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annotate cpt_gbkToGff3.xml @ 1:bb6332a85aa6 draft

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author cpt
date Mon, 05 Jun 2023 02:43:04 +0000
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1 <tool id="edu.tamu.cpt.gff3.customGbkToGff" name="(CPT) Genbank to GFF3: " version="20.1.0.0">
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2 <description> CPT made Biobython-based solution</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 '$__tool_directory__/gbk_to_gff3.py'
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10 '$gbkIn'
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11 '$makeMRNA'
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12 '$makeGene'
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13 --identifier "$qualID"
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14 --fastaFile '$fastaOut'
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15 > '$default']]></command>
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16 <inputs>
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17 <param label="GenBank file" name="gbkIn" type="data" format="genbank"/>
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18 <param checked="true" label="Automatically generate any missing Gene features if CDS/RBS has none" name="makeGene" type="boolean" truevalue="--makeGene" falsevalue=""/>
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19 <param checked="true" label="Automatically generate missing mRNA features for genes" name="makeMRNA" type="boolean" truevalue="--makeMRNA" falsevalue=""/>
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20 <param label="Qualifier to derive GFF ID from" name="qualID" type="text" value="locus_tag"/>
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21 </inputs>
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22 <outputs>
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23 <data format="gff3" hidden="false" name="default"/>
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24 <data format="fasta" hidden="false" name="fastaOut"/>
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25 </outputs>
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26 <tests>
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27 </tests>
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28 <help><![CDATA[
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29 **What it does**
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30
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31 A Biopython-based script to convert Genbank files to GFF3. Should resolve frame shift errors and other problems caused by the old Bioperl solution.
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32
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33 Will also attempt to automatically parent RBS, CDS, and Exon features without a locus tag to an appropriate gene feature.
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34 ]]></help>
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35 <citations>
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36 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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37 <citation type="bibtex">
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38 @unpublished{galaxyTools,
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39 author = {A. Criscione},
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40 title = {CPT Galaxy Tools},
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41 year = {2019-2021},
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42 note = {https://github.com/tamu-cpt/galaxy-tools/}
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43 }
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44 </citation>
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45 </citations>
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46 </tool>