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comparison tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @ 23:31e517610e1f draft

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v0.3.0 Updated for NCBI BLAST+ 2.7.1
author peterjc
date Sat, 30 Jun 2018 17:22:46 -0400
parents 6f386c5dc4fb
children e25d3acf6e68
comparison
equal deleted inserted replaced
22:6f386c5dc4fb 23:31e517610e1f
15 -query_gencode $query_gencode 15 -query_gencode $query_gencode
16 -evalue $evalue_cutoff 16 -evalue $evalue_cutoff
17 @BLAST_OUTPUT@ 17 @BLAST_OUTPUT@
18 @THREADS@ 18 @THREADS@
19 #if $adv_opts.adv_opts_selector=="advanced": 19 #if $adv_opts.adv_opts_selector=="advanced":
20 -db_gencode $adv_opts.db_gencode 20 -db_gencode $adv_opts.db_gencode
21 $adv_opts.strand 21 $adv_opts.strand
22 -matrix $adv_opts.matrix 22 @ADV_MATRIX@
23 @ADV_FILTER_QUERY@ 23 @ADV_FILTER_QUERY@
24 @ADV_MAX_HITS@ 24 @ADV_MAX_HITS@
25 @ADV_WORD_SIZE@ 25 @ADV_WORD_SIZE@
26 @ADV_ID_LIST_FILTER@ 26 @ADV_ID_LIST_FILTER@
27 @ADV_QCOV_HSP_PERC@ 27 @ADV_QCOV_HSP_PERC@
28 @ADV_THRESHOLD@
28 ## End of advanced options: 29 ## End of advanced options:
29 #end if 30 #end if
30 </command> 31 </command>
31 <inputs> 32 <inputs>
32 <param argument="-query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 33 <param argument="-query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
47 <!-- I'd like word_size to be optional, with minimum 2 for tblastx --> 48 <!-- I'd like word_size to be optional, with minimum 2 for tblastx -->
48 <expand macro="input_word_size" /> 49 <expand macro="input_word_size" />
49 <expand macro="input_parse_deflines" /> 50 <expand macro="input_parse_deflines" />
50 <expand macro="advanced_optional_id_files" /> 51 <expand macro="advanced_optional_id_files" />
51 <expand macro="input_qcov_hsp_perc" /> 52 <expand macro="input_qcov_hsp_perc" />
53 <expand macro="input_threshold" />
52 </expand> 54 </expand>
53 </inputs> 55 </inputs>
54 <outputs> 56 <outputs>
55 <data name="output1" format="tabular" label="tblastx $query.name vs @ON_DB_SUBJECT@"> 57 <data name="output1" format="tabular" label="tblastx $query.name vs @ON_DB_SUBJECT@">
56 <expand macro="output_change_format" /> 58 <expand macro="output_change_format" />
83 85
84 @OUTPUT_FORMAT@ 86 @OUTPUT_FORMAT@
85 87
86 ------- 88 -------
87 89
90 @CLI_OPTIONS@
91
92 -------
93
88 **References** 94 **References**
89 95
90 If you use this Galaxy tool in work leading to a scientific publication please 96 If you use this Galaxy tool in work leading to a scientific publication please
91 cite the following papers: 97 cite the following papers:
92 98