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1 <tool id="ngs-tools_sample" name="Sample (ngs-tools)" version="1.0.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.1.7">ngs-tools</requirement>
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5 </requirements>
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6 <command>
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7 ngs-tools sample
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8 --input-format $input_format.format
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9 --sample-size $size
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10 --output $output_file
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11 #if str($input_format.paired.paired_selector) == "True"
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12 --output-pair $output_file_pair
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13 #end if
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14 $input_format.paired.input_file
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15 #if str($input_format.paired.paired_selector) == "True"
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16 $input_format.paired.input_file_pair
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17 #end if
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18 </command>
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19 <inputs>
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20 <conditional name="input_format">
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21 <param name="format" type="select" label="Input format">
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22 <option value="fastq" selected="true">Fastq</option>
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23 </param>
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24 <when value="fastq">
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25 <conditional name="paired">
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26 <param name="paired_selector" type="select" label="Paired data?">
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27 <option value="True">Yes</option>
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28 <option value="False" selected="true">No</option>
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29 </param>
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30 <when value="True">
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31 <param name="input_file" type="data" format="fastq" label="FASTQ File to sample from" />
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32 <param name="input_file_pair" type="data" format="fastq" label="FASTQ Paired File to sample from" />
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33 </when>
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34 <when value="False">
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35 <param name="input_file" type="data" format="fastq" label="FASTQ File to sample from" />
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36 </when>
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37 </conditional>
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38 </when>
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39 </conditional>
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40 <param name="size" type="integer" size="6" value="100" label="Number of records to sample" />
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41 </inputs>
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42 <outputs>
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43 <data name="output_file" format="input" />
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44 <data name="output_file_pair" format="input">
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45 <filter>input_format['paired']['paired_selector'] == "True"</filter>
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46 </data>
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47 </outputs>
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48 <help>
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49
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50 **What it does**
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51
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52 This tool samples a random number of records from the input file(s). Supports
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53 paired data assuming paired files are in sync.
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54
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55 Supported formats: FASTQ.
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56
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57 --------
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58
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59 This tool is based on `ngs-tools`__ by Carlos Borroto <carlos.borroto@gmail.com>.
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60
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61 .. __: https://github.com/cjav/ngs-tools/
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62
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63 </help>
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64 </tool>
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