diff save_images.xml @ 0:6e0f244acd32 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/save_images.xml	Thu Mar 26 17:42:45 2020 -0400
@@ -0,0 +1,239 @@
+<tool id="cp_save_images" name="SaveImages" version="@CP_VERSION@">
+    <description>saves image or movie files</description>
+  
+    <macros>
+        <import>macros.xml</import>
+        <xml name="file_format">
+            <param name="file_format" label="Saved file format" type="select">
+                <option value="jpeg">jpeg</option>
+                <option value="npy">npy</option>
+                <option value="png">png</option>
+                <option value="tiff">tiff</option>
+            </param>
+        </xml>
+        <xml name="bit_depth">
+            <param name="bit_depth" label="Image bit depth" type="select">
+                <option value="8-bit integer">8-bit integer</option>
+                <option value="16-bit integer">16-bit integer</option>
+                <option value="32-bit floating point">32-bit floating point</option>
+            </param>
+        </xml>
+    </macros>
+    
+    <expand macro="py_requirements"/>
+    <expand macro="cmd_modules" />
+
+    <configfiles>
+        <inputs name="inputs" />
+        <configfile name="script_file">
+import json
+import sys
+import os
+
+FOURSPACES=@SPACES@
+
+input_json_path = sys.argv[1]
+input_pipeline= sys.argv[2]
+
+params = json.load(open(input_json_path, "r"))
+
+def writesi():
+    _str = "\nSaveImages:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:13|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
+
+    _str += FOURSPACES + "Select the type of image to save:%s\n" % params['con_type_of_image']['type_of_image']
+
+    _str += FOURSPACES + "Select the image to save:%s\n" % params['image_to_save']
+
+    method_for_constructing = params['con_method_for_constructing']['method_for_constructing']
+    _str += FOURSPACES + "Select method for constructing file names:%s\n" % method_for_constructing
+
+    if method_for_constructing == "From image filename":
+        img_name_file_prefix = params['con_method_for_constructing']['name_for_file_prefix']
+        append_suffix = params['con_method_for_constructing']['con_append_suffix']['append_suffix']
+
+        if append_suffix == "Yes":
+            text_append = params['con_method_for_constructing']['con_append_suffix']['text_to_append']
+        else:
+            text_append = ""
+    else:
+        img_name_file_prefix = "None"
+        append_suffix = "No"
+        text_append = ""
+
+    _str += FOURSPACES + "Select image name for file prefix:%s\n" % img_name_file_prefix
+
+    if method_for_constructing == "Sequential numbers":
+        file_prefix = params['con_method_for_constructing']['file_prefix']
+        no_of_digits = params['con_method_for_constructing']['no_of_digits']
+
+        _str += FOURSPACES + "Enter file prefix:%s\n" % file_prefix
+    elif method_for_constructing == "Single name":
+        _str += FOURSPACES + "Enter single file name:%s\n" % params['con_method_for_constructing'][
+            'single_file_name']
+
+        no_of_digits = 4
+    else:
+        _str += FOURSPACES + "Enter single file name:OrigBlue\n"
+        no_of_digits = 4
+        append_suffix = params['con_method_for_constructing']['con_append_suffix']['append_suffix']
+
+    _str += FOURSPACES + "Number of digits:%d\n" % no_of_digits
+    _str += FOURSPACES + "Append a suffix to the image file name?:%s\n" % append_suffix
+    _str += FOURSPACES + "Text to append to the image name:%s\n" % text_append
+
+    save_format = params['con_type_of_image']['con_save_file_format']['file_format']
+
+    _str += FOURSPACES + "Saved file format:%s\n" % save_format
+
+    if save_format == "tiff":
+        bit_depth = params['con_type_of_image']['con_save_file_format']['bit_depth']
+    else:
+        bit_depth = "8-bit integer"
+
+    _str += FOURSPACES + "Output file location:Default Output Folder\\x7Coutput\n"
+    _str += FOURSPACES + "Image bit depth:%s\n" % bit_depth
+    _str += FOURSPACES + "Overwrite existing files without warning?:%s\n" % params['overwrite_without_warning']
+    _str += FOURSPACES + "When to save:%s\n" % params['when_to_save']
+    _str += FOURSPACES + "Record the file and path information to the saved image?:%s\n" % params['record_info']
+    _str += FOURSPACES + "Create subfolders in the output folder?:%s\n" % params['subfolder_in_output']
+    _str += FOURSPACES + "Base image folder:Elsewhere...\n"
+
+    return _str
+
+with open(input_pipeline) as fin:
+    lines = fin.readlines()
+
+    k, v = lines[4].strip().split(':')
+
+    module_count = int(v)
+    new_count = module_count + 1
+    lines[4] = k + ":%d\n" % new_count
+
+    with open("output", "w") as f:
+        f.writelines(lines)
+        f.write(writesi())
+
+f.close()
+        </configfile>
+    </configfiles>
+
+    <inputs>
+        <expand macro="input_pipeline_macro" />
+        <conditional name="con_type_of_image">
+            <param name="type_of_image" type="select" label="Select the type of image to save" >
+                <option value="Image">Image</option>
+                <option value="Mask">Mask</option>
+                <option value="Cropping">Cropping</option>
+                <option value="Movie">Movie</option>
+            </param>
+            <when value="Image">
+                <conditional name="con_save_file_format">
+                    <expand macro="file_format" />
+                    <when value="tiff">
+                        <expand macro="bit_depth" />
+                    </when>
+                    <when value="jpeg" />
+                    <when value="npy" />
+                    <when value="png" />
+                </conditional>
+            </when>
+            <when value="Mask">
+                <expand macro="file_format" />
+            </when>
+            <when value="Cropping">
+                <expand macro="file_format" />
+            </when>
+            <when value="Movie">
+                <expand macro="bit_depth" />
+            </when>                        
+        </conditional>
+        <param name="image_to_save" label="Select the image to save" type="text" />
+        <conditional name="con_method_for_constructing">
+            <param name="method_for_constructing" label="Select method for constructing file names" type="select" >
+                <option value="From image filename">From image filename</option>
+                <option value="Sequential numbers">Sequential numbers</option>
+                <option value="Single name">Single name</option>          
+            </param>
+            <when value="From image filename">
+                <param name="name_for_file_prefix" label="Select image name for file prefix" type="text">
+                  <expand macro="text_validator" />
+                </param>
+                <conditional name="con_append_suffix">
+                    <param name="append_suffix" type="select" display="radio" label="Append a suffix to the image file name?">
+                        <option value="No">No</option>
+                        <option value="Yes">Yes</option>
+                    </param>
+                    <when value="Yes">
+                        <param name="text_to_append" label="Text to append to the image name" type="text">
+                          <expand macro="text_validator" />
+                        </param>
+                    </when>
+                    <when value="No" />
+                </conditional>
+            </when>
+            <when value="Sequential numbers">
+                <param name="file_prefix" label="Enter file prefix" type="text"/>
+                <param name="no_of_digits" label="Number of digits" type="integer" value="4" min="0"/>
+            </when>
+            <when value="Single name">
+                <param name="single_file_name" label="Enter single_file_name" type="text">
+                  <expand macro="text_validator" />
+                </param>
+            </when>
+        </conditional>
+        <param name="overwrite_without_warning" label="Overwrite existing files without warning?" type="select" >
+            <option value="No">No</option>
+            <option value="Yes">Yes</option>
+        </param>
+        <param name="when_to_save" label="When to save" type="select" >
+            <option value="Every cycle">Every cycle</option>
+            <option value="First cycle">First cycle</option>
+            <option value="Last cycle">Last cycle</option>
+        </param>
+        <param name="record_info" label="Record the file and path information to the saved image?" type="select" display="radio">
+            <option value="No">No</option>
+            <option value="Yes">Yes</option>
+        </param>
+        <param name="subfolder_in_output" label="Create subfolders in the output folder?" type="select" display="radio">
+            <option value="No">No</option>        
+        </param>      
+    </inputs>
+
+    <outputs>
+        <expand macro="output_pipeline_macro" />
+    </outputs>
+
+    <tests>
+        <test>
+            <expand macro="test_input_pipeline_param" />
+            
+            <conditional name="con_type_of_image">
+                <param name="type_of_image" value="Image" />
+                <conditional name="con_save_file_format">
+                    <param name="file_format" value="tiff" />
+                    <param name="bit_depth" value="8-bit integer" />
+                </conditional>
+            </conditional>
+            <param name="image_to_save" value="ImageDisplay" />
+            <conditional name="con_method_for_constructing" >
+                <param name="method_for_constructing" value="From image filename" />
+                <param name="name_for_file_prefix" value="DNA" />
+                <conditional name="con_append_suffix">
+                    <param name="append_suffix" value="Yes" />
+                    <param name="text_to_append" value="_nucleiNumbers" />
+                </conditional>
+            </conditional>
+            <param name="overwrite_without_warning" value="Yes" />
+            <param name="when_to_save" value="Every cycle" />
+            <param name="record_info" value="No" />
+            <param name="subfolder_in_output" value="No" />
+
+            <expand macro="test_out_file" file="save_images.txt" />
+
+        </test>
+    </tests>
+
+    <expand macro="help" module="RelateObjects" />
+    <expand macro="citations" />
+
+</tool>