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1 <tool id="proteindb_from_gff3" name="Extract proteins from gff3" version="1.0.1">
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2 <requirements>
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3 <requirement type="package" version="1.2.6">protk</requirement>
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4 </requirements>
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5
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6 <description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description>
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7
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8 <command>
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9 augustus_to_proteindb.rb $gff_file -o $output $coords
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10 </command>
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11
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12
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13
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14
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15 <stdio>
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16 <exit_code range="1:" level="fatal" description="Failure" />
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17 </stdio>
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18
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19 <inputs>
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20 <param name="gff_file" type="data" format="gff3" label="Augustus Generated gff3 File" />
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21 <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--info" falsevalue="" />
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22 </inputs>
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23
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24 <outputs>
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25 <data format="fasta" name="output" />
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26 </outputs>
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27
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28
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29 <help>
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30
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31 **What it does**
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32
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33 Extract proteins from gff3 and encode genomic coordinates in the fasta header.
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34 Currently this only works with gff3 generated using the Augustus gene finder
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35
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36 ----
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37
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38 **References**
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39
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40
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41 </help>
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42
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43 </tool>
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