Mercurial > repos > nathandunn > monarchinitiative
comparison monarch-pathways-for-genes.xml @ 3:52d9016a156f draft
planemo upload commit dd3ea82b498d011701d1bfbc9fd4c9a93afc3826
| author | nathandunn |
|---|---|
| date | Mon, 27 Jun 2016 09:45:58 -0400 |
| parents | 3107c58d5c85 |
| children |
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| 2:3107c58d5c85 | 3:52d9016a156f |
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| 1 <tool id="monarch-variants-for-diseases" name="Pull Variants from Diseases" version="0.1.0"> | 1 <tool id="monarch-pathways-for-genes" name="Pull Pathways from Genes" version="0.1.0"> |
| 2 <requirements/> | 2 <requirements/> |
| 3 <stdio> | 3 <stdio> |
| 4 <exit_code range="1:" /> | 4 <exit_code range="1:" /> |
| 5 </stdio> | 5 </stdio> |
| 6 <command><![CDATA[ | 6 <command><![CDATA[ |
| 21 curl -s 'https://solr.monarchinitiative.org/solr/golr/select?defType=edismax&qt=standard&indent=on&wt=csv&rows=100000&start=0&fl=object,object_label,relation,relation_label,subject,subject_label,evidence,evidence_label,source,is_defined_by,qualifier&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&facet.method=enum&csv.encapsulator=&csv.separator=%09&csv.header=true&csv.mv.separator=%7C&fq=($inputString)&fq=object_category:%22pathway%22&facet.field=subject_taxon_closure_label&facet.field=object_taxon_closure_label&q=*:*' | tail -n +2 > $output1 | 21 curl -s 'https://solr.monarchinitiative.org/solr/golr/select?defType=edismax&qt=standard&indent=on&wt=csv&rows=100000&start=0&fl=object,object_label,relation,relation_label,subject,subject_label,evidence,evidence_label,source,is_defined_by,qualifier&facet=true&facet.mincount=1&facet.sort=count&json.nl=arrarr&facet.limit=25&facet.method=enum&csv.encapsulator=&csv.separator=%09&csv.header=true&csv.mv.separator=%7C&fq=($inputString)&fq=object_category:%22pathway%22&facet.field=subject_taxon_closure_label&facet.field=object_taxon_closure_label&q=*:*' | tail -n +2 > $output1 |
| 22 | 22 |
| 23 | 23 |
| 24 ]]></command> | 24 ]]></command> |
| 25 <inputs> | 25 <inputs> |
| 26 <param name="input1" type="data" format="tabular" multiple="true" label="Disease" /> | 26 <param name="input1" type="data" format="tabular" multiple="true" label="Genes" /> |
| 27 <param name="conditional1" type="select" multiple="false" display="radio" label="Conditional"> | 27 <param name="conditional1" type="select" multiple="false" display="radio" label="Conditional"> |
| 28 <option value="AND">and</option> | 28 <option value="AND">and</option> |
| 29 <option value="OR">or</option> | 29 <option value="OR">or</option> |
| 30 </param> | 30 </param> |
| 31 </inputs> | 31 </inputs> |
| 49 <output name="output1" file="pathways-for-genes-union.tsv"/> | 49 <output name="output1" file="pathways-for-genes-union.tsv"/> |
| 50 </test> | 50 </test> |
| 51 </tests> | 51 </tests> |
| 52 <help><![CDATA[ | 52 <help><![CDATA[ |
| 53 Pulls data from monarch web services as TSV given a disease. | 53 Pulls data from monarch web services as TSV given a disease. |
| 54 subject,subject_label,subject_taxon,subject_taxon_label,subject_gene,subject_gene_label,relation,relation_label,object,object_label,evidence,evidence_label,source,is_defined_by,qualifier | 54 object,object_label,relation,relation_label,subject,subject_label,evidence,evidence_label,source,is_defined_by,qualifier |
| 55 ]]></help> | 55 ]]></help> |
| 56 <citations> | 56 <citations> |
| 57 <citation type="doi">doi:10.5281/zenodo.56412</citation> | 57 <citation type="doi">doi:10.5281/zenodo.56412</citation> |
| 58 </citations> | 58 </citations> |
| 59 </tool> | 59 </tool> |