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changeset 1:0b7db679fff8 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6a3036d24b5ec074936f8f8283b7e176f6f1ce70"
author bgruening
date Thu, 09 Apr 2020 08:12:15 -0400
parents 9c8ee01c0b22
children 3c3cd68d6d5a
files common.xml test-data/common.txt test-data/convert_objects_to_image.txt test-data/display_data_on_image.txt test-data/enhance_or_suppress_features.txt test-data/export_to_spreadsheet.txt test-data/gray_to_color.txt test-data/identify_primary_objects.txt test-data/mask_image.txt test-data/measure_granularity.txt test-data/measure_image_area_occupied.txt test-data/measure_image_intensity.txt test-data/measure_image_quality.txt test-data/measure_object_intensity.txt test-data/measure_object_size_shape.txt test-data/measure_texture.txt test-data/relate_objects.txt test-data/save_images.txt
diffstat 18 files changed, 27 insertions(+), 24 deletions(-) [+]
line wrap: on
line diff
--- a/common.xml	Thu Mar 26 16:23:56 2020 -0400
+++ b/common.xml	Thu Apr 09 08:12:15 2020 -0400
@@ -182,9 +182,9 @@
         _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
         _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
 
-        _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" + x_spacing
-        _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" + y_spacing
-        _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" + z_spacing
+        _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" % x_spacing
+        _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" % y_spacing
+        _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" % z_spacing
     else:
         _str += FOURSPACES + "Select the image type:Grayscale image\n"
         _str += FOURSPACES + "Name to assign these images:DNA\n"
@@ -218,9 +218,9 @@
                 _str += FOURSPACES + "Maximum intensity:255.0\n"
 
             if process_3d == "Yes":
-                _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" + x_spacing
-                _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" + y_spacing
-                _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" + z_spacing
+                _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" % x_spacing
+                _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" % y_spacing
+                _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" % z_spacing
 
     return _str
 
@@ -305,8 +305,11 @@
                             <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)_(?P&lt;field6>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5_field6</option>
                             <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)__(?P&lt;field6>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5__field6</option>
                         </param>
-                        <param name="folder_name_regex" type="text" value="(?P&lt;Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$" label="Regular expression to extract from folder name"> 
+                        <param name="folder_name_regex" type="select" label="Select folder name pattern to extract from folder name" help="Folder names must comply with one of the patterns.For example, folder name images-exp1 matches the pattern field1-field2. If none of the patterns are suitable, please use other Galaxy tools to rename your folder first.  "> 
                             <sanitizer sanitize="false"/>
+                            <option value="(?P&lt;field1>.*)">field1</option>
+                            <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)">field1-field2</option>
+                            <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)">field1_field2</option>
                         </param>
                         <param name="extract_metadata_from" type="select" label="Extract metadata from">
                             <option value="All images">All images</option>
--- a/test-data/common.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/common.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/convert_objects_to_image.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/convert_objects_to_image.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/display_data_on_image.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/display_data_on_image.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/enhance_or_suppress_features.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/enhance_or_suppress_features.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/export_to_spreadsheet.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/export_to_spreadsheet.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/gray_to_color.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/gray_to_color.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/identify_primary_objects.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/identify_primary_objects.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/mask_image.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/mask_image.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/measure_granularity.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/measure_granularity.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/measure_image_area_occupied.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/measure_image_area_occupied.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/measure_image_intensity.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/measure_image_intensity.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/measure_image_quality.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/measure_image_quality.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/measure_object_intensity.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/measure_object_intensity.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/measure_object_size_shape.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/measure_object_size_shape.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/measure_texture.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/measure_texture.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/relate_objects.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/relate_objects.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location:
--- a/test-data/save_images.txt	Thu Mar 26 16:23:56 2020 -0400
+++ b/test-data/save_images.txt	Thu Apr 09 08:12:15 2020 -0400
@@ -18,7 +18,7 @@
     Metadata extraction method:Extract from file/folder names
     Metadata source:File name
     Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<Date>[0-9]{4}_[0-9]{2}_[0-9]{2})$
+    Regular expression to extract from folder name:(?P<field1>.*)
     Extract metadata from:All images
     Select the filtering criteria:and (file does contain "")
     Metadata file location: