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1 <tool id="megablast_wrapper" name="Megablast" version="1.1.0">
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2 <description> compare short reads against htgs, nt, and wgs databases</description>
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3 <command interpreter="python">
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4 megablast_wrapper.py
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5 --db_build="${ filter( lambda x: str( x[0] ) == str( $source_select ), $__app__.tool_data_tables[ 'blastdb' ].get_fields() )[0][-1] }"
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6 --input=$input_query
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7 --word_size=$word_size
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8 --identity_cutoff=$iden_cutoff
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9 --eval_cutoff=$evalue_cutoff
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10 --filter_query=$filter_query
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11 --index_dir=${GALAXY_DATA_INDEX_DIR}
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12 --output=$output1
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13 </command>
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14 <inputs>
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15 <param name="input_query" type="data" format="fasta" label="Compare these sequences"/>
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16 <param name="source_select" type="select" display="radio" label="against target database">
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17 <options from_data_table="blastdb" />
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18 </param>
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19 <param name="word_size" type="select" label="using word size" help="Size of best perfect match (-W)">
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20 <option value="28">28</option>
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21 <option value="16">16</option>
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22 </param>
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23 <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity (-p)" help="no cutoff if 0" />
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24 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff (-e)" />
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25 <param name="filter_query" type="select" label="Filter out low complexity regions? (-F)">
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26 <option value="T">Yes</option>
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27 <option value="F">No</option>
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data name="output1" format="tabular"/>
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32 </outputs>
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33 <requirements>
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34 <requirement type="package">megablast</requirement>
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35 </requirements>
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36 <tests>
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37 <test>
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38 <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/>
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39 <!-- source_select needs to match the entry in the blastdb.loc file, which includes the last update date if appropriate -->
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40 <param name="source_select" value="/galaxy/data/blastdb/phiX/phiX" />
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41 <param name="word_size" value="28" />
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42 <param name="iden_cutoff" value="99.0" />
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43 <param name="evalue_cutoff" value="10.0" />
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44 <param name="filter_query" value="T" />
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45 <output name="output1" file="megablast_wrapper_test1.out"/>
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46 </test>
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47 </tests>
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48 <help>
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49
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50 .. class:: warningmark
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51
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52 **Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing.
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53
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54 -----
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55
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56 **What it does**
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57
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58 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.
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59
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60 -----
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61
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62 **Output format**
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63
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64 Output of this tool contains 13 columns delimited by Tabs:
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65
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66 1. Id of your sequence
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67 2. GI of the database hit
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68 3. Length of the database hit
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69 4. % identity
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70 5. Alignment length
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71 6. # mismatches
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72 7. # gaps
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73 8. Start position in your sequence
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74 9. End position in your sequence
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75 10. Start position in database hit
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76 11. End position in database hit
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77 12. E-value
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78 13. Bit score
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79
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80 -------
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81
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82 **Reference**
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83
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84 Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.
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85
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86 </help>
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87 </tool>
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