Mercurial > repos > devteam > megablast_wrapper
annotate megablast_wrapper.xml @ 1:b2c29f4b6b6c draft default tip
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:25:15 -0400 |
| parents | fb0d744e32fa |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="megablast_wrapper" name="Megablast" version="1.2.0"> |
| 2 <description> compare short reads against htgs, nt, and wgs databases</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.2.26+">blast+</requirement> | |
| 5 <requirement type="package" version="0.7.1">bx-python</requirement> | |
| 6 </requirements> | |
| 7 <command interpreter="python"> | |
| 8 megablast_wrapper.py | |
| 9 --db_build="${source_select.fields.path}" | |
| 10 --input=$input_query | |
| 11 --word_size=$word_size | |
| 12 --identity_cutoff=$iden_cutoff | |
| 13 --eval_cutoff=$evalue_cutoff | |
| 14 --filter_query=$filter_query | |
| 15 --index_dir=${GALAXY_DATA_INDEX_DIR} | |
| 16 --output=$output1 | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param name="input_query" type="data" format="fasta" label="Compare these sequences"/> | |
| 20 <param name="source_select" type="select" display="radio" label="against target database"> | |
| 21 <options from_data_table="blastdb" /> | |
| 22 </param> | |
| 23 <param name="word_size" type="select" label="using word size" help="Size of best perfect match (-word_size)"> | |
| 24 <option value="28">28</option> | |
| 25 <option value="16">16</option> | |
| 26 </param> | |
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b2c29f4b6b6c
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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changeset
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27 <param name="iden_cutoff" type="float" value="90.0" label="report hits above this identity (-perc_identity)" help="no cutoff if 0" /> |
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b2c29f4b6b6c
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
28 <param name="evalue_cutoff" type="float" value="0.001" label="set expectation value cutoff (-evalue)" /> |
| 0 | 29 <param name="filter_query" type="select" label="Filter out low complexity regions? (-dust)"> |
| 30 <option value="yes">Yes</option> | |
| 31 <option value="no">No</option> | |
| 32 </param> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 35 <data name="output1" format="tabular"/> | |
| 36 </outputs> | |
| 37 <tests> | |
| 38 <test> | |
| 39 <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/> | |
| 40 <!-- source_select needs to match the entry in the blastdb.loc file, which includes the last update date if appropriate --> | |
| 41 <param name="source_select" value="phiX" /> | |
| 42 <param name="word_size" value="28" /> | |
| 43 <param name="iden_cutoff" value="99.0" /> | |
| 44 <param name="evalue_cutoff" value="10.0" /> | |
| 45 <param name="filter_query" value="yes" /> | |
| 46 <output name="output1" file="megablast_wrapper_test1.out"/> | |
| 47 </test> | |
| 48 </tests> | |
| 49 <help> | |
| 50 | |
| 51 .. class:: warningmark | |
| 52 | |
| 53 **Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing. | |
| 54 | |
| 55 ----- | |
| 56 | |
| 57 **What it does** | |
| 58 | |
| 59 This tool runs **megablast** function of BLAST+ blastn tool - a high performance nucleotide local aligner developed by Webb Miller and colleagues. | |
| 60 | |
| 61 ----- | |
| 62 | |
| 63 **Output format** | |
| 64 | |
| 65 Output of this tool contains 13 columns delimited by Tabs: | |
| 66 | |
| 67 1. Id of your sequence | |
| 68 2. GI of the database hit | |
| 69 3. Length of the database hit | |
| 70 4. % identity | |
| 71 5. Alignment length | |
| 72 6. # mismatches | |
| 73 7. # gaps | |
| 74 8. Start position in your sequence | |
| 75 9. End position in your sequence | |
| 76 10. Start position in database hit | |
| 77 11. End position in database hit | |
| 78 12. E-value | |
| 79 13. Bit score | |
| 80 | |
| 81 ------- | |
| 82 | |
| 83 **Reference** | |
| 84 | |
| 85 Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214. | |
| 86 | |
| 87 </help> | |
| 88 </tool> |