diff starting_modules.py @ 4:035a58c7f54a draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"

--- a/starting_modules.py	Mon May 11 07:45:48 2020 -0400
+++ b/starting_modules.py	Sat Feb 06 09:59:30 2021 +0000
@@ -1,6 +1,5 @@
 import json
 import sys
-import os
 
 FOURSPACES = "    "
 
@@ -13,7 +12,7 @@
     filter_images = params['images']['filter_images']
 
     _str = "\nImages:[module_num:1|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
-    _str += FOURSPACES+":\n"
+    _str += FOURSPACES + ":\n"
     _str += FOURSPACES + "Filter images?:%s\n" % filter_images
     _str += FOURSPACES + "Select the rule criteria:and (extension does isimage) (directory doesnot startwith \".\")\n"
 
@@ -45,7 +44,7 @@
         _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
         _str += FOURSPACES + "Use case insensitive matching?:No\n"
     else:
-        _str += FOURSPACES + "Metadata data type:Text\n"  #default Text,not possible to select in Galaxy
+        _str += FOURSPACES + "Metadata data type:Text\n"  # default Text,not possible to select in Galaxy
         _str += FOURSPACES + "Metadata types:{}\n"
         _str += FOURSPACES + "Extraction method count:%d\n" % method_count
 
@@ -70,19 +69,18 @@
             _str += FOURSPACES + "Extract metadata from:%s\n" % methods["con_metadata_extract_from"]["extract_metadata_from"]
 
             if methods["con_metadata_extract_from"]["extract_metadata_from"] == "Images matching a rule":
-                rule_str =""
+                rule_str = ""
                 for r in methods["con_metadata_extract_from"]["r_match"]:
                     if r["con_match"]["rule_type"] == "extension":
                         rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \
-                                    r["con_match"]["match_type"]+")"
+                                    r["con_match"]["match_type"] + ")"
                     else:
-                        rule_str +=" (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " +\
-                                   r["con_match"]["contain"] + " \"" + r["con_match"]["match_value"] +"\")"
+                        rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " +\
+                            r["con_match"]["contain"] + " \"" + r["con_match"]["match_value"] + "\")"
 
-
-                _str += FOURSPACES + "Select the filtering criteria:" + methods["con_metadata_extract_from"]["match_all_any"] + rule_str +"\n"
+                _str += FOURSPACES + "Select the filtering criteria:" + methods["con_metadata_extract_from"]["match_all_any"] + rule_str + "\n"
             else:
-                _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n" #this line is required even if it's not used
+                _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n"  # this line is required even if it's not used
 
             _str += FOURSPACES + "Metadata file location:\n"
             _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
@@ -127,7 +125,7 @@
         _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
 
     else:
-        #the below lines are not relevant to "images matching rules", but needed in pipeline file
+        # the below lines are not relevant to "images matching rules", but needed in pipeline file
         _str += FOURSPACES + "Select the image type:Grayscale image\n"
         _str += FOURSPACES + "Name to assign these images:DNA\n"
         _str += FOURSPACES + "Match metadata:[]\n"
@@ -147,18 +145,18 @@
         for rule in nameandtypes["con_assign_a_name_to"]["r_match_rule"]:
 
             rule_str = ""
-            if len(rule["r_match"]) >0 :
+            if len(rule["r_match"]) > 0:
                 for r in rule["r_match"]:
-                        if r["con_match"]["rule_type"] == "file" or r["con_match"]["rule_type"] == "directory":
-                            rule_str += " (" + r["con_match"]["rule_type"] + " "+r["con_match"]["operator"]+" "+\
-                                        r["con_match"]["contain"]+" \"" + r["con_match"]["match_value"] +"\")"
-                        else:
-                            rule_str += " ("+ r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \
-                                        r["con_match"]["match_type"] + ")"
+                    if r["con_match"]["rule_type"] == "file" or r["con_match"]["rule_type"] == "directory":
+                        rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \
+                            r["con_match"]["contain"] + " \"" + r["con_match"]["match_value"] + "\")"
+                    else:
+                        rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \
+                            r["con_match"]["match_type"] + ")"
             else:
-                rule_str = " (file does contain \"\")"  #need to have a value even if it is not used
+                rule_str = " (file does contain \"\")"  # need to have a value even if it is not used
 
-            _str += FOURSPACES + "Select the rule criteria:" + rule["match_all_any"] + rule_str +"\n"
+            _str += FOURSPACES + "Select the rule criteria:" + rule["match_all_any"] + rule_str + "\n"
 
             img_or_obj = rule["con_select_image_type"]["select_image_type"]
 
@@ -171,8 +169,7 @@
 
             _str += FOURSPACES + "Select the image type:%s\n" % img_or_obj
 
-
-            intensity_range="Image metadata" #default value
+            intensity_range = "Image metadata"  # default value
             if img_or_obj == "Grayscale image" or img_or_obj == "Color image":
                 intensity_range = rule["con_select_image_type"]["con_set_intensity"]["set_intensity_range_from"]
 
@@ -183,7 +180,6 @@
             else:
                 _str += FOURSPACES + "Maximum intensity:255.0\n"
 
-
     return _str
 
 
@@ -192,7 +188,7 @@
 
     _str = "\nGroups:[module_num:4|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
 
-    group_images =  groups["con_groups"]["group_images"]
+    group_images = groups["con_groups"]["group_images"]
 
     _str += FOURSPACES + "Do you want to group your images?:%s\n" % group_images
     _str += FOURSPACES + "grouping metadata count:1\n"
@@ -224,4 +220,4 @@
     output_str = img_str + metadata_str + nameandtypes_str + groups_str
 
     f.write(output_str)
-    f.close()
\ No newline at end of file
+    f.close()