Mercurial > repos > drosofff > msp_blastparser_and_hits

comparison BlastParser_and_hits.xml @ 4:22641bb68b91 draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Mon, 29 Jun 2015 06:06:11 -0400
parents e0985bad7b92
children a941981a298c
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3:fa936e163bbd 4:22641bb68b91
1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.1.0"> 1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.2.0">
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.
13 #if $additional_filters.use_filters == "yes":
14 --filter_relativeCov $additional_filters.filter_relativeCov
15 --filter_maxScore $additional_filters.filter_maxScore
16 --filter_meanScore $additional_filters.filter_meanScore
17 #end if
18
12 </command> 19 </command>
13 <inputs> 20 <inputs>
14 <param name="sequences" type="data" format="fasta" label="fasta sequences that have been blasted" /> 21 <param name="sequences" type="data" format="fasta" label="fasta sequences that have been blasted" />
15 <param name="blast" type="data" format="tabular" label="The blast output you wish to parse" /> 22 <param name="blast" type="data" format="tabular" label="The blast output you wish to parse" />
16 <param name="flanking" type="text" size="5" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/> 23 <param name="flanking" type="text" size="5" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/>
17 <param name="mode" type="select" label="Verbose or short reporting mode" help="display or not the oases contigs"> 24 <param name="mode" type="select" label="Verbose or short reporting mode" help="display or not the oases contigs">
18 <option value="verbose" default="true">verbose</option> 25 <option value="verbose" default="true">verbose</option>
19 <option value="short">do not report oases contigs</option> 26 <option value="short">do not report oases contigs</option>
20 </param> 27 </param>
28 <conditional name="additional_filters">
29 <param name="use_filters" type="select" label="Use Additional Filters?">
30 <option value="no">No</option>
31 <option value="yes">Yes</option>
32 </param>
33 <when value="no">
34 </when>
35 <when value="yes">
36 <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/>
37 <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/>
38 <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/>
39 </when>
40 </conditional>
21 </inputs> 41 </inputs>
22 <outputs> 42 <outputs>
23 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/> 43 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
24 <data name="fastaOutput" format="fasta" label="hits"/> 44 <data name="fastaOutput" format="fasta" label="hits"/>
25 </outputs> 45 </outputs>