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

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
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 detect_errors="aggressive"> 9 <command detect_errors="aggressive">
10 <![CDATA[
10 ## The command is a Cheetah template which allows some Python based syntax. 11 ## 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 12 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
12 blastn 13 blastn
13 -query '$query' 14 #if $query.is_of_type('fasta.gz'):
15 -query <(gunzip -c '${query}')
16 #else:
17 -query '${query}'
18 #end if
14 @BLAST_DB_SUBJECT@ 19 @BLAST_DB_SUBJECT@
15 -task $blast_type 20 -task '${blast_type}'
16 -evalue $evalue_cutoff 21 -evalue '${evalue_cutoff}'
17 @BLAST_OUTPUT@ 22 @BLAST_OUTPUT@
18 @THREADS@ 23 @THREADS@
19 #if $adv_opts.adv_opts_selector=="advanced": 24 #if $adv_opts.adv_opts_selector=="advanced":
20 $adv_opts.strand 25 ${adv_opts.strand}
21 @ADV_FILTER_QUERY@ 26 @ADV_FILTER_QUERY@
22 @ADV_MAX_HITS@ 27 @ADV_MAX_HITS@
23 @ADV_WORD_SIZE@ 28 @ADV_WORD_SIZE@
24 #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): 29 #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ):
25 -perc_identity $adv_opts.identity_cutoff 30 -perc_identity '${adv_opts.identity_cutoff}'
26 #end if 31 #end if
27 $adv_opts.ungapped 32 ${adv_opts.ungapped}
28 @ADV_ID_LIST_FILTER@ 33 @ADV_ID_LIST_FILTER@
29 @ADV_QCOV_HSP_PERC@ 34 @ADV_QCOV_HSP_PERC@
35 ## only use window size if dc-megablast mode is used
36 #if ($blast_type == "dc-megablast"):
37 -window_size @ADV_WINDOW_SIZE@
38 #end if
39 @ADV_GAPOPEN@
40 @ADV_GAPEXTEND@
30 ## End of advanced options: 41 ## End of advanced options:
31 #end if 42 #end if
43 ]]>
32 </command> 44 </command>
33 <inputs> 45 <inputs>
34 <param argument="-query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 46 <param argument="-query" type="data" format="fasta,fasta.gz" label="Nucleotide query sequence(s)"/>
35 <expand macro="input_conditional_nucleotide_db" /> 47 <expand macro="input_conditional_nucleotide_db" />
36 <param name="blast_type" argument="-task" type="select" display="radio" label="Type of BLAST"> 48 <param name="blast_type" argument="-task" type="select" display="radio" label="Type of BLAST">
37 <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option> 49 <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option>
38 <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option> 50 <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option>
39 <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option> 51 <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option>
51 <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' --> 63 <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' -->
52 <param name="filter_query" argument="-dust" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> 64 <param name="filter_query" argument="-dust" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" />
53 <expand macro="input_strand" /> 65 <expand macro="input_strand" />
54 <expand macro="input_max_hits" /> 66 <expand macro="input_max_hits" />
55 <param name="identity_cutoff" argument="-perc_identity" type="float" min="0" max="100" value="0" label="Percent identity cutoff" help="Use zero for no cutoff" /> 67 <param name="identity_cutoff" argument="-perc_identity" type="float" min="0" max="100" value="0" label="Percent identity cutoff" help="Use zero for no cutoff" />
56 68 <expand macro="input_word_size" />
57 <!-- I'd like word_size to be optional, with minimum 4 for blastn -->
58 <param argument="-word_size" type="integer" min="0" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4" />
59 <param argument="-ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> 69 <param argument="-ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
60 <expand macro="input_parse_deflines" /> 70 <expand macro="input_parse_deflines" />
61 <expand macro="advanced_optional_id_files" /> 71 <expand macro="advanced_optional_id_files" />
62 <expand macro="input_qcov_hsp_perc" /> 72 <expand macro="input_qcov_hsp_perc" />
73 <!-- the help text here is unique to the blastx application, so macro not used -->
74 <param name="window_size" type="integer" optional="true" min="0"
75 label="Multiple hits window size: use 0 to specify 1-hit algorithm, leave blank for default"
76 help="Only relevant for dc-megablast, and otherwise ignored. Default window size changes with substitution matrix and BLAST type.
77 Entering a non-negative integer will override the default."/>
78 <expand macro="input_gapopen"/>
79 <expand macro="input_gapextend"/>
63 </expand> 80 </expand>
64 </inputs> 81 </inputs>
65 <outputs> 82 <outputs>
66 <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@"> 83 <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@">
67 <expand macro="output_change_format" /> 84 <expand macro="output_change_format" />
89 <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" /> 106 <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" />
90 </test> 107 </test>
91 <test> 108 <test>
92 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> 109 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
93 <param name="db_opts_selector" value="file" /> 110 <param name="db_opts_selector" value="file" />
111 <param name="subject" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" />
112 <param name="database" value="" />
113 <param name="evalue_cutoff" value="1e-40" />
114 <param name="out_format" value="6" />
115 <param name="adv_opts_selector" value="basic" />
116 <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" />
117 </test>
118 <test>
119 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
120 <param name="db_opts_selector" value="file" />
94 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> 121 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />
95 <param name="database" value="" /> 122 <param name="database" value="" />
96 <param name="evalue_cutoff" value="1e-40" /> 123 <param name="evalue_cutoff" value="1e-40" />
97 <param name="out_format" value="cols" /> 124 <param name="out_format" value="cols" />
98 <param name="std_cols" value="qseqid,sseqid,pident" /> 125 <param name="std_cols" value="qseqid,sseqid,pident" />
166 193
167 @OUTPUT_FORMAT@ 194 @OUTPUT_FORMAT@
168 195
169 ------- 196 -------
170 197
198 @CLI_OPTIONS@
199
200 -------
201
171 **References** 202 **References**
172 203
173 If you use this Galaxy tool in work leading to a scientific publication please 204 If you use this Galaxy tool in work leading to a scientific publication please
174 cite the following papers: 205 cite the following papers:
175 206