diff measure_texture.xml @ 0:0f751bb492de 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/measure_texture.xml	Thu Mar 26 16:30:56 2020 -0400
@@ -0,0 +1,132 @@
+<tool id="cp_measure_texture" name="MeasureTexture" version="@CP_VERSION@">
+    <description>measures the degree and nature of textures within images and objects to quantify their roughness and smoothness</description>
+  
+    <macros>
+        <import>macros.xml</import>
+        <xml name="measureImgObj">
+            <repeat name="rpt_obj_to_measure" title="Add another object">
+                <param name="obj_to_measure" label="Select objects to measure" type="text" />       
+            </repeat>
+        </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 writemi():
+    _str = "\nMeasureTexture:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:5|show_window:False|notes:\\x5B\\'PARAMS\\x3A\\', \\'- Texture scale\'\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
+
+    img_count = len(params['rpt_image_to_measure'])
+    obj_count = len(params['con_img_obj']['rpt_obj_to_measure'])
+    scale_count = len(params['rpt_scale_to_measure'])
+
+    img_obj = params['con_img_obj']['img_obj']
+
+    _str += FOURSPACES + "Hidden:%d\n" % img_count
+    _str += FOURSPACES + "Hidden:%d\n" % obj_count
+    _str += FOURSPACES + "Hidden:%d\n" % scale_count
+
+    for img in params['rpt_image_to_measure']:
+        _str += FOURSPACES + "Select an image to measure:%s\n" % img['image_to_measure']
+
+    if img_obj == "Images":
+        _str += FOURSPACES + "Select objects to measure:None\n"
+    else:
+        for obj in params['con_img_obj']['rpt_obj_to_measure']:
+            _str += FOURSPACES + "Select objects to measure:%s\n" % obj['obj_to_measure']
+
+    for scale in params['rpt_scale_to_measure']:
+        _str += FOURSPACES + "Texture scale to measure:%s\n" % str(scale['scale_to_measure'])
+
+    _str += FOURSPACES + "Measure images or objects?:%s\n" % params['con_img_obj']['img_obj']
+
+    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(writemi())
+
+f.close()
+        </configfile>    
+    </configfiles>
+  
+    <inputs>
+
+        <expand macro="input_pipeline_macro" />
+        <repeat name="rpt_image_to_measure" title="Add another image">
+            <param name="image_to_measure" label="Select an image to measure" type="text" >
+                <expand macro="text_validator" />
+            </param>
+        </repeat>
+
+        <conditional name="con_img_obj">
+            <param name="img_obj" label="Measure images or objects?" type="select">
+                <option value="Images">Images</option>
+                <option value="Objects">Objects</option>
+                <option value="Both">Both</option>
+            </param>
+            <when value="Objects">
+                <expand macro="measureImgObj" />
+            </when>
+            <when value="Both">
+                <expand macro="measureImgObj" />
+            </when>
+            <when value="Images" />
+        </conditional>
+        <repeat name="rpt_scale_to_measure" title="Add another scale">
+            <param name="scale_to_measure" label="Texture scale to measure" type="integer" value="3" min="0" />
+        </repeat>
+    </inputs>
+
+    <outputs>
+        <expand macro="output_pipeline_macro" />
+    </outputs>
+
+    <tests>
+        <test>
+            <expand macro="test_input_pipeline_param" />
+            <repeat name="rpt_image_to_measure">
+                <param name="image_to_measure" value="DNA" />
+            </repeat>
+            <conditional name="con_img_obj">
+                <param name="img_obj" value="Objects" />
+                <repeat name="rpt_obj_to_measure">
+                    <param name="obj_to_measure" value="Nuclei" />
+                </repeat>
+            </conditional>
+
+            <repeat name="rpt_scale_to_measure">
+                <param name="scale_to_measure" value="3" />
+            </repeat>
+
+            <expand macro="test_out_file" file="measure_texture.txt" />
+        </test>
+    </tests>
+
+    <expand macro="help" module="MeasureObjectSizeShape" />
+    <expand macro="citations" /> 
+</tool>