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10
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1 <tool id="PileupVariant" name="PileupVariant" version="1.10">
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0
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2 <description>Keep only mpileup line with variant</description>
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3 <command interpreter="perl">
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10
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4 #if $exclude.do=="YES"
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5 PileupVariant.pl -input_pileup_file $input_pileup_file -input_exclusion_file $input_exclusion_file -log_file $log_file > $output_pileup_file
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6 #else
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7 PileupVariant.pl -input_pileup_file $input_pileup_file -log_file $log_file > $output_pileup_file
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8 #end if
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9
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0
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10 </command>
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11 <inputs>
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7
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12 <param name="input_pileup_file" type="data" format="pileup" label="Select a suitable input file from your history"/>
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10
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13 <conditional name="exclude">
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14 <param name="do" type="select" label="Exclude some position">
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15 <option value="NO">NO</option>
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16 <option value="YES">YES</option>
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17 </param>
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18 <when value="YES">
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19 <param name="input_exclusion_file" type="data" format="pileup" label="Select a suitable input file from your history"/>
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20 </when>
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21 <when value="NO">
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22
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23 </when>
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24 </conditional>
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0
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25 </inputs>
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26 <outputs>
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7
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27 <data name="output_pileup_file" format="pileup" label="${tool.name} on ${on_string}"/>
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28 <data name="log_file" format="txt" label="${tool.name} LOG on ${on_string}"/>
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0
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29 </outputs>
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30
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31 <help>
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32
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33
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34
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35 </help>
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36 </tool>
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