Mercurial > repos > drosofff > msp_blastparser_and_hits

annotate BlastParser_and_hits.xml @ 0:3959a271cf3f draft

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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">
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2 <description>for virus discovery</description>
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3 <requirements></requirements>
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4 <command interpreter="python">
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5 BlastParser_and_hits.py
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6 --sequences $sequences
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7 --blast $blast
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8 --tabularOutput $tabularOutput
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9 --fastaOutput $fastaOutput
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10 --flanking $flanking
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11 </command>
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12 <inputs>
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13 <param name="sequences" type="data" format="fasta" label="fasta sequences that have been blasted" />
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14 <param name="blast" type="data" format="tabular" label="The blast output you wish to parse" />
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15 <param name="flanking" type="text" size="5" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/>
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16 </inputs>
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17 <outputs>
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18 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
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19 <data name="fastaOutput" format="fasta" label="hits"/>
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20 </outputs>
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21
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22 <tests>
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23 <test>
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24 <param ftype="fasta" name="sequences" value="input.fa" />
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25 <param ftype="tabular" name="blast" value="blast.tab" />
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26 <param name="flanking" value="5" />
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27 <output name="tabularOutput" ftype="tabular" file="output.tab" />
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28 <output name="fastaOutput" ftype="fasta" file="output.fa" />
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29 </test>
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30 </tests>
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31
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32 <help>
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33
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34 **What it does**
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35
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36 Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly
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37
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38 </help>
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39 <test>
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40 </test>
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41
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42 </tool>