Mercurial > repos > cpt > cpt_wig_rebase
annotate wig_rebase.xml @ 3:4451729a0a3b draft default tip
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author | cpt |
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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 '$wigFile' |
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12 |
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13 '$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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55 |
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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> |