Mercurial > repos > nathandunn > biolinkplanteome
comparison gene-associations.xml @ 1:66ece4fd024f draft default tip
planemo upload commit 20eeb677e99874173440a365f2db04e315e7ebed
| author | nathandunn |
|---|---|
| date | Wed, 28 Jun 2017 10:27:08 -0400 |
| parents | 028a3ffc17b4 |
| children |
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| 0:028a3ffc17b4 | 1:66ece4fd024f |
|---|---|
| 2 <macros> | 2 <macros> |
| 3 <import>macros.xml</import> | 3 <import>macros.xml</import> |
| 4 </macros> | 4 </macros> |
| 5 <expand macro="frontmatter" /> | 5 <expand macro="frontmatter" /> |
| 6 <command><![CDATA[ | 6 <command><![CDATA[ |
| 7 curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/bioentity/gene/$input/$association/?rows=$rows&fetch_objects=true' > $output | 7 curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/api/bioentity/gene/$input/$association/?rows=$rows&fetch_objects=true' > $output |
| 8 ]]></command> | 8 ]]></command> |
| 9 <inputs> | 9 <inputs> |
| 10 <param name="input" type="text" format="txt" multiple="false" label="Gene"/> | 10 <param name="input" type="text" format="txt" multiple="false" label="Gene (e.g. MaizeGDB:9024907)"/> |
| 11 <param name="association" type="select" multiple="false" display="radio" label="Type"> | 11 <param name="association" type="select" multiple="false" display="radio" label="Type"> |
| 12 <option value="diseases">Diseases (e.g,. NCBIGene:4750, Orphanet:173505)</option> | 12 <option value="diseases">Diseases</option> |
| 13 <option value="function">Function (e.g,. NCBIGene:4750, Orphanet:173505)</option> | 13 <option value="function">Function</option> |
| 14 <option value="homologs">Homologs (e.g,. NCBIGene:4750, Orphanet:173505)</option> | 14 <!--<option value="homologs">Homologs</option>--> |
| 15 <option value="interactions">Interactions (e.g,. NCBIGene:4750, Orphanet:173505)</option> | 15 <!--<option value="interactions">Interactions</option>--> |
| 16 <option value="phenotypes">Phenotypes (e.g,. NCBIGene:4750, Orphanet:173505)</option> | 16 <option value="phenotypes">Phenotypes</option> |
| 17 </param> | 17 </param> |
| 18 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/> | 18 <param name="rows" type="text" format="txt" multiple="false" value="1000" label="Num Rows"/> |
| 19 </inputs> | 19 </inputs> |
| 20 <expand macro="outputs" /> | 20 <expand macro="outputs" /> |
| 21 <tests> | 21 <tests> |
| 22 <test> | 22 <test> |
| 23 <param name="input" value="NCBIGene:4750"/> | 23 <param name="input" value="MaizeGDB:9024907"/> |
| 24 <param name="association" value="diseases"/> | 24 <param name="association" value="diseases"/> |
| 25 <output name="output" file="diseases-for-gene.json"/> | 25 <output name="output" file="diseases-for-gene.json"/> |
| 26 </test> | 26 </test> |
| 27 <test> | 27 <test> |
| 28 <param name="input" value="NCBIGene:4750"/> | 28 <param name="input" value="MaizeGDB:9024907"/> |
| 29 <param name="association" value="function"/> | 29 <param name="association" value="function"/> |
| 30 <output name="output" file="function-for-gene.json"/> | 30 <output name="output" file="function-for-gene.json"/> |
| 31 </test> | 31 </test> |
| 32 <!--<test>--> | |
| 33 <!--<param name="input" value="MaizeGDB:9024907"/>--> | |
| 34 <!--<param name="association" value="homologs"/>--> | |
| 35 <!--<output name="output" file="homologs-for-gene.json"/>--> | |
| 36 <!--</test>--> | |
| 37 <!--<test>--> | |
| 38 <!--<param name="input" value="MaizeGDB:9024907"/>--> | |
| 39 <!--<param name="association" value="interactions"/>--> | |
| 40 <!--<output name="output" file="interactions-for-gene.json"/>--> | |
| 41 <!--</test>--> | |
| 32 <test> | 42 <test> |
| 33 <param name="input" value="NCBIGene:4750"/> | 43 <param name="input" value="MaizeGDB:9024907"/> |
| 34 <param name="association" value="homologs"/> | |
| 35 <output name="output" file="homologs-for-gene.json"/> | |
| 36 </test> | |
| 37 <test> | |
| 38 <param name="input" value="NCBIGene:4750"/> | |
| 39 <param name="association" value="interactions"/> | |
| 40 <output name="output" file="interactions-for-gene.json"/> | |
| 41 </test> | |
| 42 <test> | |
| 43 <param name="input" value="NCBIGene:4750"/> | |
| 44 <param name="association" value="phenotypes"/> | 44 <param name="association" value="phenotypes"/> |
| 45 <output name="output" file="phenotypes-for-gene.json"/> | 45 <output name="output" file="phenotypes-for-gene.json"/> |
| 46 </test> | 46 </test> |
| 47 </tests> | 47 </tests> |
| 48 <expand macro="citations" /> | 48 <expand macro="citations" /> |