand macro="input_max_hits" /> |
45 <expand macro="input_word_size" /> | 46 <expand macro="input_word_size" /> |
46 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> | 47 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> |
47 <expand macro="input_parse_deflines" /> | 48 <expand macro="input_parse_deflines" /> |
49 <expand macro="advanced_optional_id_files" /> | |
48 </expand> | 50 </expand> |
49 </inputs> | 51 </inputs> |
50 <outputs> | 52 <outputs> |
51 <data name="output1" format="tabular" label="blastx $query.name vs @ON_DB_SUBJECT@"> | 53 <data name="output1" format="tabular" label="blastx $query.name vs @ON_DB_SUBJECT@"> |
52 <expand macro="output_change_format" /> | 54 <expand macro="output_change_format" /> |
121 If you use this Galaxy tool in work leading to a scientific publication please | 123 If you use this Galaxy tool in work leading to a scientific publication please |
122 cite the following papers: | 124 cite the following papers: |
123 | 125 |
124 @REFERENCES@ | 126 @REFERENCES@ |
125 </help> | 127 </help> |
128 <expand macro="blast_citations" /> | |
126 </tool> | 129 </tool> |