Mercurial > repos > drosofff > msp_blastparser_and_hits
comparison BlastParser_and_hits.xml @ 10:ddebfe3fb11a draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 1863d04c44d7bf6386624e76263ec27e61d1e632
author | drosofff |
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date | Fri, 05 Feb 2016 05:45:52 -0500 |
parents | d1c1a8c380af |
children | 77346ecf5a28 |
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9:d1c1a8c380af | 10:ddebfe3fb11a |
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1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.4.1"> | 1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.4.2"> |
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 $blast.name | 22 --dataset_name "$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" /> |
27 <param name="blast" type="data" format="tabular" label="The blast output you wish to parse" /> | 27 <param name="blast" type="data" format="tabular" label="The blast output you wish to parse" /> |