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annotate phenotype-gene-associations.xml @ 1:8fdad43e4250 draft

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planemo upload commit 2e06360e9b6f5ca9e6d254430878008fa6a57a03
author nathandunn
date Wed, 21 Jun 2017 19:00:33 -0400
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1 <tool id="monarch-phenotype-gene-associations" name="Phenotype Gene Associations" version="0.1.0">
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2 <requirements/>
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3 <stdio>
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4 <exit_code range="1:" />
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5 </stdio>
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6 <command><![CDATA[
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7 curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/phenotype/$input/gene/$taxid/ids?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="Phenotype ID (e.g. MP:0001569)" />
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11 <param name="taxid" type="text" format="txt" multiple="false" label="Taxon ID (e.g. NCBITaxon:10090)" />
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12 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
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13 </inputs>
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14 <outputs>
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15 <data name="output" format="json" />
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="input" value="MP:0001569"/>
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20 <param name="taxid" value="NCBITaxon:10090"/>
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21 <output name="output" file="phenotype-for-phenotype-and-taxon.json"/>
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22 </test>
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23 </tests>
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24 <help><![CDATA[
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25 Pulls data from Monarch Initiative BioLink API web services as JSON.
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26 https://api.monarchinitiative.org/api/
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27 ]]></help>
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28 <citations>
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29 <citation type="doi">doi:10.5281/zenodo.56412</citation>
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30 </citations>
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31 </tool>
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