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1 <tool id="cnvsim" name="Simulate CNV" version="0.9.2">
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8
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2 <description>in NGS short reads </description>
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3 <command interpreter="python" detect_errors="exit_code">
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4 #if $type.simulation_type=="whole_genome"
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5 cnv-sim.py -n $number_of_reads -l $read_length -g $regions_count -a $amplifications_percentage -d $deletions_percentage -cn_min $minimum_copy_number -cn_max $maximum_copy_number -r_min $minimum_region_length -r_max $maximum_region_length genome $reference
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8
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6 #else
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7 cnv-sim.py -n $number_of_reads -l $read_length -g $regions_count -a $amplifications_percentage -d $deletions_percentage -cn_min $minimum_copy_number -cn_max $maximum_copy_number -r_min $minimum_region_length -r_max $maximum_region_length exome $reference $target
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8
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8 #end if
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9 </command>
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10 <inputs>
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11 <conditional name="type">
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12 <param name="simulation_type" type="select" label="Simulation Type">
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12
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13 <option value="whole_genome">CNV Simulation in Whole Genome Sequencing</option>
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14 <option value="targeted_exome">CNV Simulation in Targeted Exome Sequencing</option>
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15 </param>
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16 <when value="whole_genome">
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17 <param format="fasta" name="reference" type="data" label="Reference Genome" help="Reference genome to generate reads from"/>
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18 </when>
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19 <when value="targeted_exome">
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20 <param format="fasta" name="reference" type="data" label="Reference Genome" help="Reference genome to generate reads from"/>
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21 <param format="bed" name="target" type="data" label="Target Regions" help="a list of exonic regions"/>
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22 </when>
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23 </conditional>
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24 <param name="number_of_reads" type="integer" value="100000" label="Number of Reads" help="determines the number of reads to be generated for the control and simulated CNV (approximately)"/>
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25 <param name="read_length" type="integer" value="100" label="Read Length (bp)" help="determines the read length fot the generated FASTQ files"/>
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26
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27 <param name="regions_count" type="integer" value="30" label="Regions Count" help="determines how many randomly-generated regions will show CNVs"/>
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28 <param name="minimum_region_length" type="integer" value="1000" label="Minimum Region Length" help="Minimum length of each CNV region"/>
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29 <param name="maximum_region_length" type="integer" value="100000" label="Maximum Region Length" help="Minimum length of each CNV region"/>
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30 <param name="amplifications_percentage" type="float" value="0.5" label="Percentage of amplifications" help="determines what fraction of the regions will show amplifications (range: 0.0-1.0)"/>
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31 <param name="deletions_percentage" type="float" value="0.5" label="Percentage of deletions" help="determines what fraction of the regions will show deletions (range: 0.0-1.0)"/>
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32 <param name="minimum_copy_number" type="integer" value="3" label="Variation minimum" help="determines the minumum number of amplifications/deletions introduced in each region"/>
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33 <param name="maximum_copy_number" type="integer" value="10" label="Variation maximum" help="determines the maximum number of amplifications/deletions introduced in each region"/>
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34
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35 </inputs>
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36 <outputs>
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37 <data format="bed" name="cnv_list" from_work_dir="simulation_output/copynumber.bed" label="CNV List from ${tool.name} on ${on_string}"/>
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38 <data format="fastq" name="control_1" from_work_dir="simulation_output/control_1.fastq" label="Control reads 1 from ${tool.name} on ${on_string}"/>
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39 <data format="fastq" name="control_2" from_work_dir="simulation_output/control_2.fastq" label="Control reads 2 from ${tool.name} on ${on_string}"/>
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40 <data format="fastq" name="cnv_1" from_work_dir="simulation_output/cnv_1.fastq" label="CNV reads 1 from ${tool.name} on ${on_string}"/>
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41 <data format="fastq" name="cnv_2" from_work_dir="simulation_output/cnv_2.fastq" label="CNV reads 2 from ${tool.name} on ${on_string}"/>
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42 </outputs>
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43 <help><![CDATA[
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44 .. class:: infomark
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45 '''TIP''' This tool requires *fasta* format.
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46 ----
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47 **CNV Simulator**
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48 In genomics, Copy Number Variations (CNVs) is a type of structural variation in a genome where sections of the genome are duplicated or deleted. The number of variations (duplications/deletions) varies between individuals in the human population.
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49
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50 The Copy Number Variation Simulator (CNV-Sim) is a simulation tool that extends the functionality of existing next-generation sequencing read simulators to introduce copy number variations in the generated reads. The resulting reads encompass amplifications as well as deletions according to a predefined list of variant regions.
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51
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52 CNV-Sim aids testing and benchmarking tools for copy number variation detection and analysis. The tool offers two types of simulation:
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53
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54 CNV-Sim offers two types of simulation:
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55 1. CNV simulation in whole genome. CNV-Sim utilizes the functionality of ART to introduce variations in the genome.
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56 2. CNV simulation in targeted exome. CNV-Sim utilizes the functionality of Wessim to introduce variations in the targets.
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57
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58 Homepage: http://nabavilab.github.io/CNV-Sim/
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59 ]]></help>
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60 </tool> |
