Mercurial > repos > nathandunn > biolinkplanteome

annotate variant-associations.xml @ 0:028a3ffc17b4 draft

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author nathandunn
date Fri, 23 Jun 2017 15:04:12 -0400
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028a3ffc17b4 planemo upload commit b095175f34e78ceded24a6e1da99b328f50db86d
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1 <tool id="planteome-variant-associations" name="Variant Associations" version="0.1.0">
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <expand macro="frontmatter" />
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6 <command><![CDATA[
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7 curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/bioentity/variant/$input/$association/?rows=$rows&fetch_objects=true' > $output
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8 ]]></command>
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9 <inputs>
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10 <param name="input" type="text" format="txt" multiple="false" label="Variant (e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783)" />
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11 <param name="association" type="select" multiple="false" display="radio" label="Type">
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12 <option value="genes">Genes</option>
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13 <option value="genotypes">Genotypes</option>
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14 <option value="phenotypes">Phenotypes</option>
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15 </param>
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16 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
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17 </inputs>
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18 <expand macro="outputs" />
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19 <tests>
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20 <test>
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21 <param name="input" value="ZFIN:ZDB-ALT-010427-8"/>
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22 <param name="association" value="genes"/>
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23 <output name="output" file="genes-for-variant.json"/>
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24 </test>
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25 <test>
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26 <param name="input" value="ZFIN:ZDB-ALT-010427-8"/>
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27 <param name="association" value="genotypes"/>
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28 <output name="output" file="genotypes-for-variant.json"/>
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29 </test>
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30 <test>
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31 <param name="input" value="ClinVarVariant:65929"/>
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32 <param name="association" value="phenotypes"/>
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33 <output name="output" file="phenotypes-for-variant.json"/>
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34 </test>
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35 </tests>
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36 <expand macro="citations" />
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37 </tool>
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