Mercurial > repos > nathandunn > biolinkmonarchinitiative

annotate phenotype-gene-associations.xml @ 3:d40860663861 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 1a35e82b210719d58263c618f9a67801db26d391
author nathandunn
date Sat, 02 Dec 2017 16:41:34 -0500
parents 88e1bd76b069
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
1 <tool id="monarch-phenotype-gene-associations" name="Phenotype Gene Associations" version="0.1.0">
2
88e1bd76b069 planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e
nathandunn
parents: 0
diff changeset
2 <macros>
88e1bd76b069 planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e
nathandunn
parents: 0
diff changeset
3 <import>macros.xml</import>
88e1bd76b069 planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e
nathandunn
parents: 0
diff changeset
4 </macros>
88e1bd76b069 planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e
nathandunn
parents: 0
diff changeset
5 <expand macro="frontmatter" />
0
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
6 <command><![CDATA[
2
88e1bd76b069 planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e
nathandunn
parents: 0
diff changeset
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
0
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
8 ]]></command>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
9 <inputs>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
10 <param name="input" type="text" format="txt" multiple="false" label="Phenotype ID (e.g. MP:0001569)" />
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
11 <param name="taxid" type="text" format="txt" multiple="false" label="Taxon ID (e.g. NCBITaxon:10090)" />
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
12 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
13 </inputs>
2
88e1bd76b069 planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e
nathandunn
parents: 0
diff changeset
14 <expand macro="outputs" />
0
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
15 <tests>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
16 <test>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
17 <param name="input" value="MP:0001569"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
18 <param name="taxid" value="NCBITaxon:10090"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
19 <output name="output" file="phenotype-for-phenotype-and-taxon.json"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
20 </test>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
21 </tests>
2
88e1bd76b069 planemo upload commit 91b079b5648caa7a8795ec0957a4b11e104d986e
nathandunn
parents: 0
diff changeset
22 <expand macro="citations" />
0
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
23 </tool>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
24