[2] | 1 | <tool id="megablast_wrapper" name="Megablast" version="1.0.5"> |
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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="$source_select" |
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| 6 | --input=$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_file="blastdb.loc"> |
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| 18 | <column name="name" index="0"/> |
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| 19 | <column name="value" index="0"/> |
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| 20 | </options> |
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| 21 | </param> |
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| 22 | <param name="word_size" type="select" label="using word size" help="Size of best perfect match"> |
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| 23 | <option value="28">28</option> |
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| 24 | <option value="16">16</option> |
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| 25 | </param> |
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| 26 | <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity" help="no cutoff if 0" /> |
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| 27 | <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> |
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| 28 | <param name="filter_query" type="select" label="Filter out low complexity regions?"> |
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| 29 | <option value="T">Yes</option> |
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| 30 | <option value="F">No</option> |
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| 31 | </param> |
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| 32 | </inputs> |
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| 33 | <outputs> |
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| 34 | <data name="output1" format="tabular"/> |
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| 35 | </outputs> |
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| 36 | <requirements> |
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| 37 | <requirement type="package">megablast</requirement> |
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| 38 | </requirements> |
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| 39 | <tests> |
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| 40 | <test> |
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| 41 | <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/> |
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| 42 | <!-- source_select needs to match the entry in the blastdb.loc file, which includes the last update date if appropriate --> |
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| 43 | <param name="source_select" value="phiX" /> |
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| 44 | <param name="word_size" value="28" /> |
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| 45 | <param name="iden_cutoff" value="99.0" /> |
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| 46 | <param name="evalue_cutoff" value="10.0" /> |
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| 47 | <param name="filter_query" value="T" /> |
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| 48 | <output name="output1" file="megablast_wrapper_test1.out"/> |
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| 49 | </test> |
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| 50 | </tests> |
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| 51 | <help> |
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| 52 | |
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| 53 | .. class:: warningmark |
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| 54 | |
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| 55 | **Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. |
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| 56 | |
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| 57 | ----- |
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| 58 | |
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| 59 | **What it does** |
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| 60 | |
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| 61 | 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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| 62 | |
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| 63 | ----- |
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| 64 | |
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| 65 | **Output format** |
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| 66 | |
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| 67 | Output of this tool contains 13 columns delimited by Tabs: |
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| 68 | |
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| 69 | 1. Id of your sequence |
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| 70 | 2. GI of the database hit |
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| 71 | 3. Length of the database hit |
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| 72 | 4. % identity |
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| 73 | 5. Alignment length |
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| 74 | 6. # mismatches |
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| 75 | 7. # gaps |
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| 76 | 8. Start position in your sequence |
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| 77 | 9. End position in your sequence |
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| 78 | 10. Start position in database hit |
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| 79 | 11. End position in database hit |
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| 80 | 12. E-value |
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| 81 | 13. Bit score |
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| 82 | |
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| 83 | ------- |
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| 84 | |
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| 85 | **Reference** |
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| 86 | |
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| 87 | Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214. |
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| 88 | |
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| 89 | </help> |
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| 90 | </tool> |
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