Mercurial > repos > devteam > ncbi_blast_plus

comparison tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @ 22:6f386c5dc4fb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
author peterjc
date Mon, 18 Sep 2017 06:21:27 -0400
parents 697f40151eaf
children 31e517610e1f
comparison
equal deleted inserted replaced
21:7538e2bfcd41 22:6f386c5dc4fb
4 <token name="@BINARY@">blastx</token> 4 <token name="@BINARY@">blastx</token>
5 <import>ncbi_macros.xml</import> 5 <import>ncbi_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="parallelism" /> 7 <expand macro="parallelism" />
8 <expand macro="preamble" /> 8 <expand macro="preamble" />
9 <command> 9 <command detect_errors="aggressive">
10 ## The command is a Cheetah template which allows some Python based syntax. 10 ## The command is a Cheetah template which allows some Python based syntax.
11 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces 11 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
12 blastx 12 blastx
13 -query "$query" 13 -query '$query'
14 @BLAST_DB_SUBJECT@ 14 @BLAST_DB_SUBJECT@
15 -query_gencode $query_gencode 15 -query_gencode $query_gencode
16 -task $blast_type 16 -task $blast_type
17 -evalue $evalue_cutoff 17 -evalue $evalue_cutoff
18 @BLAST_OUTPUT@ 18 @BLAST_OUTPUT@
28 @ADV_QCOV_HSP_PERC@ 28 @ADV_QCOV_HSP_PERC@
29 ## End of advanced options: 29 ## End of advanced options:
30 #end if 30 #end if
31 </command> 31 </command>
32 <inputs> 32 <inputs>
33 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 33 <param argument="-query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>
34 34
35 <expand macro="input_conditional_protein_db" /> 35 <expand macro="input_conditional_protein_db" />
36 <expand macro="input_query_gencode" /> 36 <expand macro="input_query_gencode" />
37 <param name="blast_type" type="select" display="radio" label="Type of BLAST"> 37 <param name="blast_type" argument="-task" type="select" display="radio" label="Type of BLAST">
38 <option value="blastx">blastx - Traditional BLASTX to compare translated nucleotide query to protein database</option> 38 <option value="blastx">blastx - Traditional BLASTX to compare translated nucleotide query to protein database</option>
39 <option value="blastx-fast">blastx-fast - Use longer words for seeding, faster but less accurate</option> 39 <option value="blastx-fast">blastx-fast - Use longer words for seeding, faster but less accurate</option>
40 </param> 40 </param>
41 <expand macro="input_evalue" /> 41 <expand macro="input_evalue" />
42 42
46 <expand macro="input_filter_query_default_true" /> 46 <expand macro="input_filter_query_default_true" />
47 <expand macro="input_strand" /> 47 <expand macro="input_strand" />
48 <expand macro="input_scoring_matrix" /> 48 <expand macro="input_scoring_matrix" />
49 <expand macro="input_max_hits" /> 49 <expand macro="input_max_hits" />
50 <expand macro="input_word_size" /> 50 <expand macro="input_word_size" />
51 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> 51 <param argument="-ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
52 <expand macro="input_parse_deflines" /> 52 <expand macro="input_parse_deflines" />
53 <expand macro="advanced_optional_id_files" /> 53 <expand macro="advanced_optional_id_files" />
54 <expand macro="input_qcov_hsp_perc" /> 54 <expand macro="input_qcov_hsp_perc" />
55 </expand> 55 </expand>
56 </inputs> 56 </inputs>
105 <param name="adv_opts_selector" value="basic" /> 105 <param name="adv_opts_selector" value="basic" />
106 <output name="output1" file="blastx_rhodopsin_vs_four_human_all.tabular" ftype="tabular" /> 106 <output name="output1" file="blastx_rhodopsin_vs_four_human_all.tabular" ftype="tabular" />
107 </test> 107 </test>
108 </tests> 108 </tests>
109 <help> 109 <help>
110 110
111 @SEARCH_TIME_WARNING@ 111 @SEARCH_TIME_WARNING@
112 112
113 **What it does** 113 **What it does**
114 114
115 Search a *protein database* using a *translated nucleotide query*, 115 Search a *protein database* using a *translated nucleotide query*,