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comparison VarAmpliCNV_Anno.xml @ 1:5c324f9a4e20 draft default tip

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author geert-vandeweyer
date Fri, 25 Sep 2020 08:30:57 +0000
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0:febc6023d37b 1:5c324f9a4e20
1 <tool id="VarAmpliCNV_Anno" name="Annotate Amplicons" version="0.1.0" python_template_version="3.5">
2 <requirements>
3 <container type="docker">cmgantwerpen/varamplicnv:1.0.0</container>
4
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 processAmpliconRegion.py
8
9 ## input amplicon file
10 -a '$AmpInput'
11
12 ## ROI input
13 -r '$roiInput'
14
15 ## snpInput (probes to discard)
16 #if $snpInput
17 -s $snpInput
18 #end if
19
20 ## output files
21 -D '$dedupOut'
22 -R '$roiOut'
23
24
25 ]]></command>
26 <inputs>
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." />
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." />
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)." />
30 </inputs>
31 <outputs>
32 <data name="dedupOut" format="bed" label="VarAmpliCNV on ${on_string}: DeDuplicated Amplicon List" />
33 <data name="roiOut" format="bed" label="VarAmpliCNV on ${on_string}: ROI-Annotated Amplicon List" />
34 </outputs>
35 <help>
36 **VarAmpliCNV : BED file PreProcessing**
37
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.
39
40 **Parameters are :**
41
42 * Amplicon Design File (BED) : This is the *exact* BED file provided by HaloPlex, containing the restriction fragments.
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
44 * Ignore list (BED) : (optional) Provide amplicons present in amplicon design, to exclude during the analysis
45
46 **Output files :**
47
48 * DeDuplicated amplicon List (BED) : Use this file in subsequent steps (GC and Counting).
49 * ROI-Annotated List : This file is needed during CNV-calling.
50 </help>
51 </tool>