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1 <tool id="rtg_readsim" name="Simulate reads">
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2 <description>with RTG readsim</description>
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3 <command interpreter="bash">galaxy-rtg-wrapper.sh readsim
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4 -t ${input.extra_files_path}
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5 #if str($input2) != "None":
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6 -T ${input2.extra_files_path}
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7 #end if
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8 #if $limit.sType == "numreads":
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9 -n $limit.n
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10 #else
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11 -c $limit.c
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12 #end if
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13 -m $m
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14 -M $M
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15 --machine $machine.sMachine
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16 #if $machine.sMachine == "illumina_se":
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17 -r $machine.r
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18 #else if $machine.sMachine == "illumina_pe":
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19 -L $machine.L
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20 -R $machine.R
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21 #else if $machine.sMachine == "454_pe":
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22 --454-min-total-size $machine.454-min
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23 --454-max-total-size $machine.454-max
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24 #end if
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25 --seed $seed
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26 -o ${output.extra_files_path} >$output</command>
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27 <inputs>
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28
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29 <param name="input" type="data" format="rtg_sdf" label="SDF containing input genome"/>
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30 <param name="input2" type="data" format="rtg_sdf" label="SDF with second genome for simulating diploid genomes" optional="true" />
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31 <param name="m" type="integer" value="200" label="Minimum fragment length" help="Total number of reads"/>
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32 <param name="M" type="integer" value="400" label="Minimum fragment length" help="Total number of reads"/>
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33
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34 <conditional name="limit">
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35 <param name="sType" type="select" label="Select read limit">
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36 <option value="numreads">Fixed number of reads</option>
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37 <option value="coverage">Fixed coverage</option>
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38 </param>
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39 <when value="numreads">
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40 <param name="n" type="integer" value="1000" label="Number of reads" help="Total number of reads"/>
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41 </when>
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42 <when value="coverage">
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43 <param name="c" type="float" value="1" label="Coverage" help="Total coverage"/>
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44 </when>
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45 </conditional>
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46
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47 <conditional name="machine">
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48 <param name="sMachine" type="select" label="Select machine type">
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49 <option value="illumina_pe">Illumina paired-end</option>
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50 <option value="illumina_se">Illumina single-end</option>
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51 <option value="454_pe">454 paired-end</option>
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52 </param>
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53 <when value="illumina_se">
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54 <param name="r" type="integer" value="100" label="Read length" help="Target read length on left side"/>
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55 </when>
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56 <when value="illumina_pe">
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57 <param name="L" type="integer" value="100" label="Left read length" help="Target read length on left side"/>
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58 <param name="R" type="integer" value="100" label="Right read length" help="Target read length on right side"/>
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59 </when>
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60 <when value="454_pe">
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61 <param name="454-min" type="integer" value="500" label="Minimum total length" help="Minimum sum of left and right read lengths"/>
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62 <param name="454-max" type="integer" value="300" label="Maximum total length" help="Maximum sum of left and right read lengths"/>
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63 </when>
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64 </conditional>
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65 <param name="seed" type="integer" value="42" label="Seed" help="Seed for the random number generator"/>
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66 </inputs>
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67 <outputs>
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68 <data format="rtg_sdf" name="output" />
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69 </outputs>
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70
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71 <help>
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72 This tool creates an SDF containing randomly generated reads.
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73 </help>
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74
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75 </tool>
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