jpayne@0: <tool id="random_select" name="Choose Randomly" version="0.1.0" profile="16.10">
jpayne@0:     <description>one pair of reads from a collection of paired reads</description>
jpayne@0:     <requirements>
jpayne@0:     </requirements>
jpayne@0:     <command detect_errors="exit_code"><![CDATA[
jpayne@0:         #if not $seed
jpayne@0:         #from hashlib import md5
jpayne@0:         #set $seed = md5(str($input.name)).hexdigest()
jpayne@0:         #end if
jpayne@0:         echo "seed: " $seed &&
jpayne@0:         echo $seed > $output_seed &&
jpayne@0:         #import random
jpayne@0:         #set $_ = random.seed($seed)
jpayne@0:         #set $choice = random.choice(list($input))
jpayne@0:         cp $choice.forward $selection.forward && cp $choice.reverse $selection.reverse
jpayne@0:     ]]></command>
jpayne@0:     <inputs>
jpayne@0: 		<param label="List of paired datasets" name="input" type="data_collection" collection_type="list:paired" format="fastqsanger" />
jpayne@0:         <param label="Random seed (optional)" name="seed" type="text" />
jpayne@0:     </inputs>
jpayne@0:     <outputs>
jpayne@0:     	<collection name="selection" label="Selected pair" type="paired">
jpayne@0:     		<data name="forward" format="fastqsanger" />
jpayne@0:             <data name="reverse" format="fastqsanger" />
jpayne@0:         </collection>
jpayne@0:         <data name="output_seed" label="Seed" format_source="seed" hidden="true" />
jpayne@0:     </outputs>
jpayne@0:     <tests>
jpayne@0:         <test>
jpayne@0:             <param name="mul" value="single" />
jpayne@0:             <param name="seed" value="TESTTEST" />
jpayne@0:             <param name="input">
jpayne@0:                 <collection type="list">
jpayne@0:                     <element name="sample1">
jpayne@0:                         <collection type="paired">
jpayne@0:                             <element name="forward" value="sample1_1.fastq" />
jpayne@0:                             <element name="reverse" value="sample1_2.fastq" />
jpayne@0:                         </collection>
jpayne@0:                     </element>
jpayne@0:                     <element name="sample2">
jpayne@0:                         <collection type="paired">
jpayne@0:                             <element name="forward" value="sample2_1.fastq" />
jpayne@0:                             <element name="reverse" value="sample2_2.fastq" />
jpayne@0:                         </collection>
jpayne@0:                     </element>
jpayne@0:                     <element name="sample3">
jpayne@0:                         <collection type="paired">
jpayne@0:                             <element name="forward" value="sample3_1.fastq" />
jpayne@0:                             <element name="reverse" value="sample3_2.fastq" />
jpayne@0:                         </collection>
jpayne@0:                     </element>
jpayne@0:                     <element name="sample4">
jpayne@0:                         <collection type="paired">
jpayne@0:                             <element name="forward" value="sample4_1.fastq" />
jpayne@0:                             <element name="reverse" value="sample4_2.fastq" />
jpayne@0:                         </collection>
jpayne@0:                     </element>
jpayne@0:                 </collection>
jpayne@0:             </param>
jpayne@0:             <output_collection name="selection" type="paired" >
jpayne@0:                 <element name="forward" file="sample4_1.fastq" />
jpayne@0:                 <element name="reverse" file="sample4_2.fastq" />
jpayne@0:             </output_collection>
jpayne@0:         </test>
jpayne@0:     </tests>
jpayne@0:     <help>Choose one pair at random from a paired dataset. 
jpayne@0:             If you re-use the seed, the choice should be the same 
jpayne@0:             (this is for reproducability of analysis.) 
jpayne@0:             Provide a blank seed value to use a seed created 
jpayne@0:             as an MD5 sum of the dataset's name.
jpayne@0:     </help>
jpayne@0:     <citations>
jpayne@0:     </citations>
jpayne@0: </tool>