<tool id="monarch-bioentityset-overrepresentation" name="Bioentity Set Get Over Representation" version="0.1.0">
	<macros>
		<import>macros.xml</import>
	</macros>
    <requirements>
        <requirement type="package" version="1.5">jq</requirement>
    </requirements>
	<expand macro="frontmatter" />
	<command><![CDATA[
#*
curl --silent -X GET --header 'Accept: application/json' 'https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/?object_category=phenotype&subject=NCBIGene%3A6295&subject=NCBIGene%3A1258&subject=NCBIGene%3A3614&subject=NCBIGene%3A26121&subject=NCBIGene%3A7275&subject=NCBIGene%3A55857&subject=NCBIGene%3A79797&subject=NCBIGene%3A10594&subject=NCBIGene%3A64218&subject=NCBIGene%3A7401&ontology=hp&subject_category=gene&taxon=NCBITaxon%3A9606&object_category=phenotype&max_p_value=0.05' > $output
*#
#set $subject_string = ''
#set $subject = $subject.replace(' ', '')
#set $subject = $subject.replace(',', ' ')
#for $word in $subject.split(' ')
#set $subject_string += '&subject='+str($word)
#end for

#set $background_string = ''
#set $background = $background.replace(' ', '')
#set $background = $background.replace(',', ' ')
#for $word in $background.split(' ')
#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_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" />
		<param  name="subject" type="text" format="txt" multiple="true" label="Entity ids to be examined, e.g. NCBIGene:6295,NCBIGene:1258 ,NCBIGene:3614 ,NCBIGene:26121 ,NCBIGene:7275 ,NCBIGene:55857 ,NCBIGene:79797 ,NCBIGene:10594 ,NCBIGene:64218 ,NCBIGene:7401"
        />
		<param  name="background" type="text" format="txt" multiple="true" label="Entity ids in background set, e.g. NCBIGene:84570, NCBIGene:3630; used in over-representation tests" />
		<param  name="ontology" type="text" format="txt" multiple="false" value="hp" label="ontology id. Must be obo id. Examples: go, mp, hp, uberon (optional: will be inferred if left blank)" />
		<param  name="subject_category" type="text" format="txt" multiple="false" label="Other types may be used e.g. disease but statistics may not make sense" value="gene"/>
		<param  name="taxon" type="text" format="txt" multiple="true" label="must be NCBITaxon CURIE. Example: NCBITaxon:9606" />
		<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>
	<outputs>
		<data name="output_json" format="json"/>
		<data 
			name="output_tsv" 
			format="tsv"
			>
		</data>
	</outputs>
	<tests>
		<!--

		emulate: https://api-dev.monarchinitiative.org/api/bioentityset/overrepresentation/
		?object_category=phenotype
subject=NCBIGene%3A6295
subject=NCBIGene%3A1258
subject=NCBIGene%3A3614
subject=NCBIGene%3A26121
subject=NCBIGene%3A7275
subject=NCBIGene%3A55857
subject=NCBIGene%3A79797
subject=NCBIGene%3A10594
subject=NCBIGene%3A64218
subject=NCBIGene%3A7401
ontology=hp
subject_category=gene
taxon=NCBITaxon%3A9606
object_category=phenotype
max_p_value=0.05-->
		<test>
			<param name="object_category" value="phenotype"/>
			<param name="subject" value="NCBIGene%3A6295,NCBIGene%3A1258,NCBIGene%3A3614,NCBIGene%3A26121,NCBIGene%3A7275,NCBIGene%3A55857,NCBIGene%3A79797,NCBIGene%3A10594,NCBIGene%3A64218,NCBIGene%3A7401"/>
			<param name="ontology" value="hp"/>
			<param name="subject_category" value="gene"/>
			<param name="taxon" value="NCBITaxon:9606"/>
			<param name="object_category" value="phenotype"/>
			<param name="max_p_value" value="0.05"/>
			<output name="output_json" file="bioentityset-overrepresentation.json"/>
			<output name="output_tsv" file="bioentityset-overrepresentation.tsv"/>
		</test>
	</tests>
	<expand macro="citations" />
</tool>