Mercurial > repos > nathandunn > biolinkplanteome

annotate get-object.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-get-object" name="Get Object" 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/$type$input$associations?rows=$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="Object ID" />
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11 <param name="type" type="select" multiple="false" display="radio" label="Type">
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12 <option value="">Any</option>
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13 <option value="gene/">Gene (e.g. NCBIGene:84570)</option>
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14 <option value="genotype/">Genotype (e.g. ZFIN:ZDB-FISH-150901-6607)</option>
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15 </param>
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16 <param name="associations" type="select" multiple="false" display="radio" label="Render Associations">
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17 <option value="/associations/">True</option>
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18 <option value="" checked="true">False</option>
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19 </param>
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20 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
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21 </inputs>
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22 <expand macro="outputs" />
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23 <tests>
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24 <test>
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25 <param name="input" value="OMIM:605543"/>
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26 <param name="type" value=""/>
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27 <output name="output" file="bioentity-object-for-disease.json"/>
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28 </test>
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29 <test>
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30 <param name="input" value="OMIM:605543"/>
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31 <param name="type" value=""/>
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32 <param name="associations" value="/associations/"/>
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33 <output name="output" file="bioentity-associations-for-disease.json"/>
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34 </test>
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35 <test>
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36 <param name="input" value="NCBIGene:84570"/>
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37 <param name="association" value="gene/"/>
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38 <output name="output" file="bioentity-object-for-gene.json"/>
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39 </test>
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40 <test>
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41 <param name="input" value="ZFIN:ZDB-FISH-150901-6607"/>
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42 <param name="association" value="genotype/"/>
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43 <output name="output" file="bioentity-object-for-genotype.json"/>
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44 </test>
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45 </tests>
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46 <expand macro="citations" />
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47 </tool>
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