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1 <tool id="trips_create_annotation" name="Create TRIPS-Viz annotation" version="1.0">
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0
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2 <description>Covert GFF3/GTF and transcriptome FASTA to custom annotation sqlite</description>
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3 <requirements>
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4 <requirement type="package" version="0.19.0">pysam</requirement>
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5 <requirement type="package" version="2.0.0">sqlitedict</requirement>
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6 <requirement type="package" version="3.37.1">sqlite</requirement>
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7 <requirement type="package" version="3.0.2">intervaltree</requirement>
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0
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8
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9 </requirements>
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10 <command><![CDATA[
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11 python $__tool_directory__/create_annotation_sqlite.py ${input1} ${input2} ${input3} ${input4} ${input5} ${input6}
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12 ]]></command>
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13 <inputs>
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14 <param name="input1" type="text" label="Transcriptome name" />
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15 <param name="input2" type="data" format="gff" label="Transcriptome Annotation file (GFF/GTF)" />
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16 <param name="input3" type="data" format="fasta" label="Transcriptome FASTA File" />
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17 <param name="input4" type="integer" value="0" label="Psuedo UTR length" help="This value will be added used to create UTRs of this length. This is useful when looking at transcriptomes without annotated UTRs"/>
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18 <param name="input5" type="text" label="Transcript ID" help="An example of a transcript_id from the annotation file, e.g ENST000000123456.1"/>
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19 <param name="input6" type="text" label="Gene Name" help="An example of a gene name from the annotation file" />
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20 </inputs>
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21 <outputs>
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22 <data name="output1" format="sqlite"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input1" value="test_org" ftype="text"/>
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27 <param name="input2" value="test.gtf" ftype="gff"/>
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28 <param name="input3" value="test.fasta" ftype="fasta"/>
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29 <param name="input4" value="0" ftype="integer"/>
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30 <param name="input5" value="YDL248W" ftype="text"/>
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31 <param name="input6" value="YDL248W" ftype="text"/>
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32 <output name="output1" file="test_org.sqlite" ftype="sqlite" lines_diff="4" />
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33 </test>
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34 </tests>
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35 <help>
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36 **What it does**
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37
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38 Builds a custom transcirptome annoatation stored in sqlite format for you organism.
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39 </help>
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40 <citations/>
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41 </tool>
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42
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