Mercurial > repos > jowong > spotyping
comparison spotyping.xml @ 0:376f0194b92a draft
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| author | jowong |
|---|---|
| date | Sun, 04 Nov 2018 20:36:13 -0500 |
| parents | |
| children | 6d7d31716caa |
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| -1:000000000000 | 0:376f0194b92a |
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| 1 <tool id="spotyping" name="Spoligotype Prediction" version="0.1.0"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="2.1">spotyping</requirement> | |
| 4 </requirements> | |
| 5 <command> | |
| 6 python SpoTyping.py | |
| 7 #if str( $data_input.data_selector ) == "paired" | |
| 8 $data_input.input1.forward $data_input.input1.reverse | |
| 9 #end if | |
| 10 #if str( $data_input.data_selector ) == "single" | |
| 11 $data_input.input2.element_identifier | |
| 12 #end if | |
| 13 ></command> | |
| 14 <inputs> | |
| 15 <conditional name="data_input"> | |
| 16 <param name="data_selector" type="select" label="Single or Paired-end Data" help="Select between paired and single end data to add name to dataset"> | |
| 17 <option value="paired">Paired</option> | |
| 18 <option value="single">Single</option> | |
| 19 </param> | |
| 20 <when value="paired"> | |
| 21 <param name="input1" format="data" type="data_collection" collection_type="paired" label="Select a paired collection" help="a paired data"/> | |
| 22 </when> | |
| 23 <when value="single"> | |
| 24 <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/> | |
| 25 </when> | |
| 26 </conditional> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data name="output1" label="spoligotyping results" format="data" from_work_dir="SpoTyping"/> | |
| 30 <data name="output2" label="spoligotyping log" format="data" from_work_dir="SpoTyping.log"/> | |
| 31 <data name="output3" label="query" format="data" from_work_dir="*.xls"/> | |
| 32 </outputs> | |
| 33 <help><![CDATA[ | |
| 34 Usage: python SpoTyping.py [options] FASTQ_1/FASTA FASTQ_2(optional) | |
| 35 ]]></help> | |
| 36 <citations> | |
| 37 <citation type="bibtex"> | |
| 38 @misc{githubSpoTyping, | |
| 39 author = {Xia, Eryu}, | |
| 40 year = {2016}, | |
| 41 title = {SpoTyping}, | |
| 42 publisher = {GitHub}, | |
| 43 journal = {GitHub repository}, | |
| 44 url = {https://github.com/xiaeryu/SpoTyping}, | |
| 45 }</citation> | |
| 46 </citations> | |
| 47 </tool> |