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1 <?xml version="1.0"?>
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2 <tool id="edu.tamu.cpt.gff3.remove_annots" name="Remove Annotation Feature" version="19.1.0.1" profile="16.04">
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3 <description>that's unused in our GFF tools</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>cpt-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"><![CDATA[
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10 python $__tool_directory__/remove_annotations.py
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11 $gff3_data
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12 $remark
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13 $region
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14 > $default]]></command>
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15 <inputs>
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16 <expand macro="gff3_input" />
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17 <param checked="true" label="Remove 'remark' features" name="remark" type="boolean" truevalue="--remark" falsevalue="" />
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18 <param checked="true" label="Remove 'region' features" name="region" type="boolean" truevalue="--region" falsevalue="" />
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19 </inputs>
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20 <outputs>
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21 <data format="gff3" name="default"/>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="gff3_data" value="RemoveAnnote_In.gff3" />
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26 <param name="remark" value="--remark" />
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27 <param name="region" value= "--region" />
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28 <output name="default" file="RemoveAnnote_Out.gff3" />
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29 </test>
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30 </tests>
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31 <help><![CDATA[
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32 **What it does**
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33
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34 For an input GFF3, this tool specifically removes the feature entry with remark and/or region type (column 3) as needed for compatibility
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35 with certain tools. These feature typically encompasses the entire length of the sequence upon which the GFF3 is based.
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36
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37 Example input:
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38 Miro annotation remark 1 167935 . . . gff-version=3;sequence-region=%28%27Miro%27%2C 0%2C 172788%29
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39
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40 Miro cpt gene 1231 5436 . . . ID=CDS1;
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41
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42 Example output:
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43 Miro cpt gene 1231 5436 . . . ID=CDS1;
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44
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45
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46 ]]></help>
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47 <expand macro="citations" />
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48 </tool>
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