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1 <?xml version="1.0"?>
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2 <tool id="edu.tamu.cpt2.util.glimmer3_to_gff3" name="Glimmer3 to GFF3" version="19.1.0.0">
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3 <description>convert formats</description>
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4 <macros>
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5 <import>cpt-macros.xml</import>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="aggressive">
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10 @GENOME_SELECTOR_PRE@
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11
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12 python $__tool_directory__/cpt_convert_glimmer_to_gff3.py
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13 $glimmer
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14 @GENOME_SELECTOR@
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15 > $data
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16 </command>
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17 <inputs>
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18 <param label="Glimmer Output" name="glimmer" type="data" format="tabular,txt"/>
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19 <expand macro="genome_selector" />
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20 </inputs>
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21 <outputs>
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22 <data format="gff3" name="data">
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23 </data>
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="reference_genome_source" value="history" />
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28 <param name="genome_fasta" value="ConvGlim_In.fasta" />
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29 <param name="glimmer" value="ConvGlim_In.out" />
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30 <output name="data" file="ConvGlim_Out.gff3" />
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31 </test>
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32 </tests>
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33 <help>
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34 **What it does**
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35
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36 Converts an input Glimmer3 table to the GFF3 format. If the Glimmer3 output indicates a gene wrapping
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37 around over the sequence boundary (as if circular) then it will only convert the upstream fragment and
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38 label it as "_truncated" in the resulting GFF.
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39 </help>
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40 <expand macro="citations" />
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41 </tool>
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