changeset 0:5d6ff635462f draft default tip

planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Tue Jun 26 08:57:11 2018 -0400
@@ -0,0 +1,17 @@
+<?xml version="1.0"?>
+<datatypes>
+    <datatype_files>
+        <datatype_file name="gmql.py" />
+    </datatype_files>
+        <registration>
+            <!-- GMQL Custom datatypes -->
+            <datatype extension="gmql_user" type="galaxy.datatypes.tabular:Tabular" subclass="True" />
+            <datatype extension="gmql_query" type="galaxy.datatypes.data:Text" subclass="True"/>
+            <datatype extension="gmql_repository" type="galaxy.datatypes.tabular:Tabular" subclass="True" />
+            <datatype extension="meta" type="galaxy.datatypes.tabular:Tabular" subclass="True" />
+            <datatype extension="gdm" type="galaxy.datatypes.gmql:Gdm" display_in_upload="True" />
+        </registration>
+        <sniffers>
+            <sniffer type="galaxy.datatypes.gmql:Gdm" />
+        </sniffers>
+</datatypes>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gmql.py	Tue Jun 26 08:57:11 2018 -0400
@@ -0,0 +1,69 @@
+# Custom datatypes for the use of the GMQL framework within Galaxy
+# ----------------------------------------------------------------------------
+# Luana Brancato, [e-mail]
+# ----------------------------------------------------------------------------
+
+from galaxy.datatypes import metadata
+from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes.tabular import Tabular
+from galaxy.datatypes.sniff import get_headers
+
+import logging
+
+class Gdm ( Tabular ):
+    """Tab delimited data in Gdm format"""
+
+    file_ext = "gdm"
+    column_names = ['chr','left','right','strand','name','score']
+
+
+    MetadataElement( name='columns', default='6', desc='Number of Columns', readonly=True, visible=False )
+    MetadataElement( name='column_types', default=['str','int','int','str','str','float'],
+                     param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False)
+
+
+    def display_peek(self, dataset):
+        """Returns formatted html of peek"""
+
+        return self.make_html_table(dataset, column_names=self.column_names)
+
+    def sniff(self, filename):
+        """
+        Determines whether a file is in gdm format
+
+        GDM files have at least 6 required fields.
+        (Actually in the format definition only the first 5 are mandatory, but the ones returned by the system have
+        always at least 6).
+
+        Required fields must be tab separated.
+
+        Columns 0, 3, 4 must be strings.
+        Columns 1, 2, 5 numbers.
+
+        Column 5 (Score) can be not provided.
+
+
+        """
+
+
+        headers = get_headers(filename, '\t', count=10)
+
+
+        try:
+            for hdr in headers:
+                if hdr and hdr[0] and not hdr[0].startswith('#'):
+                    if len(hdr) != 6:
+                        return False
+                    try:
+                        int(hdr[1])
+                        int(hdr[2])
+                    except:
+                        return False
+                    if hdr[5] != '.':
+                        try:
+                            float(hdr[5])
+                        except:
+                            return False
+                    return True
+        except:
+            return False