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1 <tool id="megablast_wrapper" name="Megablast" version="1.2.0">
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2 <description> compare short reads against htgs, nt, and wgs databases</description>
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3 <requirements>
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4 <requirement type="package" version="2.2.26+">blast+</requirement>
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5 <requirement type="package" version="0.7.1">bx-python</requirement>
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6 </requirements>
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7 <command interpreter="python">
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8 megablast_wrapper.py
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9 --db_build="${source_select.fields.path}"
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10 --input=$input_query
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11 --word_size=$word_size
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12 --identity_cutoff=$iden_cutoff
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13 --eval_cutoff=$evalue_cutoff
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14 --filter_query=$filter_query
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15 --index_dir=${GALAXY_DATA_INDEX_DIR}
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16 --output=$output1
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17 </command>
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18 <inputs>
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19 <param name="input_query" type="data" format="fasta" label="Compare these sequences"/>
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20 <param name="source_select" type="select" display="radio" label="against target database">
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21 <options from_data_table="blastdb" />
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22 </param>
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23 <param name="word_size" type="select" label="using word size" help="Size of best perfect match (-word_size)">
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24 <option value="28">28</option>
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25 <option value="16">16</option>
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26 </param>
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27 <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity (-perc_identity)" help="no cutoff if 0" />
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28 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff (-evalue)" />
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29 <param name="filter_query" type="select" label="Filter out low complexity regions? (-dust)">
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30 <option value="yes">Yes</option>
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31 <option value="no">No</option>
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32 </param>
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33 </inputs>
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34 <outputs>
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35 <data name="output1" format="tabular"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/>
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40 <!-- source_select needs to match the entry in the blastdb.loc file, which includes the last update date if appropriate -->
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41 <param name="source_select" value="phiX" />
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42 <param name="word_size" value="28" />
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43 <param name="iden_cutoff" value="99.0" />
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44 <param name="evalue_cutoff" value="10.0" />
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45 <param name="filter_query" value="yes" />
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46 <output name="output1" file="megablast_wrapper_test1.out"/>
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47 </test>
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48 </tests>
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49 <help>
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50
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51 .. class:: warningmark
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52
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53 **Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing.
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54
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55 -----
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56
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57 **What it does**
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58
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59 This tool runs **megablast** function of BLAST+ blastn tool - a high performance nucleotide local aligner developed by Webb Miller and colleagues.
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60
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61 -----
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62
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63 **Output format**
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64
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65 Output of this tool contains 13 columns delimited by Tabs:
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66
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67 1. Id of your sequence
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68 2. GI of the database hit
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69 3. Length of the database hit
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70 4. % identity
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71 5. Alignment length
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72 6. # mismatches
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73 7. # gaps
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74 8. Start position in your sequence
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75 9. End position in your sequence
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76 10. Start position in database hit
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77 11. End position in database hit
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78 12. E-value
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79 13. Bit score
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80
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81 -------
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82
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83 **Reference**
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84
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85 Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.
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86
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87 </help>
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88 </tool>
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