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1 <tool id="sixframe_translate" name="Generate 6-frame translation" 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>Translates DNA/RNA to protein</description>
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8
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9 <command>
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10 sixframe.rb $fasta_file -o $output $strip_header $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="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
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22 <param name="strip_header" type="boolean" label="Strip header info" help="" truevalue="--strip-header" falsevalue="" />
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23 <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--coords" falsevalue="" />
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24 </inputs>
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25
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26 <outputs>
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27 <data format="fasta" name="output" />
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28 </outputs>
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29
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30 <tests>
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31 <test>
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32 <param name="fasta_file" value="small_genome.fasta" format="fasta"/>
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33 <output name="output" format="fasta">
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34 <assert_contents>
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35 <has_text text="SVQHWFYRFQAGHPRVFCPKNGPRRLW" />
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36 </assert_contents>
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37 </output>
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38 </test>
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39 </tests>
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40
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41
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42 <help>
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43
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44 **What it does**
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45
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46 Generates 6 frame translations suitable for proteogenomics workflows
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47
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48 ----
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49
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50 **References**
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51
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52
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53 </help>
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54
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55 </tool>
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