Mercurial > repos > nathandunn > biolinkmonarchinitiative
diff bioentityset-overrepresentation.xml @ 4:49b46f044d48 draft
planemo upload commit 0dbcda86caba8f8fead7cb6fde0ae3e73d398f1e
| author | nathandunn |
|---|---|
| date | Mon, 04 Dec 2017 19:35:12 -0500 |
| parents | d40860663861 |
| children | 6eaaeedf2f37 |
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--- a/bioentityset-overrepresentation.xml Sat Dec 02 16:41:34 2017 -0500 +++ b/bioentityset-overrepresentation.xml Mon Dec 04 19:35:12 2017 -0500 @@ -21,7 +21,15 @@ #set $background_string += '&background='+str($word) #end for -curl --silent -X GET --header 'Accept: application/json' 'https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/?object_category=$object_category$subject_string&background=$background_string&ontology=$ontology&subject_category=$subject_category&taxon=$taxon&object_category=$object_category&max_p_value=$max_p_value' > $output +curl --silent -X GET --header 'Accept: application/json' 'https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/?object_category=$object_category$subject_string&background=$background_string&ontology=$ontology&subject_category=$subject_category&taxon=$taxon&object_category=$object_category&max_p_value=$max_p_value' > $output_json + +&& + +echo -e "p\tn\tp_uncorrected\tc" > $output_tsv + +&& + +cat $output_json | jq -r '.results[] | flatten | @tsv ' >> $output_tsv ]]></command> <inputs> <param name="object_category" type="text" format="txt" multiple="false" label="CATEGORY of entity at link OBJECT (target), e.g. function, phenotype, disease" /> @@ -34,9 +42,19 @@ <param name="object_category" type="text" format="txt" multiple="false" label="E.g. phenotype, function" value="phenotype" /> <param name="max_p_value" type="text" format="txt" multiple="false" value="0.05" label="Exclude results with p-value greater than this"/> </inputs> - <expand macro="outputs" /> + <outputs> + <data name="output_json" format="json"/> + <data + name="output_tsv" + format="tsv" + header_row="1" + > + </data> + </outputs> <tests> - <!--emulate: https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/ + <!-- + + emulate: https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/ ?object_category=phenotype subject=NCBIGene%3A6295 subject=NCBIGene%3A1258 @@ -61,7 +79,8 @@ <param name="taxon" value="NCBITaxon:9606"/> <param name="object_category" value="phenotype"/> <param name="max_p_value" value="0.05"/> - <output name="output" file="bioentityset-overrepresentation.json"/> + <output name="output_json" file="bioentityset-overrepresentation.json"/> + <output name="output_tsv" file="bioentityset-overrepresentation.tsv"/> </test> </tests> <expand macro="citations" />