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comparison BlastParser_and_hits.xml @ 15:1991c830504a draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07
author drosofff
date Wed, 09 Nov 2016 11:32:32 -0500
parents 6dfa79a6908a
children 0e51eef139ab
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14:6dfa79a6908a 15:1991c830504a
1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.4.3"> 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><![CDATA[
5 BlastParser_and_hits.py 5 python '$__tool_directory__'/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" />
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" />
28 <param name="flanking" type="text" size="5" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/> 28 <param name="flanking" type="integer" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/>
29 <param name="mode" type="select" label="Extensive or compact reporting mode" help="display (extensive) or not (compact) the oases contigs"> 29 <param name="mode" type="select" label="Extensive or compact reporting mode" help="display (extensive) or not (compact) the oases contigs">
30 <option value="verbose" default="true">extensive</option> 30 <option value="verbose" selected="true">extensive</option>
31 <option value="short">compact</option> 31 <option value="short">compact</option>
32 </param> 32 </param>
33 <conditional name="additional_filters"> 33 <conditional name="additional_filters">
34 <param name="use_filters" type="select" label="Use Additional Filters?"> 34 <param name="use_filters" type="select" label="Use Additional Filters?">
35 <option value="no">No</option> 35 <option value="no">No</option>