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1 <tool id="gff3_to_fasta" name="Extract proteins from gff3" version="1.1.0">
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2 <requirements>
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3 <container type="docker">iracooke/protk-1.4.1</container>
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4 <requirement type="package" version="1.4">protk</requirement>
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5 </requirements>
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6
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7 <description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description>
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8
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9 <command>
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10 augustus_to_proteindb.rb $gff_file -o $output $coords
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11 </command>
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12
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13
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14
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15
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16 <stdio>
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17 <exit_code range="1:" level="fatal" description="Failure" />
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18 </stdio>
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19
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20 <inputs>
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21 <param name="gff_file" type="data" format="gff3" label="Augustus Generated gff3 File" />
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22 <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--info" falsevalue="" />
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23 </inputs>
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24
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25 <outputs>
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26 <data format="fasta" name="output" />
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27 </outputs>
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28
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29 <tests>
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30 <!-- Just test that the tool runs and produces vaguely correct output -->
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31 <test>
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32 <param name="gff_file" value="augustus_sample.gff" format="gff3"/>
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33 <output name="output" file="augustus_sample.fasta" format="fasta"/>
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34 </test>
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35 </tests>
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36
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37
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38 <help>
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39
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40 **What it does**
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41
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42 Extract proteins from gff3 and encode genomic coordinates in the fasta header.
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43 Currently this only works with gff3 generated using the Augustus gene finder
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44
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45 ----
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46
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47 **References**
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48
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49
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50 </help>
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51
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52 </tool>
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