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1 <tool id="edu.tamu.cpt.gff3.require_sd" name="Gff3 Filter: Require SD" version="19.1.0.0">
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2 <description>ensures CDSs have an SD</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>cpt-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 @GENOME_SELECTOR_PRE@
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10
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11 python $__tool_directory__/gff3_require_sd.py
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12
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13 @GENOME_SELECTOR@
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14 @INPUT_GFF@
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15
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16 > $stdout
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17
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18 ]]></command>
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19 <inputs>
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20 <expand macro="genome_selector" />
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21 <expand macro="gff3_input" />
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22 </inputs>
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23 <outputs>
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24 <data format="gff3" name="stdout" label="$gff3_data.name filtered for SD presence"/>
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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="reference_genome_source" value="history" />
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29 <param name="genome_fasta" value="T7_ReqSDIn.fasta" />
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30 <param name="gff3_data" value="T7_ReqSDIn.gff3" />
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31
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32 <output name="stdout" file="T7_ReqSDOut.gff3" />
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33 </test>
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34 <test>
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35 <param name="reference_genome_source" value="history" />
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36 <param name="genome_fasta" value="Miro_ReqSDIn.fa" />
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37 <param name="gff3_data" value="Miro_ReqSDIn.gff3" />
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38
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39 <output name="stdout" file="Miro_ReqSDOut.gff3" />
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 **What it does**
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44
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45 Ensures every CDS has an upstream Shine-Dalgarno site defined. ShineFind is used to add SD subfeatures to CDSs without one.
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46
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47 .. class:: warningmark
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48
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49 This tool removes non-CDS type features, and CDS features without an SD site (RBS features are ignored).
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50
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51 ]]></help>
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52 <expand macro="citations" />
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53 </tool>
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