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annotate bulk-operations.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-bulk-operations" name="Bulk Operations" 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/mart/$association/$object_category/$taxon?rows=$rows&fetch_objects=true' > $output
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8 ]]></command>
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9 <inputs>
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10 <param name="taxon" type="text" format="txt" multiple="false" label="Taxon (e.g. NCBITaxon:9606)"/>
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11 <param name="object_category" type="text" format="txt" multiple="false" label="Object Category (e.g. phenotype, disease)"/>
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12 <param name="association" type="select" multiple="false" display="radio" label="Type">
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13 <option value="gene">Gene</option>
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14 <option value="disease">Disease</option>
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15 <option value="case">Case</option>
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16 </param>
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17 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
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18 </inputs>
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19 <expand macro="outputs" />
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20 <tests>
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21 <!--NOTE: these take way too long to run because fo the large amount of data involved-->
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22 <!--<test>-->
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23 <!--<param name="type" value="gene"/>-->
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24 <!--<param name="taxon" value="NCBITaxon:9606"/>-->
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25 <!--<param name="rows" value="1"/>-->
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26 <!--<param name="object_category" value="phenotype"/>-->
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27 <!--<output name="output" file="gene-mart-for-phenotype.json"/>-->
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28 <!--</test>-->
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29 <!--<test>-->
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30 <!--<param name="type" value="disease"/>-->
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31 <!--<param name="taxon" value="NCBITaxon:9606"/>-->
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32 <!--<param name="rows" value="1"/>-->
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33 <!--<param name="object_category" value="phenotype"/>-->
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34 <!--<output name="output" file="disease-mart-for-phenotype.json"/>-->
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35 <!--</test>-->
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36 <!--<test>-->
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37 <!--<param name="type" value="case"/>-->
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38 <!--<param name="taxon" value="NCBITaxon:9606"/>-->
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39 <!--<param name="rows" value="1"/>-->
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40 <!--<param name="object_category" value="phenotype"/>-->
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41 <!--<output name="output" file="case-mart-for-phenotype.json"/>-->
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42 <!--</test>-->
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43 </tests>
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44 <expand macro="citations" />
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45 </tool>
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