Mercurial > repos > drosofff > msp_blastparser_and_hits
comparison BlastParser_and_hits.xml @ 4:60b6bd959929 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
| author | drosofff |
|---|---|
| date | Fri, 15 Jan 2016 12:29:30 -0500 |
| parents | 8f5d48294f70 |
| children | 78c34df2dd8d |
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| 3:8f5d48294f70 | 4:60b6bd959929 |
|---|---|
| 1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.3.2"> | 1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.3.3"> |
| 2 <description>for virus discovery</description> | 2 <description>for virus discovery</description> |
| 3 <requirements></requirements> | 3 <requirements></requirements> |
| 4 <command interpreter="python"> | 4 <command interpreter="python"> |
| 5 BlastParser_and_hits.py | 5 BlastParser_and_hits.py |
| 6 --sequences $sequences | 6 --sequences $sequences |
| 12 ## Additional parameters. | 12 ## Additional parameters. |
| 13 #if $additional_filters.use_filters == "yes": | 13 #if $additional_filters.use_filters == "yes": |
| 14 --filter_relativeCov $additional_filters.filter_relativeCov | 14 --filter_relativeCov $additional_filters.filter_relativeCov |
| 15 --filter_maxScore $additional_filters.filter_maxScore | 15 --filter_maxScore $additional_filters.filter_maxScore |
| 16 --filter_meanScore $additional_filters.filter_meanScore | 16 --filter_meanScore $additional_filters.filter_meanScore |
| 17 --filter_term_in "$additional_filters.filter_term_in" | |
| 18 --filter_term_out "$additional_filters.filter_term_out" | |
| 17 #end if | 19 #end if |
| 18 --al_sequences $al_sequences | 20 --al_sequences $al_sequences |
| 19 --un_sequences $un_sequences | 21 --un_sequences $un_sequences |
| 20 | 22 |
| 21 </command> | 23 </command> |
| 36 </when> | 38 </when> |
| 37 <when value="yes"> | 39 <when value="yes"> |
| 38 <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/> | 40 <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/> |
| 39 <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/> | 41 <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/> |
| 40 <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/> | 42 <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/> |
| 43 <param name="filter_term_in" type="text" value="" label="filter the subject list with a keyword" help=""/> | |
| 44 <param name="filter_term_out" type="text" value="" label="filter the subject list excluding a keyword" help=""/> | |
| 41 </when> | 45 </when> |
| 42 </conditional> | 46 </conditional> |
| 43 </inputs> | 47 </inputs> |
| 44 <outputs> | 48 <outputs> |
| 45 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/> | 49 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/> |