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comparison BlastParser_and_hits.xml @ 0:69ea2a13947f draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Sun, 21 Jun 2015 14:31:29 -0400
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1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.1.0">
2 <description>for virus discovery</description>
3 <requirements></requirements>
4 <command interpreter="python">
5 BlastParser_and_hits.py
6 --sequences $sequences
7 --blast $blast
8 --tabularOutput $tabularOutput
9 --fastaOutput $fastaOutput
10 --flanking $flanking
11 --mode $mode
12 </command>
13 <inputs>
14 <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" />
16 <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">
18 <option value="verbose" default="true">verbose</option>
19 <option value="short">do not report oases contigs</option>
20 </param>
21 </inputs>
22 <outputs>
23 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
24 <data name="fastaOutput" format="fasta" label="hits"/>
25 </outputs>
26
27 <tests>
28 <test>
29 <param ftype="fasta" name="sequences" value="input.fa" />
30 <param ftype="tabular" name="blast" value="blast.tab" />
31 <param name="flanking" value="5" />
32 <param name="mode" value="verbose" />
33 <output name="tabularOutput" ftype="tabular" file="output.tab" />
34 <output name="fastaOutput" ftype="fasta" file="output.fa" />
35 </test>
36 </tests>
37
38 <help>
39
40 **What it does**
41
42 Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly
43
44 </help>
45 </tool>