workflow example OK

src/jflow/parameter.py

@@ -454,6 +454,8 @@ class InputFileList(ParameterList, AbstractFile):
             return list.__init__(self, [default])
         elif default.__class__.__name__ == "list":
             return list.__init__(self, default)
+        elif default.__class__.__name__ == "InputFileList":
+            return list.__init__(self, default)
 
 
 class OutputFileList(ParameterList, AbstractFile):

src/jflow/workflow.py

@@ -240,24 +240,25 @@ class Workflow(threading.Thread):
                                           group=param.group, display_name=param.display_name)
                     self.__setattr__(param.name, new_param)
                 elif param.__class__ == InputFileList:
+                    path2test = args[param.name]
+                    if not path2test.__class__.__name__ == "list":
+                        path2test = [path2test]
+                    default_vals = []
                     # handle url inputs
-                    default_vals, is_uri = [], False
-                    if args[param.name].__class__.__name__ == "list":
-                        for path in args[param.name]:
-                            new_url, is_uri = self._download_urlfile(path)
-                            if is_uri: default_vals.append(new_url)
-                    else:
-                        new_url, is_uri = self._download_urlfile(args[param.name])
-                        if is_uri: default_vals.append(new_url)
-                    # handle upload inputs
-                    try: is_local = os.path.isfile(args[param])
-                    except: is_local = False
-                    if not is_uri and not is_local and param.type.__name__ == "inputfile" or param.type.__name__ == "browsefile":
-                        if args[param.name].__class__.__name__ == "list":
-                            for path in args[param.name]:
-                                default_vals.append(os.path.join(self.jflow_config_reader.get_tmp_directory(), (path)))
-                        else:
-                            default_vals.append(os.path.join(self.jflow_config_reader.get_tmp_directory(), (args[param.name])))
+                    for path in path2test:
+                        new_url, is_uri = self._download_urlfile(path)
+                        if is_uri: 
+                            default_vals.append(new_url)
+                            path2test.remove(path)
+                    # handle localfile
+                    for path in path2test:    
+                        if os.path.isfile(path):
+                            default_vals.append(path)
+                            path2test.remove(path)
+                    # handle upload inputs 
+                    if param.type.__name__ == "inputfile" or param.type.__name__ == "browsefile":
+                        for path in path2test:
+                            default_vals.append(os.path.join(self.jflow_config_reader.get_tmp_directory(), (path)))
                     self.__getattribute__(param.name).extend(default_vals)
                 elif param.__class__ ==  ParameterList:
                     self.__getattribute__(param.name).extend(args[param.name])

workflows/alignment/__init__.py

@@ -35,9 +35,5 @@ class Alignment (Workflow):
         # index the reference genome
         bwaindex = self.add_component("BWAIndex", [self.reference_genome])
         # align reads against indexed genome
-        #bwa = self.add_component("BWA", [bwaindex.databank, self.args["read_1"], self.args["read_2"]])
-        
-        
-        
-        
+        bwa = self.add_component("BWA", [bwaindex.databank, self.read_1, self.read_2])
         
\ No newline at end of file

workflows/components/bwa.py

@@ -19,7 +19,7 @@ import os
 from subprocess import Popen, PIPE
 
 from jflow.component import Component
-from jflow.iotypes import OutputFile, OutputFileList, InputFile, InputFileList, Formats
+from jflow.parameter import Formats
 
 from weaver.function import ShellFunction
 from weaver.abstraction import Map
@@ -29,25 +29,24 @@ from jflow.abstraction import MultiMap
 class BWA (Component):
     
     def define_parameters(self, reference_genome, read1, read2=None, algorithm="aln"):
-        self.read1 = InputFileList(read1, Formats.FASTQ)
-        self.read2 = None
+        self.add_input_file("reference_genome", "Which reference file should be used", default=reference_genome, required=True)
+        self.add_input_file("read1", "Which read1 files should be used", file_format=Formats.FASTQ, default=read1, required=True, is_list=True)
+        self.add_input_file("read2", "Which read2 files should be used", file_format=Formats.FASTQ, default=read2, is_list=True)
+        self.add_parameter("algorithm", "Which algorithm should be used to align the reads", default=algorithm, choices=["aln", "bwasw"])
         if algorithm == "aln":
-            self.sai1 = OutputFileList(self.get_outputs('{basename_woext}.sai', self.read1))
+            self.add_output_file("sai1", "The BWA sai1 file", pattern='{basename_woext}.sai', basename=self.read1, is_list=True)
         else: 
             self.sai1 = None
         if read2: 
-            self.read2 = InputFileList(read2, Formats.FASTQ)
             if algorithm == "aln":
-                self.sai2 = OutputFileList(self.get_outputs('{basename_woext}.sai', self.read2))
+                self.add_output_file("sai2", "The BWA sai2 file", pattern='{basename_woext}.sai', basename=self.read2, is_list=True)
             else: 
                 self.sai2 = None
-            self.bam_files = OutputFileList(self.get_outputs('{basename_woext}.bam', [self.read1, self.read2]), Formats.BAM)
+            self.add_output_file("bam_files", "The BWA bam file", pattern='{basename_woext}.bam', basename=[self.read1, self.read2], file_format=Formats.BAM, is_list=True)
         else:
             self.sai2 = None
-            self.bam_files = OutputFileList(self.get_outputs('{basename_woext}.bam', self.read1), Formats.BAM)
-        self.algorithm = algorithm
-        self.reference_genome = InputFile(reference_genome)
-        self.stderr = os.path.join(self.output_directory, 'bwa.stderr')
+            self.add_output_file("bam_files", "The BWA bam file", pattern='{basename_woext}.bam', basename=self.read1, file_format=Formats.BAM, is_list=True)
+        self.add_output_file("stderr", "The BWA stderr file", basename='bwa.stderr')
         
     def process(self):        
         if self.algorithm=="bwasw":
@@ -77,7 +76,7 @@ class BWA (Component):
                 bwasamse = ShellFunction(self.get_exec_path("bwa") + " samse " + self.reference_genome + \
                                          " $1 $2 2>> " + self.stderr + " | " + self.get_exec_path("samtools") + " view -bS - > $3 2>> " + self.stderr, cmd_format='{EXE} {IN} {OUT}')
                 bwasamse = MultiMap(bwasamse, inputs=[self.sai1, self.read1], outputs=self.bam_files, includes=self.reference_genome)
-
+                
     def get_version(self):
         cmd = [self.get_exec_path("bwa")]
         p = Popen(cmd, stdout=PIPE, stderr=PIPE)