Mercurial > repos > nathandunn > biolinkmonarchinitiative

annotate genotype-associations.xml @ 1:8fdad43e4250 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e06360e9b6f5ca9e6d254430878008fa6a57a03
author nathandunn
date Wed, 21 Jun 2017 19:00:33 -0400
parents 4f6fba8332ec
children 88e1bd76b069
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-genotype-associations" name="Genotype Associations" version="0.1.0">
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
2 <requirements/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
3 <stdio>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
4 <exit_code range="1:" />
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
5 </stdio>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
6 <command><![CDATA[
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
7 curl -X GET --header 'Accept: application/json' 'https://api.monarchinitiative.org/api/bioentity/genotype/$input/$association/?rows=$rows&fetch_objects=true' > $output
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="Genotype (e.g. ZFIN:ZDB-FISH-150901-4286)" />
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
11 <param name="association" type="select" multiple="false" display="radio" label="Type">
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
12 <option value="diseases">Diseases </option>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
13 <option value="genes">Genes</option>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
14 <option value="genotypes">Genotypes</option>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
15 <option value="phenotypes">Phenotypes</option>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
16 </param>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
17 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
18 </inputs>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
19 <outputs>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
20 <data name="output" format="json" />
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
21 </outputs>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
22 <tests>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
23 <test>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
24 <param name="input" value="ZFIN:ZDB-FISH-150901-4286"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
25 <param name="association" value="diseases"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
26 <output name="output" file="diseases-for-genotype.json"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
27 </test>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
28 <test>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
29 <param name="input" value="ZFIN:ZDB-FISH-150901-4286"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
30 <param name="association" value="genes"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
31 <output name="output" file="genes-for-genotype.json"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
32 </test>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
33 <test>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
34 <param name="input" value="ZFIN:ZDB-FISH-150901-4286"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
35 <param name="association" value="genotypes"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
36 <output name="output" file="genotypes-for-genotype.json"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
37 </test>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
38 <test>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
39 <param name="input" value="ZFIN:ZDB-FISH-150901-4286"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
40 <param name="association" value="phenotypes"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
41 <output name="output" file="phenotypes-for-genotype.json"/>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
42 </test>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
43 </tests>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
44 <help><![CDATA[
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
45 Pulls data from Monarch Initiative BioLink API web services as JSON.
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
46 https://api.monarchinitiative.org/api/
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
47 ]]></help>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
48 <citations>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
49 <citation type="doi">doi:10.5281/zenodo.56412</citation>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
50 </citations>
4f6fba8332ec planemo upload commit 570b5e3caa1a2bd2d9937fb6acc3ea991bfeaa10-dirty
nathandunn
parents:
diff changeset
51 </tool>