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1 <tool id="random_select" name="Choose Randomly" version="0.1.0" profile="16.10">
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2 <description>one pair of reads from a collection of paired reads</description>
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3 <requirements>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 #if not $seed
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7 #from hashlib import md5
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8 #set $seed = md5(str($input.name)).hexdigest()
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9 #end if
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10 echo "seed: " $seed &&
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11 echo $seed > $output_seed &&
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12 #import random
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13 #set $_ = random.seed($seed)
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14 #set $choice = random.choice(list($input))
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15 cp $choice.forward $selection.forward && cp $choice.reverse $selection.reverse
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16 ]]></command>
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17 <inputs>
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18 <param label="List of paired datasets" name="input" type="data_collection" collection_type="list:paired" format="fastqsanger" />
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19 <param label="Random seed (optional)" name="seed" type="text" />
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20 </inputs>
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21 <outputs>
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22 <collection name="selection" label="Selected pair" type="paired">
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23 <data name="forward" format="fastqsanger" />
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24 <data name="reverse" format="fastqsanger" />
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25 </collection>
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26 <data name="output_seed" label="Seed" format_source="seed" hidden="true" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="mul" value="single" />
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31 <param name="seed" value="TESTTEST" />
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32 <param name="input">
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33 <collection type="list">
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34 <element name="sample1">
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35 <collection type="paired">
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36 <element name="forward" value="sample1_1.fastq" />
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37 <element name="reverse" value="sample1_2.fastq" />
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38 </collection>
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39 </element>
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40 <element name="sample2">
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41 <collection type="paired">
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42 <element name="forward" value="sample2_1.fastq" />
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43 <element name="reverse" value="sample2_2.fastq" />
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44 </collection>
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45 </element>
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46 <element name="sample3">
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47 <collection type="paired">
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48 <element name="forward" value="sample3_1.fastq" />
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49 <element name="reverse" value="sample3_2.fastq" />
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50 </collection>
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51 </element>
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52 <element name="sample4">
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53 <collection type="paired">
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54 <element name="forward" value="sample4_1.fastq" />
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55 <element name="reverse" value="sample4_2.fastq" />
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56 </collection>
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57 </element>
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58 </collection>
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59 </param>
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60 <output_collection name="selection" type="paired" >
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61 <element name="forward" file="sample4_1.fastq" />
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62 <element name="reverse" file="sample4_2.fastq" />
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63 </output_collection>
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64 </test>
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65 </tests>
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66 <help>Choose one pair at random from a paired dataset.
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67 If you re-use the seed, the choice should be the same
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68 (this is for reproducability of analysis.)
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69 Provide a blank seed value to use a seed created
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70 as an MD5 sum of the dataset's name.
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71 </help>
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72 <citations>
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73 </citations>
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74 </tool> |
