# HG changeset patch
# User nathandunn
# Date 1498244652 14400
# Node ID 028a3ffc17b45be351e0c9654cee1fce1c729f0a
planemo upload commit b095175f34e78ceded24a6e1da99b328f50db86d
diff -r 000000000000 -r 028a3ffc17b4 LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Fri Jun 23 15:04:12 2017 -0400
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+BSD 3-Clause License
+
+Copyright (c) 2017, Nathan Dunn
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+ contributors may be used to endorse or promote products derived from
+ this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff -r 000000000000 -r 028a3ffc17b4 README.md
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+# Biolink-planteome
+
+[![Build Status](https://travis-ci.org/nathandunn/biolink-planteome.svg?branch=master)](https://travis-ci.org/nathandunn/biolink-planteome)
+[![DOI](https://zenodo.org/badge/94568425.svg)](https://zenodo.org/badge/latestdoi/94568425)
+
+
+Wrapper around the [planteome Iniatitive Biolink API](https://biolink.planteome.org/api/).
+
+Available on the [Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/repository?repository_id=c46e72ccdb506940).
+
+The [planteome Intiative](http://planteome.org/) is a warehouse that integrates, aligns, and re-distributes cross-species gene, genotype, variant, disease, and phenotype data using ontology associations.
+
+The [Biolink API](https://github.com/biolink/biolink-api) is an open API biologically and biomedically relevant entities, and the relationships between them.
+
+
+
+![Screen Shot](images/ScreenShot1.png)
+
+
diff -r 000000000000 -r 028a3ffc17b4 associations.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/associations.xml Fri Jun 23 15:04:12 2017 -0400
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+
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+ macros.xml
+
+
+ $output
+ #else if $type == 'from'
+ curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/association/$type/$subject?rows=$rows&fetch_objects=true' > $output
+ #else if $type == 'to'
+ curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/association/$type/$object?rows=$rows&fetch_objects=true' > $output
+ #else if $type == 'between'
+ curl --silent -X GET --header 'Accept: application/json' 'http://biolink.planteome.org/apiapi/association/$type/$subject/$object?rows=$rows&fetch_objects=true' > $output
+ #end if
+ ]]>
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diff -r 000000000000 -r 028a3ffc17b4 bioentity-associations.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bioentity-associations.xml Fri Jun 23 15:04:12 2017 -0400
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+
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+ macros.xml
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+ $output
+ ]]>
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diff -r 000000000000 -r 028a3ffc17b4 bulk-operations.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bulk-operations.xml Fri Jun 23 15:04:12 2017 -0400
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+ macros.xml
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+ $output
+ ]]>
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diff -r 000000000000 -r 028a3ffc17b4 disease-associations.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/disease-associations.xml Fri Jun 23 15:04:12 2017 -0400
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+
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+ macros.xml
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+ $output
+ ]]>
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diff -r 000000000000 -r 028a3ffc17b4 gene-associations.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gene-associations.xml Fri Jun 23 15:04:12 2017 -0400
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+ macros.xml
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+ $output
+ ]]>
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diff -r 000000000000 -r 028a3ffc17b4 genotype-associations.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/genotype-associations.xml Fri Jun 23 15:04:12 2017 -0400
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+
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+ macros.xml
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+ $output
+ ]]>
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diff -r 000000000000 -r 028a3ffc17b4 get-object.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/get-object.xml Fri Jun 23 15:04:12 2017 -0400
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+
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+ macros.xml
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+ $output
+ ]]>
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diff -r 000000000000 -r 028a3ffc17b4 images/ScreenShot1.png
Binary file images/ScreenShot1.png has changed
diff -r 000000000000 -r 028a3ffc17b4 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Jun 23 15:04:12 2017 -0400
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+ doi:10.5281/zenodo.815635
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diff -r 000000000000 -r 028a3ffc17b4 phenotype-gene-associations.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phenotype-gene-associations.xml Fri Jun 23 15:04:12 2017 -0400
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+ macros.xml
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+ $output
+ ]]>
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diff -r 000000000000 -r 028a3ffc17b4 search-operations.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/search-operations.xml Fri Jun 23 15:04:12 2017 -0400
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+ macros.xml
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+ $output
+ ]]>
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diff -r 000000000000 -r 028a3ffc17b4 substance-associations.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/substance-associations.xml Fri Jun 23 15:04:12 2017 -0400
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+ macros.xml
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+ $output
+ ]]>
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diff -r 000000000000 -r 028a3ffc17b4 test-data/associations-for-variant.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/associations-for-variant.json Fri Jun 23 15:04:12 2017 -0400
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+{"associations": [{"subject_extension": null, "slim": null, "publications": null, "object": {"xrefs": null, "taxon": {"label": "Danio rerio", "id": "NCBITaxon:7955"}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "fgf8a/fgf8a; shha/shha [n.s.]", "deprecated": null, "id": "ZFIN:ZDB-FISH-150901-25704", "description": null, "consider": null}, "id": "3fe46d0c-e666-48fd-a95e-7b3591d40f57", "type": null, "evidence_graph": {"nodes": [{"lbl": "tbx392", "id": "ZFIN:ZDB-ALT-010427-8"}, {"lbl": "fgf8a/fgf8a; shha/shha", "id": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8-_ZDB-GENE-990415-72-ZDB-ALT-980203-1091-ZDB-ALT-980203-1091"}, {"lbl": "shha", "id": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8"}, {"lbl": "shha/shha", "id": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8"}, {"lbl": "fgf8a/fgf8a; shha/shha [n.s.]", "id": "ZFIN:ZDB-FISH-150901-25704"}], "edges": [{"sub": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8", "pred": "GENO:0000382", "obj": "ZFIN:ZDB-ALT-010427-8"}, {"sub": "ZFIN:ZDB-FISH-150901-25704", "pred": "GENO:0000382", "obj": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8-_ZDB-GENE-990415-72-ZDB-ALT-980203-1091-ZDB-ALT-980203-1091"}, {"sub": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8", "pred": "GENO:0000382", "obj": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8"}, {"sub": "ZFIN:ZDB-FISH-150901-25704", "pred": "GENO:0000382", "obj": "ZFIN:ZDB-FISH-150901-25704"}, {"sub": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8-_ZDB-GENE-990415-72-ZDB-ALT-980203-1091-ZDB-ALT-980203-1091", "pred": "GENO:0000382", "obj": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8"}]}, "subject": {"xrefs": null, "taxon": {"label": null, "id": null}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "tbx392", "deprecated": null, "id": "ZFIN:ZDB-ALT-010427-8", "description": null, "consider": null}, "provided_by": ["http://data.monarchinitiative.org/ttl/zfin.ttl"], "relation": {"types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": null, "deprecated": null, "id": null, "description": null, "consider": null}, "qualifiers": null, "object_extension": null, "evidence_types": null}, {"subject_extension": null, "slim": null, "publications": null, "object": {"xrefs": null, "taxon": {"label": "Danio rerio", "id": "NCBITaxon:7955"}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "shha/shha [n.s.]; myog", "deprecated": null, "id": "ZFIN:ZDB-FISH-150901-19342", "description": null, "consider": null}, "id": "ea094031-5086-478a-baf1-3297c258a429", "type": null, "evidence_graph": {"nodes": [{"lbl": "tbx392", "id": "ZFIN:ZDB-ALT-010427-8"}, {"lbl": "shha/shha [n.s.]; myog", "id": "ZFIN:ZDB-FISH-150901-19342"}, {"lbl": "shha", "id": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8"}, {"lbl": "shha/shha", "id": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8"}, {"lbl": "shha/shha [n.s.]", "id": "ZFIN:ZDB-FISH-150901-6607"}], "edges": [{"sub": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8", "pred": "GENO:0000382", "obj": "ZFIN:ZDB-ALT-010427-8"}, {"sub": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8", "pred": "GENO:0000382", "obj": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8"}, {"sub": "ZFIN:ZDB-FISH-150901-6607", "pred": "GENO:0000382", "obj": "ZFIN:ZDB-FISH-150901-6607"}, {"sub": "ZFIN:ZDB-FISH-150901-19342", "pred": "GENO:0000382", "obj": "ZFIN:ZDB-FISH-150901-6607"}, {"sub": "ZFIN:ZDB-FISH-150901-6607", "pred": "GENO:0000382", "obj": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8"}]}, "subject": {"xrefs": null, "taxon": {"label": null, "id": null}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "tbx392", "deprecated": null, "id": "ZFIN:ZDB-ALT-010427-8", "description": null, "consider": null}, "provided_by": ["http://data.monarchinitiative.org/ttl/zfin.ttl"], "relation": {"types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": null, "deprecated": null, "id": null, "description": null, "consider": null}, "qualifiers": null, "object_extension": null, "evidence_types": null}, {"subject_extension": null, "slim": null, "publications": null, "object": {"xrefs": null, "taxon": {"label": "Danio rerio", "id": "NCBITaxon:7955"}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "ndr2/ndr2; shha/shha [n.s.]", "deprecated": null, "id": "ZFIN:ZDB-FISH-150901-12204", "description": null, "consider": null}, "id": "c0883e4f-2925-478f-bfae-621a2164fff5", "type": null, "evidence_graph": {"nodes": [{"lbl": "ndr2/ndr2; shha/shha [n.s.]", "id": "ZFIN:ZDB-FISH-150901-12204"}, {"lbl": "tbx392", "id": "ZFIN:ZDB-ALT-010427-8"}, {"lbl": "shha", "id": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8"}, {"lbl": "shha/shha", "id": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8"}, {"lbl": "ndr2/ndr2; shha/shha", "id": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8-_ZDB-GENE-990415-181-ZDB-ALT-980203-605-ZDB-ALT-980203-605"}], "edges": [{"sub": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8", "pred": "GENO:0000382", "obj": "ZFIN:ZDB-ALT-010427-8"}, {"sub": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8", "pred": "GENO:0000382", "obj": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8"}, {"sub": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8-_ZDB-GENE-990415-181-ZDB-ALT-980203-605-ZDB-ALT-980203-605", "pred": "GENO:0000382", "obj": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8"}, {"sub": "ZFIN:ZDB-FISH-150901-12204", "pred": "GENO:0000382", "obj": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8-ZDB-ALT-010427-8-_ZDB-GENE-990415-181-ZDB-ALT-980203-605-ZDB-ALT-980203-605"}, {"sub": "ZFIN:ZDB-FISH-150901-12204", "pred": "GENO:0000382", "obj": "ZFIN:ZDB-FISH-150901-12204"}]}, "subject": {"xrefs": null, "taxon": {"label": null, "id": null}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "tbx392", "deprecated": null, "id": "ZFIN:ZDB-ALT-010427-8", "description": null, "consider": null}, "provided_by": ["http://data.monarchinitiative.org/ttl/zfin.ttl"], "relation": {"types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": null, "deprecated": null, "id": null, "description": null, "consider": null}, "qualifiers": null, "object_extension": null, "evidence_types": null}, {"subject_extension": null, "slim": null, "publications": null, "object": {"xrefs": null, "taxon": {"label": "Danio rerio", "id": "NCBITaxon:7955"}, "types": null, "categories": null, "replaced_by": null, "synonyms": null, "label": "shha/shha [n.s.]", "deprecated": null, "id": "ZFIN:ZDB-FISH-150901-10317", "description": null, "consider": null}, "id": "d52846ef-ed3b-4277-bdc6-dc572d335e5c", "type": null, "evidence_graph": {"nodes": [{"lbl": "tbx392", "id": "ZFIN:ZDB-ALT-010427-8"}, {"lbl": "shha/shha", "id": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010426-4-ZDB-ALT-010427-8"}, {"lbl": "shha", "id": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8"}, {"lbl": "shha/shha [n.s.]", "id": "ZFIN:ZDB-FISH-150901-10317"}], "edges": [{"sub": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010427-8", "pred": "GENO:0000382", "obj": "ZFIN:ZDB-ALT-010427-8"}, {"sub": "ZFIN:ZDB-FISH-150901-10317", "pred": "GENO:0000382", "obj": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010426-4-ZDB-ALT-010427-8"}, {"sub": ":.well-known/genid/ZDB-GENE-980526-166-ZDB-ALT-010426-4-ZDB-ALT-010427-8", "pred": "GENO:0000382", "obj": 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