Mercurial > repos > devteam > ncbi_blast_plus
comparison tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 15:c16c30e9ad5b draft
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
author | peterjc |
---|---|
date | Sun, 05 Jul 2015 10:37:27 -0400 |
parents | 2fe07f50a41e |
children | b5f1f599d1fb |
comparison
equal
deleted
inserted
replaced
14:2fe07f50a41e | 15:c16c30e9ad5b |
---|---|
1 <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.01"> | 1 <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.03"> |
2 <description>Search nucleotide database with nucleotide query sequence(s)</description> | 2 <description>Search nucleotide database with 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@">blastn</token> | 6 <token name="@BINARY@">blastn</token> |
7 <import>ncbi_macros.xml</import> | 7 <import>ncbi_macros.xml</import> |
8 </macros> | 8 </macros> |
9 <expand macro="requirements" /> | 9 <expand macro="preamble" /> |
10 <command> | 10 <command> |
11 ## 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. |
12 ## 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 |
13 blastn | 13 blastn |
14 -query "$query" | 14 -query "$query" |
17 -evalue $evalue_cutoff | 17 -evalue $evalue_cutoff |
18 @BLAST_OUTPUT@ | 18 @BLAST_OUTPUT@ |
19 @THREADS@ | 19 @THREADS@ |
20 #if $adv_opts.adv_opts_selector=="advanced": | 20 #if $adv_opts.adv_opts_selector=="advanced": |
21 $adv_opts.strand | 21 $adv_opts.strand |
22 @ADVANCED_OPTIONS@ | 22 @ADV_FILTER_QUERY@ |
23 @ADV_MAX_HITS@ | |
24 @ADV_WORD_SIZE@ | |
23 #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): | 25 #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): |
24 -perc_identity $adv_opts.identity_cutoff | 26 -perc_identity $adv_opts.identity_cutoff |
25 #end if | 27 #end if |
26 $adv_opts.ungapped | 28 $adv_opts.ungapped |
27 @ADV_ID_LIST_FILTER@ | 29 @ADV_ID_LIST_FILTER@ |
30 @ADV_QCOV_HSP_PERC@ | |
28 ## End of advanced options: | 31 ## End of advanced options: |
29 #end if | 32 #end if |
30 </command> | 33 </command> |
31 | |
32 <expand macro="stdio" /> | |
33 | |
34 <inputs> | 34 <inputs> |
35 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> | 35 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> |
36 | |
37 <expand macro="input_conditional_nucleotide_db" /> | 36 <expand macro="input_conditional_nucleotide_db" /> |
38 | |
39 <param name="blast_type" type="select" display="radio" label="Type of BLAST"> | 37 <param name="blast_type" type="select" display="radio" label="Type of BLAST"> |
40 <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option> | 38 <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option> |
41 <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option> | 39 <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option> |
42 <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option> | 40 <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option> |
43 <option value="dc-megablast">dc-megablast - Discontiguous megablast used to find more distant (e.g., interspecies) sequences</option> | 41 <option value="dc-megablast">dc-megablast - Discontiguous megablast used to find more distant (e.g., interspecies) sequences</option> |
62 <validator type="in_range" min="0" /> | 60 <validator type="in_range" min="0" /> |
63 </param> | 61 </param> |
64 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> | 62 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> |
65 <expand macro="input_parse_deflines" /> | 63 <expand macro="input_parse_deflines" /> |
66 <expand macro="advanced_optional_id_files" /> | 64 <expand macro="advanced_optional_id_files" /> |
65 <expand macro="input_qcov_hsp_perc" /> | |
67 </expand> | 66 </expand> |
68 </inputs> | 67 </inputs> |
69 <outputs> | 68 <outputs> |
70 <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@"> | 69 <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@"> |
71 <expand macro="output_change_format" /> | 70 <expand macro="output_change_format" /> |
102 <param name="std_cols" value="qseqid,sseqid,pident" /> | 101 <param name="std_cols" value="qseqid,sseqid,pident" /> |
103 <param name="ext_cols" value="qlen,slen" /> | 102 <param name="ext_cols" value="qlen,slen" /> |
104 <param name="adv_opts_selector" value="basic" /> | 103 <param name="adv_opts_selector" value="basic" /> |
105 <output name="output1" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" /> | 104 <output name="output1" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" /> |
106 </test> | 105 </test> |
106 <!-- Disable for ToolShed where *.loc tests not yet supported | |
107 See https://github.com/peterjc/galaxy_blast/issues/53 | |
108 <test> | |
109 <param name="query" value="chimera.fasta" ftype="fasta" /> | |
110 <param name="db_opts_selector" value="db" /> | |
111 <param name="database" value="three_human_mRNA" /> | |
112 <param name="out_format" value="6" /> | |
113 <param name="adv_opts_selector" value="advanced" /> | |
114 <param name="max_hits" value="1" /> | |
115 <output name="output1" file="blastn_chimera_vs_three_human_max1.tabular" ftype="tabular" /> | |
116 </test> | |
117 <test> | |
118 <param name="query" value="chimera.fasta" ftype="fasta" /> | |
119 <param name="db_opts_selector" value="db" /> | |
120 <param name="database" value="three_human_mRNA" /> | |
121 <param name="out_format" value="0" /> | |
122 <param name="adv_opts_selector" value="advanced" /> | |
123 <param name="max_hits" value="1" /> | |
124 <output name="output1" file="blastn_chimera_vs_three_human_max1.txt" ftype="txt" /> | |
125 </test> | |
126 --> | |
107 </tests> | 127 </tests> |
108 <help> | 128 <help> |
109 | 129 |
110 @SEARCH_TIME_WARNING@ | 130 @SEARCH_TIME_WARNING@ |
111 | 131 |