Mercurial > repos > drosofff > msp_blastparser_and_hits

comparison BlastParser_and_hits.xml @ 10:ddebfe3fb11a draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 1863d04c44d7bf6386624e76263ec27e61d1e632
author drosofff
date Fri, 05 Feb 2016 05:45:52 -0500
parents d1c1a8c380af
children 77346ecf5a28
comparison
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9:d1c1a8c380af 10:ddebfe3fb11a
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" />