Mercurial > repos > cpt > cpt_wig_rebase

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author cpt
date Fri, 05 Jan 2024 05:57:58 +0000
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1 <tool id="edu.tamu.cpt.wig.rebase" name="Rebase Wig Analysis Results" version="19.1.0.0">
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2 <description>against parent features</description>
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3 <macros>
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4 <import>macros.xml</import>
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5
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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 '$__tool_directory__/wig_rebase.py'
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10 '$parent'
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11 '$wigFile'
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13 '$protein2dna'
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14 --map_by "$map_by"
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15 > '$output']]></command>
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16 <inputs>
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17 <param label="Parent GFF3 annotations" name="parent" format="gff3" type="data"/>
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18 <param label="Wig Results" name="wigFile" format="wig" type="data"/>
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19 <param label="Map protein translated results to original DNA data" name="protein2dna" type="boolean" truevalue="--protein2dna" falsevalue=""/>
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20 <param label="Mapping Key" name="map_by" type="text" value="ID"/>
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21 </inputs>
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22 <outputs>
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23 <data format="wig" name="output"/>
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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="parent" value="T7_CLEAN.gff3"/>
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28 <param name="wigFile" value="T7_BW_I.wig"/>
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29 <param name="protein2dna" value="--protein2dna"/>
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30 <param name="map_by" value="ID"/>
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31 <output name="output" file="T7_BW_I_REBASE.wig"/>
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32 </test>
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33 <test>
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34 <param name="parent" value="tmhmm.parent.gff3"/>
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35 <param name="wigFile" value="tmhmm_m.wig"/>
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36 <param name="protein2dna" value="--protein2dna"/>
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37 <param name="map_by" value="ID"/>
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38 <output name="output" file="rebased_m.wig"/>
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42 **What it does**
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43
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44 Rebases wig results against a set of gff3 annotations which were involved in producing that data.
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45
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46 For example, imagine you take a gff3 file, and export the CDS sequences in
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47 order to analyse in TMHMM. Having done this, you want to view the associated
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48 Wig files in JBrowse with your TMHMM results. This tool will re-map the wig
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49 data to the correct location in the parent genome.
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50
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51 E.g. Given
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52
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53 - A feature (gp01) runs from 2000-2200
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54 - A wig file with data from 1-200
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56 The data would be re-mapped and you would receive a wig file with data from 2000-2200.
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57 ]]></help>
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58 <expand macro="citations"/>
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59 </tool>