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1 <tool id="edu.tamu.cpt.gff3.lipoP_to_gff3" name= "LipoP to GFF3" version="1.0">
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2 <description>Adds LipoP results to GFF3</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 python $__tool_directory__/lipoP_to_gff3.py
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10
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11 "$lipoIn"
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12 "$gff3In"
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13 --jBrowseOut "$jBrowseOut"
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14 $filterSP2
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15 > $stdout
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16
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17 ]]></command>
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18 <inputs>
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19 <param label="LipoP Output" name="lipoIn" type="data" format="txt"/>
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20 <param label="GFF3 for Rebasing" name="gff3In" type="data" format="gff3"/>
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21 <param label="Output to jBrowse" name="jBrowseOut" type="boolean" truevalue="True" falsevalue="" help="Strip non-cleavage features from GFF3 (for viewing in Apollo)"/>
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22 <param name="filterSP2" truevalue="--filterSP2" falsevalue="" type="boolean" label="Filter for only SPII Cleavage sites" checked="true"/>
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23 </inputs>
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24 <outputs>
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25 <data format="gff3" name="stdout"/>
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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="lipoIn" value="LipoToGFF_In.txt" />
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30 <param name="gff3In" value="LipoToGFF_In.gff3" />
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31 <param name="jBrowseOut" value="True" />
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32 <param name="filterSP2" value="True" />
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33 <output name="stdout" value="LipoToGFF_Out.gff3" />
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 **What it does**
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38
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39 Adds the cleavage sites from a LipoP run to a GFF3 file's feature list. Must use
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40 the .txt output of LipoP (ensure .html is turned off). The most common way this
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41 tool will be utilized is to take a GFF3, use the GFF3 Feature Sequence Export
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42 tool (https://cpt.tamu.edu/galaxy/root?tool_id=edu.tamu.cpt.gff3.export_seq) to
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43 get a multi-FASTA of the CDSs, run that multi-FASTA through LipoP, and then
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44 recombine the LipoP results with the original GFF3 file with this tool.
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45
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46 Currently, only CleavII results will be added with this tool.
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47
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48 "Output to jBrowse" will remove all gene features that do not have a CleavII
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49 result from the LipoP, and remove all sub features of the gene except for the
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50 cleavage sites. This is useful for viewing in Apollo, but should most likely
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51 not be used if you plan to run this output through more tools.
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52 ]]></help>
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53 <expand macro="citations-2020" />
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54 </tool>
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