Mercurial > repos > devteam > ncbi_blast_plus
comparison tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 6:a23b0627623c draft
Uploaded v0.0.15, clearer warning about searching against a FASTA file.
author | peterjc |
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date | Thu, 24 Jan 2013 12:40:41 -0500 |
parents | 393a7a35383c |
children | 1f546099212f |
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5:393a7a35383c | 6:a23b0627623c |
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1 <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.14"> | 1 <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.15"> |
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" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> | 4 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> |
5 <version_command>blastn -version</version_command> | 5 <version_command>blastn -version</version_command> |
6 <command> | 6 <command> |
53 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> | 53 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> |
54 <conditional name="db_opts"> | 54 <conditional name="db_opts"> |
55 <param name="db_opts_selector" type="select" label="Subject database/sequences"> | 55 <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
56 <option value="db" selected="True">BLAST Database</option> | 56 <option value="db" selected="True">BLAST Database</option> |
57 <option value="histdb">BLAST database from your history</option> | 57 <option value="histdb">BLAST database from your history</option> |
58 <option value="file">FASTA file from your history (pairwise e-values)</option> | 58 <option value="file">FASTA file from your history (see warning note below)</option> |
59 </param> | 59 </param> |
60 <when value="db"> | 60 <when value="db"> |
61 <param name="database" type="select" label="Nucleotide BLAST database"> | 61 <param name="database" type="select" label="Nucleotide BLAST database"> |
62 <options from_file="blastdb.loc"> | 62 <options from_file="blastdb.loc"> |
63 <column name="value" index="0"/> | 63 <column name="value" index="0"/> |
160 | 160 |
161 Search a *nucleotide database* using a *nucleotide query*, | 161 Search a *nucleotide database* using a *nucleotide query*, |
162 using the NCBI BLAST+ blastn command line tool. | 162 using the NCBI BLAST+ blastn command line tool. |
163 Algorithms include blastn, megablast, and discontiguous megablast. | 163 Algorithms include blastn, megablast, and discontiguous megablast. |
164 | 164 |
165 .. class:: warningmark | |
166 | |
167 You can also search against a FASTA file of subject nucleotide | |
168 sequences. This is *not* advised because it is slower (only one | |
169 CPU is used), but more importantly gives e-values for pairwise | |
170 searches (very small e-values which will look overly signficiant). | |
171 In most cases you should instead turn the other FASTA file into a | |
172 database first using *makeblastdb* and search against that. | |
173 | |
165 ----- | 174 ----- |
166 | 175 |
167 **Output format** | 176 **Output format** |
168 | 177 |
169 Because Galaxy focuses on processing tabular data, the default output of this | 178 Because Galaxy focuses on processing tabular data, the default output of this |