Mercurial > repos > cpt > cpt_gff_to_gbk

annotate gff2gb.xml @ 3:c8fcb7246ac3 draft

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author cpt
date Mon, 05 Jun 2023 02:44:32 +0000
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1 <tool id="edu.tamu.cpt.gff.gff2gb" name="GFF3 to GenBank" version="4.0">
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2 <description>convert gff3 to GenBank</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>cpt-macros.xml</import>
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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 @GENOME_SELECTOR_PRE@
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10
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11 'python $__tool_directory__/gff2gb.py'
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12 @INPUT_GFF@
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13 @INPUT_FASTA@
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14 --transltbl '$transltbl'
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15 > '$output']]></command>
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16 <inputs>
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17 <expand macro="input/gff3+fasta"/>
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18 <param label="Translation Table" name="transltbl" type="select">
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19 <option value="1">1. The Standard Code</option>
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20 <option value="2">2. The Vertebrate Mitochondrial Code</option>
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21 <option value="3">3. The Yeast Mitochondrial Code</option>
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22 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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23 <option value="5">5. The Invertebrate Mitochondrial Code</option>
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24 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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25 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
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26 <option value="10">10. The Euplotid Nuclear Code</option>
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27 <option value="11" selected="true">11. The Bacterial, Archaeal and Plant Plastid Code</option>
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28 <option value="12">12. The Alternative Yeast Nuclear Code</option>
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29 <option value="13">13. The Ascidian Mitochondrial Code</option>
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30 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
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31 <option value="16">16. Chlorophycean Mitochondrial Code</option>
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32 <option value="21">21. Trematode Mitochondrial Code</option>
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33 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
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34 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
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35 <option value="24">24. Pterobranchia Mitochondrial Code</option>
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36 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
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37 </param>
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38 </inputs>
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39 <outputs>
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40 <data format="genbank" hidden="false" name="output" label="${gff3_data.name} as GenBank"/>
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41 </outputs>
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42 <tests>
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43 <!-- There have been issues running the diffs for the files -->
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44 <!-- Going to use asserts and run ONE (or no) diffs -->
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45 <test>
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46 <!-- ORIGINAL TEST FILE, regenerated 10.12.2020 -->
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47 <param name="reference_genome_source" value="history"/>
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48 <param name="genome_fasta" value="miro.fa"/>
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49 <param name="gff3_data" value="miro.gff3"/>
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50 <output name="output" file="miro_from_tool.gbk" compare="sim_size" delta_frac="0.05">
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51 <assert_contents>
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52 <has_text text="RBS"/>
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53 <has_text text="gene"/>
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54 <has_text text="CDS"/>
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55 </assert_contents>
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56 </output>
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 .. class:: warningmark
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61
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62 This is a LOSSY conversion. This tool **TRUNCATES** genbank file identifiers if
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63 they are too long. Your data may not "match up" after processing through this
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64 tool.
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65
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66 **What it does**:
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67
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68 Convert gff3 data to genbank. There are many WebApollo specific conventions. A re-numbering is also done.
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69
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70 **Supported / Expected Data**
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71
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72 - gene / mRNA / (CDS, Exon)
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73 - gene / tRNA
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74 - terminator
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75
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76 ]]></help>
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77 <expand macro="citations"/>
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78 </tool>