Mercurial > repos > drosofff > msp_blastparser_and_hits
comparison BlastParser_and_hits.xml @ 11:77346ecf5a28 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e979a94ca761f94e6617b3e761bde5775846d2d8
| author | drosofff |
|---|---|
| date | Fri, 05 Feb 2016 09:40:00 -0500 |
| parents | ddebfe3fb11a |
| children | 80e4273db58d |
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| 10:ddebfe3fb11a | 11:77346ecf5a28 |
|---|---|
| 1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.4.2"> | 1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.4.3"> |
| 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 $sequences |
| 7 --blast "$blast" | 7 --blast $blast |
| 8 --tabularOutput "$tabularOutput" | 8 --tabularOutput $tabularOutput |
| 9 --fastaOutput "$fastaOutput" | 9 --fastaOutput $fastaOutput |
| 10 --flanking "$flanking" | 10 --flanking $flanking |
| 11 --mode "$mode" | 11 --mode $mode |
| 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" | 17 --filter_term_in "$additional_filters.filter_term_in" |
| 18 --filter_term_out "$additional_filters.filter_term_out" | 18 --filter_term_out "$additional_filters.filter_term_out" |
| 19 #end if | 19 #end if |
| 20 --al_sequences "$al_sequences" | 20 --al_sequences $al_sequences |
| 21 --un_sequences "$un_sequences" | 21 --un_sequences $un_sequences |
| 22 --dataset_name "$blast.element_identifier" | 22 --dataset_name "$blast.element_identifier" |
| 23 | 23 |
| 24 </command> | 24 </command> |
| 25 <inputs> | 25 <inputs> |
| 26 <param name="sequences" type="data" format="fasta" label="fasta sequences that have been blasted" /> | 26 <param name="sequences" type="data" format="fasta" label="fasta sequences that have been blasted" /> |