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1 <tool id="VarAmpliCNV_Anno" name="Annotate Amplicons" version="0.1.0" python_template_version="3.5">
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2 <requirements>
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3 <container type="docker">cmgantwerpen/varamplicnv:1.0.0</container>
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4
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 processAmpliconRegion.py
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8
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9 ## input amplicon file
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10 -a '$AmpInput'
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11
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12 ## ROI input
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13 -r '$roiInput'
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14
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15 ## snpInput (probes to discard)
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16 #if $snpInput
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17 -s $snpInput
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18 #end if
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19
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20 ## output files
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21 -D '$dedupOut'
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22 -R '$roiOut'
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23
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24
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25 ]]></command>
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26 <inputs>
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27 <param name="AmpInput" type="data" format="bed" optional="false" label="Amplicon Design File (BED)" help="This file is the HaloPlex design file, containing individual amplicons." />
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28 <param name="roiInput" type="data" format="bed" optional="false" label="ROI file (BED)" help="Region of Interest definition. Typically one line per Exon of the target genes bis." />
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29 <param name="snpInput" type="data" format="bed" optional="true" label="Ignore List (BED)" help="A subset of amplicons you do not want to analyze (e.g. a co-enriched panel)." />
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30 </inputs>
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31 <outputs>
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32 <data name="dedupOut" format="bed" label="VarAmpliCNV on ${on_string}: DeDuplicated Amplicon List" />
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33 <data name="roiOut" format="bed" label="VarAmpliCNV on ${on_string}: ROI-Annotated Amplicon List" />
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34 </outputs>
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35 <help>
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36 **VarAmpliCNV : BED file PreProcessing**
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37
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38 Preprocessing includes removing SNP (unwanted amplicons) coordinates and duplicate coordinates. It also adds Region annotations to input region of interest (ROI) used during plotting.
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39
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40 **Parameters are :**
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41
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42 * Amplicon Design File (BED) : This is the *exact* BED file provided by HaloPlex, containing the restriction fragments.
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43 * ROI file (BED) : Typically the file provided *to* HaloPlex as the basis of the design. Names in column 4 are used to annotate CNV plots
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44 * Ignore list (BED) : (optional) Provide amplicons present in amplicon design, to exclude during the analysis
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45
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46 **Output files :**
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47
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48 * DeDuplicated amplicon List (BED) : Use this file in subsequent steps (GC and Counting).
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49 * ROI-Annotated List : This file is needed during CNV-calling.
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50 </help>
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51 </tool>
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