Mercurial > repos > jpayne > random_select
comparison random_select.xml @ 0:156371cbc343 tip
planemo upload
| author | jpayne |
|---|---|
| date | Tue, 06 Feb 2018 13:30:07 -0500 |
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| -1:000000000000 | 0:156371cbc343 |
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| 1 <tool id="random_select" name="Choose Randomly" version="0.1.0" profile="16.10"> | |
| 2 <description>one pair of reads from a collection of paired reads</description> | |
| 3 <requirements> | |
| 4 </requirements> | |
| 5 <command detect_errors="exit_code"><![CDATA[ | |
| 6 #if not $seed | |
| 7 #from hashlib import md5 | |
| 8 #set $seed = md5(str($input.name)).hexdigest() | |
| 9 #end if | |
| 10 echo "seed: " $seed && | |
| 11 echo $seed > $output_seed && | |
| 12 #import random | |
| 13 #set $_ = random.seed($seed) | |
| 14 #set $choice = random.choice(list($input)) | |
| 15 cp $choice.forward $selection.forward && cp $choice.reverse $selection.reverse | |
| 16 ]]></command> | |
| 17 <inputs> | |
| 18 <param label="List of paired datasets" name="input" type="data_collection" collection_type="list:paired" format="fastqsanger" /> | |
| 19 <param label="Random seed (optional)" name="seed" type="text" /> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <collection name="selection" label="Selected pair" type="paired"> | |
| 23 <data name="forward" format="fastqsanger" /> | |
| 24 <data name="reverse" format="fastqsanger" /> | |
| 25 </collection> | |
| 26 <data name="output_seed" label="Seed" format_source="seed" hidden="true" /> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="mul" value="single" /> | |
| 31 <param name="seed" value="TESTTEST" /> | |
| 32 <param name="input"> | |
| 33 <collection type="list"> | |
| 34 <element name="sample1"> | |
| 35 <collection type="paired"> | |
| 36 <element name="forward" value="sample1_1.fastq" /> | |
| 37 <element name="reverse" value="sample1_2.fastq" /> | |
| 38 </collection> | |
| 39 </element> | |
| 40 <element name="sample2"> | |
| 41 <collection type="paired"> | |
| 42 <element name="forward" value="sample2_1.fastq" /> | |
| 43 <element name="reverse" value="sample2_2.fastq" /> | |
| 44 </collection> | |
| 45 </element> | |
| 46 <element name="sample3"> | |
| 47 <collection type="paired"> | |
| 48 <element name="forward" value="sample3_1.fastq" /> | |
| 49 <element name="reverse" value="sample3_2.fastq" /> | |
| 50 </collection> | |
| 51 </element> | |
| 52 <element name="sample4"> | |
| 53 <collection type="paired"> | |
| 54 <element name="forward" value="sample4_1.fastq" /> | |
| 55 <element name="reverse" value="sample4_2.fastq" /> | |
| 56 </collection> | |
| 57 </element> | |
| 58 </collection> | |
| 59 </param> | |
| 60 <output_collection name="selection" type="paired" > | |
| 61 <element name="forward" file="sample4_1.fastq" /> | |
| 62 <element name="reverse" file="sample4_2.fastq" /> | |
| 63 </output_collection> | |
| 64 </test> | |
| 65 </tests> | |
| 66 <help>Choose one pair at random from a paired dataset. | |
| 67 If you re-use the seed, the choice should be the same | |
| 68 (this is for reproducability of analysis.) | |
| 69 Provide a blank seed value to use a seed created | |
| 70 as an MD5 sum of the dataset's name. | |
| 71 </help> | |
| 72 <citations> | |
| 73 </citations> | |
| 74 </tool> |