view tools/metag_tools/megablast_wrapper.xml @ 1:cdcb0ce84a1b

author xuebing
date Fri, 09 Mar 2012 19:45:15 -0500
parents 9071e359b9a3
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<tool id="megablast_wrapper" name="Megablast" version="1.1.0">
    <description> compare short reads against htgs, nt, and wgs databases</description>
    <command interpreter="python">
        --db_build="${ filter( lambda x: str( x[0] ) == str( $source_select ), $__app__.tool_data_tables[ 'blastdb' ].get_fields() )[0][-1] }"
        <param name="input_query" type="data" format="fasta" label="Compare these sequences"/> 
        <param name="source_select" type="select" display="radio" label="against target database">
            <options from_data_table="blastdb" />
        <param name="word_size" type="select" label="using word size" help="Size of best perfect match (-W)">
            <option value="28">28</option>
            <option value="16">16</option>
        <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity (-p)" help="no cutoff if 0" />
        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff (-e)" />
        <param name="filter_query" type="select" label="Filter out low complexity regions? (-F)">
            <option value="T">Yes</option>
            <option value="F">No</option>
        <data name="output1" format="tabular"/>
        <requirement type="package">megablast</requirement>
            <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/>
            <!-- source_select needs to match the entry in the blastdb.loc file, which includes the last update date if appropriate --> 
            <param name="source_select" value="/galaxy/data/blastdb/phiX/phiX" />
            <param name="word_size" value="28" />
            <param name="iden_cutoff" value="99.0" />
            <param name="evalue_cutoff" value="10.0" />
            <param name="filter_query" value="T" />
            <output name="output1" file="megablast_wrapper_test1.out"/> 
.. class:: warningmark

**Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing.  


**What it does**

This tool runs **megablast** (for information about megablast, please see the reference below) a high performance nucleotide local aligner developed by Webb Miller and colleagues.


**Output format**

Output of this tool contains 13 columns delimited by Tabs:

1. Id of your sequence 
2. GI of the database hit 
3. Length of the database hit
4. % identity
5. Alignment length
6. # mismatches
7. # gaps
8. Start position in your sequence
9. End position in your sequence
10. Start position in database hit
11. End position in database hit
12. E-value
13. Bit score



Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.