Mercurial > repos > devteam > ncbi_blast_plus
comparison tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 23:31e517610e1f draft
v0.3.0 Updated for NCBI BLAST+ 2.7.1
author | peterjc |
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date | Sat, 30 Jun 2018 17:22:46 -0400 |
parents | 6f386c5dc4fb |
children | e25d3acf6e68 |
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22:6f386c5dc4fb | 23:31e517610e1f |
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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 |