diff dada2_datatype.py @ 0:60abca9ae15f draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dada2_datatype.py	Fri Mar 08 06:44:26 2019 -0500
@@ -0,0 +1,84 @@
+# -*- coding: utf-8 -*-
+"""
+dada2 datatypes
+
+Author: [e-mail]
+"""
+
+import logging
+import os,os.path,re
+from galaxy.datatypes.binary import RData
+from galaxy.datatypes.tabular import Tabular
+
+log = logging.getLogger(__name__)
+
+
+class dada_derep( Tabular ):
+    """
+    datatype for dada2's derep-class
+
+    - table shows the $uniques member of the list
+    - additional file contains the Rdata
+    """
+    file_ext = "dada2_derep"
+    composite_type = 'basic'
+    allow_datatype_change = False
+    blurb = "dereplicated sequences"
+
+    def __init__(self, **kwd):
+        """Initialize derep datatype"""
+        super(dada_derep, self).__init__(**kwd)
+        self.add_composite_file( 'Rdata', is_binary = True, optional = False )
+        self.column_names = ['unique sequence', 'abundance']
+
+class dada_dada( RData ):
+    """
+    datatype for dada2's dada-class
+    """
+    file_ext = "dada2_dada"
+    blurb = "result of dada"
+
+class dada_errorrates( Tabular ):
+    """
+    datatype for dada2's result of learnErrors
+
+    - table shows the $err_out member of the list
+    - additional file contains the Rdata
+    """
+    file_ext = "dada2_errorrates"
+    blurb = "learned error rates"
+    def __init__(self, **kwd):
+        """Initialize derep datatype"""
+        super(dada_errorrates, self).__init__(**kwd)
+        self.add_composite_file( 'Rdata', is_binary = True, optional = False )
+        self.column_names = ['transition'] + [ str(_) for _ in range(0,41) ]
+
+class dada_mergepairs( Tabular ):
+    """
+    datatype for dada2's result of mergePairs (a data frame)
+
+    - the data is stored as table (wo additional Rdata)
+    """
+    file_ext = "dada2_mergepairs"
+    blurb = "merged reads"
+    def __init__(self, **kwd):
+        """Initialize derep datatype"""
+        super(dada_mergepairs, self).__init__(**kwd)
+        self.column_names = ['abundance', 'sequence', 'forward', 'reverse', 'nmatch', 'nmismatch', 'nindel', 'prefer', 'accept']
+
+class dada_sequencetable( Tabular ):
+    """
+    datatype for dada2's result of makeSequencetable (a named integer matrix col=sequences, rows=samples)
+    """
+
+    file_ext = "dada2_sequencetable"
+    blurb = "merged reads"
+
+
+class dada_uniques( Tabular ):
+    """
+    datatype for dada2's result of makeSequencetable (a named integer matrix col=sequences, rows=samples)
+    """
+
+    file_ext = "dada2_uniques"
+    blurb = "uniques"