Mercurial > repos > recetox > recetox_datatypes

changeset 0:4c64436e0c6f draft default tip

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"planemo upload commit 9d75007f88d8f0c351951d7f47a79c7922ef3395-dirty"
author recetox
date Tue, 25 Aug 2020 13:05:18 +0000
parents
children
files datatypes_conf.xml lib/galaxy/datatypes/feather.py
diffstat 2 files changed, 53 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Tue Aug 25 13:05:18 2020 +0000
@@ -0,0 +1,38 @@
+<?xml version="1.0"?>
+<datatypes>
+    <datatype_files>
+        <datatype_file name="feather.py" />
+    </datatype_files>
+
+    <registration>
+        <datatype extension="feather" type="galaxy.datatypes.feather:Feather" display_in_upload="true">
+            <converter file="feather_to_csv_converter.xml" target_datatype="csv"/>
+        </datatype>
+
+        <datatype extension="peak_table.feather" type="galaxy.datatypes.feather:Feather" subclass="true">
+            <converter file="feather_to_csv_converter.xml" target_datatype="csv"/>
+        </datatype>
+        <datatype extension="time_table.feather" type="galaxy.datatypes.feather:Feather" subclass="true">
+            <converter file="feather_to_csv_converter.xml" target_datatype="csv"/>
+        </datatype>
+        <datatype extension="aplcms_history.feather" type="galaxy.datatypes.feather:Feather" subclass="true">
+            <converter file="feather_to_csv_converter.xml" target_datatype="csv"/>
+        </datatype>
+
+        <datatype extension="peak_list.feather" type="galaxy.datatypes.feather:Feather" subclass="true">
+            <converter file="feather_to_csv_converter.xml" target_datatype="csv"/>
+        </datatype>
+        <datatype extension="metabolites.feather" type="galaxy.datatypes.feather:Feather" subclass="true">
+            <converter file="feather_to_csv_converter.xml" target_datatype="csv"/>
+        </datatype>
+        <datatype extension="annotated_peak_list.feather" type="galaxy.datatypes.feather:Feather" subclass="true">
+            <converter file="feather_to_csv_converter.xml" target_datatype="csv"/>
+        </datatype>
+        
+        <datatype extension="metabolites.h5" type="galaxy.datatypes.binary:H5" subclass="true" />
+    </registration>
+
+    <sniffers>
+        <sniffer type="galaxy.datatypes.feather:Feather" />
+    </sniffers>
+</datatypes>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/galaxy/datatypes/feather.py	Tue Aug 25 13:05:18 2020 +0000
@@ -0,0 +1,15 @@
+from galaxy.datatypes.binary import Binary
+from galaxy.datatypes.metadata import ColumnTypesParameter, MetadataElement
+
+
+class Feather(Binary):
+    file_ext = "feather"
+    
+    
+    def sniff(self, filename):
+        try:
+            with open(filename, 'rb') as f:
+                header = f.read(6)
+            return header.startswith((b'FEA1', b'ARROW1'))
+        except Exception:
+            return False