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date Fri, 05 Jan 2024 05:50:05 +0000
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1 <tool id="edu.tamu.cpt2.util.glimmer3_to_gff3" name="Glimmer3 to GFF3" version="19.1.0.0">
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2 <description>convert formats</description>
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3 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="3.9.16">python</requirement>
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9 <requirement type="package" version="1.2.2">cpt_gffparser</requirement>
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10 <requirement type="package" version="1.81">biopython</requirement>
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11 </expand>
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12 <command detect_errors="aggressive"><![CDATA[
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13 @GENOME_SELECTOR_PRE@
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14 python '$__tool_directory__/cpt_convert_glimmer_to_gff3.py'
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15 '$glimmer'
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16 @GENOME_SELECTOR@
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17 > '$data' ]]>
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18 </command>
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19 <inputs>
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20 <param label="Glimmer Output" name="glimmer" type="data" format="tabular,txt"/>
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21 <expand macro="genome_selector"/>
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22 </inputs>
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23 <outputs>
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24 <data format="gff3" name="data">
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25 </data>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="reference_genome_source" value="history"/>
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30 <param name="genome_fasta" value="ConvGlim_In.fasta"/>
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31 <param name="glimmer" value="ConvGlim_In.out"/>
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32 <output name="data" file="ConvGlim_Out.gff3"/>
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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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38 Converts an input Glimmer3 table to the GFF3 format. If the Glimmer3 output indicates a gene wrapping
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39 around over the sequence boundary (as if circular) then it will only convert the upstream fragment and
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40 label it as "_truncated" in the resulting GFF.
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41 </help>
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42 <expand macro="citations"/>
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43 </tool>