Mercurial > repos > drosofff > msp_blastparser_and_hits

comparison BlastParser_and_hits.xml @ 2:e0985bad7b92 draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Fri, 19 Jun 2015 12:53:52 -0400
parents 3959a271cf3f
children 22641bb68b91
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1:958e769c1c86 2:e0985bad7b92
1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.0.0"> 1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.1.0">
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 </command> 12 </command>
12 <inputs> 13 <inputs>
13 <param name="sequences" type="data" format="fasta" label="fasta sequences that have been blasted" /> 14 <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="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 <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>
16 </inputs> 21 </inputs>
17 <outputs> 22 <outputs>
18 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/> 23 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
19 <data name="fastaOutput" format="fasta" label="hits"/> 24 <data name="fastaOutput" format="fasta" label="hits"/>
20 </outputs> 25 </outputs>
22 <tests> 27 <tests>
23 <test> 28 <test>
24 <param ftype="fasta" name="sequences" value="input.fa" /> 29 <param ftype="fasta" name="sequences" value="input.fa" />
25 <param ftype="tabular" name="blast" value="blast.tab" /> 30 <param ftype="tabular" name="blast" value="blast.tab" />
26 <param name="flanking" value="5" /> 31 <param name="flanking" value="5" />
32 <param name="mode" value="verbose" />
27 <output name="tabularOutput" ftype="tabular" file="output.tab" /> 33 <output name="tabularOutput" ftype="tabular" file="output.tab" />
28 <output name="fastaOutput" ftype="fasta" file="output.fa" /> 34 <output name="fastaOutput" ftype="fasta" file="output.fa" />
29 </test> 35 </test>
30 </tests> 36 </tests>
31 37
34 **What it does** 40 **What it does**
35 41
36 Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly 42 Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly
37 43
38 </help> 44 </help>
39 <test>
40 </test>
41
42 </tool> 45 </tool>