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comparison BlastParser_and_hits.xml @ 0:3959a271cf3f draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Tue, 09 Jun 2015 04:15:34 -0400
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1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.0.0">
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 </command>
12 <inputs>
13 <param name="sequences" type="data" format="fasta" label="fasta sequences that have been blasted" />
14 <param name="blast" type="data" format="tabular" label="The blast output you wish to parse" />
15 <param name="flanking" type="text" size="5" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/>
16 </inputs>
17 <outputs>
18 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
19 <data name="fastaOutput" format="fasta" label="hits"/>
20 </outputs>
21
22 <tests>
23 <test>
24 <param ftype="fasta" name="sequences" value="input.fa" />
25 <param ftype="tabular" name="blast" value="blast.tab" />
26 <param name="flanking" value="5" />
27 <output name="tabularOutput" ftype="tabular" file="output.tab" />
28 <output name="fastaOutput" ftype="fasta" file="output.fa" />
29 </test>
30 </tests>
31
32 <help>
33
34 **What it does**
35
36 Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly
37
38 </help>
39 <test>
40 </test>
41
42 </tool>