Mercurial > repos > cpt > cpt_gbk_to_5col
comparison gbk_to_five_col.xml @ 1:1bdd481d5c25 draft
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
| author | cpt |
|---|---|
| date | Mon, 05 Jun 2023 02:42:57 +0000 |
| parents | |
| children | 8f5f2142fc2b |
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| 0:66143811fe8a | 1:1bdd481d5c25 |
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| 1 <tool id="edu.tamu.cpt.genbank.GBKtoFiveCol" name="Genbank to Five Column Format" version="1.0"> | |
| 2 <description/> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 <import>cpt-macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <command detect_errors="aggressive"><![CDATA[ | |
| 9 'python $__tool_directory__/gbk_to_five_col.py' | |
| 10 "$file" | |
| 11 | |
| 12 > "$output" | |
| 13 | |
| 14 ]]></command> | |
| 15 <inputs> | |
| 16 <param label="GenBank file" name="file" type="data" format="genbank"/> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data format="tabular" name="output"> | |
| 20 </data> | |
| 21 </outputs> | |
| 22 <tests> | |
| 23 <test> | |
| 24 <param name="file" value="complex_feature_locs.gbk"/> | |
| 25 <output name="output" value="gbkto5col.tsv"/> | |
| 26 </test> | |
| 27 </tests> | |
| 28 <help> | |
| 29 Genbank Format to Five Column Format | |
| 30 ==================================== | |
| 31 | |
| 32 Output format is: | |
| 33 | |
| 34 >Feature ID | |
| 35 Line 1 | |
| 36 - Column 1: Start location (first nucleotide) of a feature | |
| 37 - Column 2: Stop location (last nucleotide) of a feature | |
| 38 - Column 3: Feature name (for example, 'CDS' or 'mRNA' or 'rRNA' or 'gene' or 'exon') | |
| 39 | |
| 40 Line2: | |
| 41 - Column 4: Qualifier name (for example, 'product' or 'number' or 'gene' or 'note') | |
| 42 - Column 5: Qualifier value | |
| 43 | |
| 44 Example Output:: | |
| 45 | |
| 46 >Feature contig00077 | |
| 47 0 22956 source | |
| 48 mol_type genomic DNA | |
| 49 organism AU1189 | |
| 50 11652 11326 CDS | |
| 51 11327 11158 | |
| 52 note tapemeasure frameshift chaperone | |
| 53 product P2 E' tapemeasure frameshift chaperone | |
| 54 gene gp14 | |
| 55 translation MNPIQSDAAAPDLQADAAAIATPAQDDPATHTLDTPLVRGTQTITSITLRKPKSGELRGVSLSDLVSLDVVALSKVLPRISSPMLTEADVASIDPADLVQLGGIFAGFFDAEGREIPTGLPDRVEDPMADIATVFGWTPPVMDAFSLAELMDWRERARVRAGAQ | |
| 56 11900 11599 CDS | |
| 57 11600 11408 | |
| 58 11910 11904 RBS | |
| 59 | |
| 60 </help> | |
| 61 <expand macro="citations"/> | |
| 62 </tool> |