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author cpt
date Fri, 05 Jan 2024 05:51:38 +0000
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1 <tool id="edu.tamu.cpt.genbank.GBKtoFiveCol" name="Genbank to Five Column Format" version="1.0">
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2 <description/>
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3 <macros>
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4 <import>macros.xml</import>
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5
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 'python $__tool_directory__/gbk_to_five_col.py'
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10 "$file"
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11
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12 > "$output"
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13
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14 ]]></command>
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15 <inputs>
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16 <param label="GenBank file" name="file" type="data" format="genbank"/>
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17 </inputs>
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18 <outputs>
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19 <data format="tabular" name="output">
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20 </data>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="file" value="complex_feature_locs.gbk"/>
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25 <output name="output" value="gbkto5col.tsv"/>
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26 </test>
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27 </tests>
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28 <help>
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29 Genbank Format to Five Column Format
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30 ====================================
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31
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32 Output format is:
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33
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34 &gt;Feature ID
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35 Line 1
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36 - Column 1: Start location (first nucleotide) of a feature
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37 - Column 2: Stop location (last nucleotide) of a feature
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38 - Column 3: Feature name (for example, 'CDS' or 'mRNA' or 'rRNA' or 'gene' or 'exon')
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39
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40 Line2:
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41 - Column 4: Qualifier name (for example, 'product' or 'number' or 'gene' or 'note')
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42 - Column 5: Qualifier value
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43
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44 Example Output::
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45
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46 &gt;Feature contig00077
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47 0 22956 source
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48 mol_type genomic DNA
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49 organism AU1189
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50 11652 11326 CDS
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51 11327 11158
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52 note tapemeasure frameshift chaperone
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53 product P2 E' tapemeasure frameshift chaperone
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54 gene gp14
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55 translation MNPIQSDAAAPDLQADAAAIATPAQDDPATHTLDTPLVRGTQTITSITLRKPKSGELRGVSLSDLVSLDVVALSKVLPRISSPMLTEADVASIDPADLVQLGGIFAGFFDAEGREIPTGLPDRVEDPMADIATVFGWTPPVMDAFSLAELMDWRERARVRAGAQ
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56 11900 11599 CDS
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57 11600 11408
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58 11910 11904 RBS
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59
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60 </help>
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61 <expand macro="citations"/>
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62 </tool>