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annotate associations.xml @ 0:028a3ffc17b4 draft

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planemo upload commit b095175f34e78ceded24a6e1da99b328f50db86d
author nathandunn
date Fri, 23 Jun 2017 15:04:12 -0400
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children 66ece4fd024f
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028a3ffc17b4 planemo upload commit b095175f34e78ceded24a6e1da99b328f50db86d
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1 <tool id="planteome-associations" name="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 #if $type == 'find'
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8 curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/association/$type/?rows=$rows&fetch_objects=true&subject=$subject' > $output
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9 #else if $type == 'from'
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10 curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/association/$type/$subject?rows=$rows&fetch_objects=true' > $output
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11 #else if $type == 'to'
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12 curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/association/$type/$object?rows=$rows&fetch_objects=true' > $output
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13 #else if $type == 'between'
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14 curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/association/$type/$subject/$object?rows=$rows&fetch_objects=true' > $output
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15 #end if
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16 ]]></command>
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17 <inputs>
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18 <param name="subject" type="text" format="txt" multiple="false" label="Subject"/>
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19 <param name="object" type="text" format="txt" multiple="false" label="Object"/>
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20 <param name="type" type="select" multiple="false" display="radio" label="Type">
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21 <option value="find">Find (subject)</option>
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22 <option value="from">From (subject)</option>
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23 <option value="to">To (object)</option>
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24 <option value="between">Between (subject -> object)</option>
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25 </param>
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26 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
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27 </inputs>
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28 <expand macro="outputs" />
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29 <tests>
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30 <test>
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31 <param name="subject" value="NCBIGene:84570"/>
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32 <param name="type" value="find"/>
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33 <output name="output" file="find-associations-for-subject.json"/>
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34 </test>
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35 <test>
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36 <param name="subject" value="NCBIGene:84570"/>
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37 <param name="type" value="from"/>
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38 <output name="output" file="from-associations-for-subject.json"/>
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39 </test>
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40 <test>
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41 <param name="object" value="MP:0013765"/>
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42 <param name="type" value="to"/>
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43 <output name="output" file="to-associations-for-object.json"/>
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44 </test>
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45 <test>
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46 <param name="subject" value="MGI:1342287"/>
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47 <param name="object" value="MP:0013765"/>
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48 <param name="type" value="between"/>
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49 <output name="output" file="between-associations.json"/>
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50 </test>
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51 </tests>
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52 <expand macro="citations" />
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53 </tool>
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54