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author cpt
date Fri, 05 Jan 2024 05:57:42 +0000
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1 <tool id="edu.tamu.cpt.gff3.filter_type" name="GFF3 Feature Type Filter" version="19.1.0.0">
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2 <description>selects features from a gff3 file based on feature type</description>
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3 <macros>
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4 <import>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 #set repeat_data = '" "'.join([ str($var.type) for $var in $repeat_0 ])
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11 python '$__tool_directory__/filter_type.py'
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12 @INPUT_GFF@
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13 "$repeat_data"
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14 '$invert'
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15 > '$output']]></command>
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16 <inputs>
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17 <expand macro="gff3_input"/>
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18 <repeat name="repeat_0" title="Feature Types">
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19 <param label="Feature type" name="type" type="text"/>
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20 </repeat>
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21 <param checked="true" label="Invert the filter" name="invert" type="boolean" truevalue="--invert" falsevalue=""/>
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22 </inputs>
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23 <outputs>
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24 <data format="gff3" name="output"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="gff3_data" value="Miro_FilterIn.gff3"/>
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29 <param name="repeat_0_0|type" value="CDS"/>
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30 <param name="invert" value="False"/>
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31 <output name="output" file="Miro_FilterOut1.gff3"/>
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32 </test>
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33 <test>
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34 <param name="gff3_data" value="Miro_FilterIn.gff3"/>
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35 <param name="repeat_0_0|type" value="CDS"/>
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36 <param name="invert" value="--invert"/>
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37 <output name="output" file="Miro_FilterOut2.gff3"/>
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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41 **What it does**
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42
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43 The tool finds the specified feature type(s) in an input GFF3 and will output
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44 **only** the specified feature type. By selecting the inversion, **everything except**
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45 the specified feature type(s) will be included in the output GFF3.
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47 For example, user may output **only** ``Shine_Dalgarno_sequence`` type features, or,
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48 inverting that, output everything but ``Shine_Dalgarno_sequence`` type features. Any
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49 feature type used in the input GFF3 can be filtered; typical options would include gene,
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50 mRNA, CDS, tRNA, and terminator. The input name format must follow sequence ontology
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51 convention (http://www.sequenceontology.org/).
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52
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53 ]]></help>
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54 <expand macro="citations"/>
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55 </tool>