diff measure_object_size_shape.xml @ 0:eba2ec72f967 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_object_size_shape.xml	Thu Mar 26 17:45:13 2020 -0400
@@ -0,0 +1,86 @@
+<tool id="cp_measure_object_size_shape" name="MeasureObjectSizeShape" version="@CP_VERSION@">
+    <description>measures several area and shape features of identified objects</description>
+  
+    <macros>
+        <import>macros.xml</import>
+    </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 writemoss():
+    _str = "\nMeasureObjectSizeShape:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:1|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
+
+    for obj in params['rpt_object']:
+        _str += FOURSPACES + "Select objects to measure:%s\n" % obj['objects_to_measure']
+
+    _str += FOURSPACES + "Calculate the Zernike features?:%s\n" % params['zernike_feature']
+
+    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(writemoss())
+
+f.close()
+        </configfile>    
+    </configfiles>
+    
+    <inputs>
+      <expand macro="input_pipeline_macro" />
+      <repeat name="rpt_object" title="Add another object">
+          <param name="objects_to_measure" label="Select objects to measure" type="text" >
+            <expand macro="text_validator" />
+          </param>
+      </repeat>
+      <param name="zernike_feature" type="select" display="radio" label="Calculate the Zernike features?">
+          <option value="Yes">Yes</option>
+          <option value="No">No</option>
+      </param>
+    </inputs>
+
+    <outputs>
+        <expand macro="output_pipeline_macro" />
+    </outputs>
+
+    <tests>
+        <test>
+            <expand macro="test_input_pipeline_param" />
+            <repeat name="rpt_object">
+                <param name="objects_to_measure" value="Nuclei" />
+            </repeat>
+            <repeat name="rpt_object">
+                <param name="objects_to_measure" value="Nucleoli" />
+            </repeat>
+            <param name="zernike_feature" value="Yes" />
+            <expand macro="test_out_file" file="measure_object_size_shape.txt" />
+        </test>
+    </tests>
+
+    <expand macro="help" module="MeasureObjectSizeShape" />
+    <expand macro="citations" /> 
+
+</tool>