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1 <tool id="spotyping" name="Spoligotype Prediction" version="0.1.1">
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0
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2 <requirements>
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3 <requirement type="package" version="2.1">spotyping</requirement>
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4 </requirements>
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5 <command>
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2
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6 SpoTyping.py
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7 #if str( $data_input.data_selector ) == "paired"
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8 $data_input.input1.forward $data_input.input1.reverse
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9 #end if
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10 #if str( $data_input.data_selector ) == "single"
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11 $data_input.input2.element_identifier
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12 #end if
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1
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13 </command>
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0
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14 <inputs>
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15 <conditional name="data_input">
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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">
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17 <option value="paired">Paired</option>
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18 <option value="single">Single</option>
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19 </param>
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20 <when value="paired">
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21 <param name="input1" format="data" type="data_collection" collection_type="paired" label="Select a paired collection" help="a paired data"/>
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22 </when>
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23 <when value="single">
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24 <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/>
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25 </when>
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26 </conditional>
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27 </inputs>
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28 <outputs>
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29 <data name="output1" label="spoligotyping results" format="data" from_work_dir="SpoTyping"/>
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30 <data name="output2" label="spoligotyping log" format="data" from_work_dir="SpoTyping.log"/>
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31 <data name="output3" label="query" format="data" from_work_dir="*.xls"/>
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32 </outputs>
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33 <help><![CDATA[
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34 Usage: python SpoTyping.py [options] FASTQ_1/FASTA FASTQ_2(optional)
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35 ]]></help>
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36 <citations>
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37 <citation type="bibtex">
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38 @misc{githubSpoTyping,
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39 author = {Xia, Eryu},
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40 year = {2016},
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41 title = {SpoTyping},
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42 publisher = {GitHub},
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43 journal = {GitHub repository},
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44 url = {https://github.com/xiaeryu/SpoTyping},
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45 }</citation>
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46 </citations>
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47 </tool>
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