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1 <tool id="rtg_cgsim" name="Simulate CG reads">
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2 <description>with RTG cgsim</description>
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3 <command interpreter="bash">galaxy-rtg-wrapper.sh cgsim
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4 -t ${input.extra_files_path}
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5 #if $limit.sType == "numreads":
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6 -n $limit.n
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7 #else
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8 -c $limit.c
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9 #end if
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10 -m $m
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11 -M $M
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12 --seed $seed
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13 -o ${output.extra_files_path} >$output</command>
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14 <inputs>
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15
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16 <param name="input" type="data" format="rtg_sdf" label="Source SDF"/>
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17 <param name="m" type="integer" value="350" label="Minimum fragment length" help=""/>
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18 <param name="M" type="integer" value="500" label="Maximum fragment length" help=""/>
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19
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20 <conditional name="limit">
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21 <param name="sType" type="select" label="Select read limit">
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22 <option value="numreads">Fixed number of reads</option>
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23 <option value="coverage">Fixed coverage</option>
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24 </param>
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25 <when value="numreads">
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26 <param name="n" type="integer" value="1000" label="Number of reads" help="Total number of reads"/>
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27 </when>
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28 <when value="coverage">
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29 <param name="c" type="float" value="1" label="Coverage" help="Total coverage"/>
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30 </when>
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31 </conditional>
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32
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33 <param name="seed" type="integer" label="Seed" value="42" help="Seed for the random number generator"/>
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34 </inputs>
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35 <outputs>
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36 <data format="rtg_sdf" name="output" />
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37 </outputs>
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38
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39 <help>
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40 This tool creates an SDF containing randomly generated CG reads.
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41 </help>
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42
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43 </tool>
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