Mercurial > repos > nathandunn > biolinkmonarchinitiative

diff bioentityset-overrepresentation.xml @ 3:d40860663861 draft

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planemo upload commit 1a35e82b210719d58263c618f9a67801db26d391
author nathandunn
date Sat, 02 Dec 2017 16:41:34 -0500
parents
children 49b46f044d48
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bioentityset-overrepresentation.xml	Sat Dec 02 16:41:34 2017 -0500
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+<tool id="monarch-bioentityset-overrepresentation" name="Bioentity Set Get Over Representation" version="0.1.0">
+	<macros>
+		<import>macros.xml</import>
+	</macros>
+	<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
+	]]></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>
+	<expand macro="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" file="bioentityset-overrepresentation.json"/>
+		</test>
+	</tests>
+	<expand macro="citations" />
+</tool>
+