add conf files to tests addrun, add projet and addanalysis

remove BasicAnalyse class from addanalysis workflow, using the
BasicAnalysis Class from components directory instead

workflows/addanalysis/__init__.py

@@ -81,7 +81,7 @@ class AddAnalysis (BasicNG6Workflow):
             if parent.id not in analyses_ids :
                     display_error_message("The parent analysis associated with id '%s' does not belong to the %s id '%s' " % (parent.id, addto, self.project_id or self.run_id) )
         
-        basicanalysis = self.add_component("BasicAnalyse", [files_to_save, self.analysis_name, 
+        basicanalysis = self.add_component("BasicAnalysis", [files_to_save, self.analysis_name, 
                         self.analysis_description, self.analysis_software, self.analysis_software_options, 
                         self.analysis_software_version, self.compression, self.delete, 
                         self.archive_name], addto=addto, parent = parent)        

workflows/addanalysis/data/addanalysis.conf

+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+--data-file
+workflows\illumina_diversity_qc\data\casava_directory_test\Project_Demo_project\Sample_Demo\Demo_AGAGAG_L001_R1_001.fastq.gz
+--analysis-name
+Add an analysis, storing fastq file
+--analysis-description
+Juste copy a fastq file
+--analysis-software
+cp
+--analysis-software-options
+-f
+--analysis-software-version
+1.2

workflows/addanalysis/components/basicanalysis.py → workflows/addproject/data/addproject.conf

-#
-# Copyright (C) 2012 INRA
-# 
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-# 
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-# 
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-#
-
-from ng6.analysis import Analysis
-
-class BasicAnalyse (Analysis):
-    
-    def define_parameters(self, files, name, description, software, options, version, compression="none", 
-                          delete=False, archive_name=None):
-        
-        self.add_input_file_list( "files", "The files to be archived.", default=files, required=True )
-        self.add_parameter( "name", "The analysis name", default=name, required = True )
-        self.add_parameter( "description", "Analysis description", default=description, required = True )
-        self.add_parameter( "software", "The analysis software", default=software, required = True )
-        self.add_parameter( "options", "The analysis software options", default=options, required = True )
-        self.add_parameter( "version", "The analysis software version", default=version, required = True )
-        self.add_parameter( "compression", "File compression once archived", default=compression)
-        self.add_parameter( "delete", "Should the input data be deleted once the process is over", type = bool, default=delete)
-        self.add_parameter( "archive_name", "Give a name to the final archive", default=archive_name)
-        self.is_editable = True
-        
-    def define_analysis(self): pass
-        
-    def process(self): pass
-        
-    def get_version(self): return ""
-    
-    def post_process(self):
-        self._archive_files(self.files, self.compression, self.archive_name, self.delete)
-        
\ No newline at end of file
+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+--name 
+Demo project 2
+
+--description 
+Test adding a project

workflows/addrun/data/addrun.conf

+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+--project-name 
+Demo project 
+--name 
+Adding a run to a project
+--description 
+Test adding a run to a project
+--date
+25/08/2018
+--data-nature
+gDNA
+--sequencer
+MiSeqX
+--species
+bug
+--type
+Lane 1
\ No newline at end of file