|
2
|
1 <tool id="cnv_sim" name="Simulate CNV" version="0.9.0">
|
|
|
2 <description>in NGS short reads </description>
|
|
|
3 <command interpreter="python" detect_errors="exit_code">
|
|
|
4 #if $type.simulation_type=="whole_genome"
|
|
|
5 cnv-sim.py genome $reference
|
|
|
6 #else
|
|
|
7 cnv-sim.py exome $reference $target
|
|
|
8 #end if
|
|
|
9 </command>
|
|
|
10 <inputs>
|
|
|
11 <conditional name="type">
|
|
|
12 <param name="simulation_type" type="select" label="Simulation Type">
|
|
|
13 <option value="whole_genome">CNV Simulation in Whole Genome</option>
|
|
|
14 <option value="whole_exome">CNV Simulation in Exome Regions</option>
|
|
|
15 </param>
|
|
|
16 <when value="whole_genome">
|
|
|
17 <param format="fasta" name="reference" type="data" label="Reference Genome"/>
|
|
|
18 </when>
|
|
|
19 <when value="whole_exome">
|
|
|
20 <param format="fasta" name="reference" type="data" label="Reference Genome"/>
|
|
|
21 <param format="bed" name="target" type="data" label="Target Regions"/>
|
|
|
22 </when>
|
|
|
23 </conditional>
|
|
|
24 </inputs>
|
|
|
25 <outputs>
|
|
|
26 <data format="bed" name="cnv_list" from_work_dir="test/CNVList.bed"/>
|
|
|
27 </outputs>
|
|
|
28 <help>
|
|
|
29 This tool generates artificial NGS short reads in FASTQ format afficted by Copy Number Variations.
|
|
|
30 </help>
|
|
|
31 </tool> |
