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1 <tool id="rtg_snpsim" name="Simulate SNPs">
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2 <description>with rtg snpsim</description>
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3 <command interpreter="bash">galaxy-rtg-snpsim-wrapper.sh ${output3} ${output3.extra_files_path} snpsim
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4 --seed $seed -i ${input.extra_files_path}
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5 -o ${output.extra_files_path}
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6 #if $str($diploid) == "true":
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7 -O ${output2.extra_files_path}
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8 #end if
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9 >$output</command>
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10 <inputs>
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11 <param name="input" type="data" format="rtg_sdf" label="SDF containing input genome"/>
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12 <param name="diploid" type="select" label="Generate diploid mutations">
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13 <option value="true">Yes</option>
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14 <option value="false" selected="true">No</option>
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15 </param>
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16 <param name="seed" type="integer" value="42" label="Seed" help="Seed for the random number generator"/>
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17 </inputs>
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18 <outputs>
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19 <data format="rtg_sdf" name="output" label="Mutated genome on data ${input.hid}"/>
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20 <data format="rtg_sdf" name="output2" label="Second mutated genome on data ${input.hid}">
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21 <filter>diploid == "true"</filter>
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22 </data>
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23 <data format="vcf" name="output3" label="SNPs file generated on data ${input.hid}" />
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24 </outputs>
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25
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26 <help>
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27 This tool creates a simulated mutation of a reference genome. Can generate either haploid or diploid mutations.
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28 </help>
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29
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30 </tool>
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