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1 <tool id="protgenerator" name="Protein Generator" version="0.0.1">
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2 <description>Protein Generator</description>
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3 <command interpreter="bash">
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4 protein_generator.sh protein_generator.jar
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5 -d "$databasename"
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6 -f "$genomeFile"
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7 #if $GlimmerFile
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8 -g "$GlimmerFile"
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9 #end if
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10 #if $SplitInterval
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11 -i "$SplitInterval"
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12 #end if
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13 -o "$output1"
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14 #if $condition1.gffFile == "yes"
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15 -p "$output2"
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16 #end if
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17 #if $condition2.accessionFile == "yes"
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18 -q "$output3"
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19 #end if
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20 #if $trans_tab_file
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21 -t "$trans_tab_file"
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22 #end if
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23 </command>
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24 <inputs>
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25 <param name="databasename" type="text" label="Database name" />
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26 <param name="genomeFile" type="data" format="faa" label="Select genome file" help="Genome file in gff format" />
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27
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28 <param name="GlimmerFile" type="data" format="txt" label="Select Glimmer File" help="Glimmer txt file. Can't be used with the Split Interval" optional="true" />
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29 <param name="SplitInterval" type="integer" label="Size of the intervals" help="Size of the intervals (number of codons) into which the genome will be split. Can't be used with the Glimmer File" optional="true" />
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30
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31 <param name="trans_tab_file" type="data" format="txt" label="Select Translation Table File" help="File containing a mapping of codons to amino acids, in the format used by NCBI." optional="true" />
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32 <conditional name="condition1">
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33 <param name="gffFile" type="select" help="write the GFF file">
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34 <option value="yes" selected="True">Yes</option>
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35 <option value="no" selected="False">No</option>
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36 </param>
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37 </conditional>
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38 <conditional name="condition2">
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39 <param name="accessionFile" type="select" label="Accession File" help="Write the accession file">
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40 <option value="yes" selected="True">Yes</option>
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41 <option value="no" selected="False">No</option>
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42 </param>
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43 </conditional>
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44 </inputs>
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45 <outputs>
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46 <data format="sam" name="output1" />
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47 <data format="gff" name="output2" label="GFF file">
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48 <filter>condition1['gffFile'] == "yes"</filter>
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49 </data>
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50 <data format="txt" name="output3" label="Accession File">
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51 <filter>condition2['accessionFile'] == "yes"</filter>
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52 </data>
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53 </outputs>
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54 <help>
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55 </help>
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56 </tool>
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