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comparison phenotype-gene-associations.xml @ 2:88e1bd76b069 draft

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planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e
author nathandunn
date Thu, 22 Jun 2017 15:28:43 -0400
parents 4f6fba8332ec
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1:8fdad43e4250 2:88e1bd76b069
1 <tool id="monarch-phenotype-gene-associations" name="Phenotype Gene Associations" version="0.1.0"> 1 <tool id="monarch-phenotype-gene-associations" name="Phenotype Gene Associations" version="0.1.0">
2 <requirements/> 2 <macros>
3 <stdio> 3 <import>macros.xml</import>
4 <exit_code range="1:" /> 4 </macros>
5 </stdio> 5 <expand macro="frontmatter" />
6 <command><![CDATA[ 6 <command><![CDATA[
7 curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/phenotype/$input/gene/$taxid/ids?rows=$rows&fetch_objects=true' > $output 7 curl --silent -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/phenotype/$input/gene/$taxid/ids?rows=$rows&fetch_objects=true' > $output
8 ]]></command> 8 ]]></command>
9 <inputs> 9 <inputs>
10 <param name="input" type="text" format="txt" multiple="false" label="Phenotype ID (e.g. MP:0001569)" /> 10 <param name="input" type="text" format="txt" multiple="false" label="Phenotype ID (e.g. MP:0001569)" />
11 <param name="taxid" type="text" format="txt" multiple="false" label="Taxon ID (e.g. NCBITaxon:10090)" /> 11 <param name="taxid" type="text" format="txt" multiple="false" label="Taxon ID (e.g. NCBITaxon:10090)" />
12 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/> 12 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
13 </inputs> 13 </inputs>
14 <outputs> 14 <expand macro="outputs" />
15 <data name="output" format="json" />
16 </outputs>
17 <tests> 15 <tests>
18 <test> 16 <test>
19 <param name="input" value="MP:0001569"/> 17 <param name="input" value="MP:0001569"/>
20 <param name="taxid" value="NCBITaxon:10090"/> 18 <param name="taxid" value="NCBITaxon:10090"/>
21 <output name="output" file="phenotype-for-phenotype-and-taxon.json"/> 19 <output name="output" file="phenotype-for-phenotype-and-taxon.json"/>
22 </test> 20 </test>
23 </tests> 21 </tests>
24 <help><![CDATA[ 22 <expand macro="citations" />
25 Pulls data from Monarch Initiative BioLink API web services as JSON.
26 https://api.monarchinitiative.org/api/
27 ]]></help>
28 <citations>
29 <citation type="doi">doi:10.5281/zenodo.56412</citation>
30 </citations>
31 </tool> 23 </tool>
32 24