Mercurial > repos > bgruening > cp_export_to_spreadsheet

comparison export_to_spreadsheet.xml @ 0:10257d6d545b draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
author bgruening
date Thu, 26 Mar 2020 16:38:48 -0400
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children c956182d4e2c
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-1:000000000000 0:10257d6d545b
1 <tool id="cp_export_to_spreadsheet" name="ExportToSpreadsheet" version="@CP_VERSION@">
2 <description>exports measurements into one or more files</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <expand macro="py_requirements"/>
8 <expand macro="cmd_modules" />
9
10 <configfiles>
11 <inputs name="inputs"/>
12 <configfile name="script_file">
13 import json
14 import sys
15 import os
16
17 FOURSPACES=@SPACES@
18
19 input_json_path = sys.argv[1]
20 input_pipeline= sys.argv[2]
21
22 params = json.load(open(input_json_path, "r"))
23
24
25 def write_etss():
26 _str = "\nExportToSpreadsheet:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:12|show_window:True|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
27 _str += FOURSPACES + "Select the column delimiter:%s\n" % params["delimiter"]
28 _str += FOURSPACES + "Add image metadata columns to your object data file?:%s\n" % params["add_metadata_column_to_object"]
29
30 measurement = params["con_measurement_export"]
31
32 _str += FOURSPACES + "Select the measurements to export:%s\n" % measurement['export_measurement']
33 _str += FOURSPACES + "Calculate the per-image mean values for object measurements?:%s\n" % params['calc_mean']
34 _str += FOURSPACES + "Calculate the per-image median values for object measurements?:%s\n" % params['calc_median']
35 _str += FOURSPACES + "Calculate the per-image standard deviation values for object measurements?:%s\n" % params['calc_standard_deviation']
36 _str += FOURSPACES + "Output file location:%s\\x7C\n" % params['output_file_location']
37
38 create_gene = params["con_create_gene_pattern"]["create_gene_pattern"]
39
40 if create_gene == "No":
41 _str += FOURSPACES + "Create a GenePattern GCT file?:%s\n" % create_gene
42 _str += FOURSPACES + "Select source of sample row name:Metadata\n"
43 _str += FOURSPACES + "Select the image to use as the identifier:None\n"
44 _str += FOURSPACES + "Select the metadata to use as the identifier:None\n"
45 else:
46 _str += FOURSPACES + "Create a GenePattern GCT file?:%s\n" % create_gene
47 _str += FOURSPACES + "Select the image to use as the identifier:None\n"
48 _str += FOURSPACES + "Select the metadata to use as the identifier:None\n"
49
50 export_all_measurements = params["con_export_all_measurements"]["export_all_measurements"]
51
52 if export_all_measurements == "Yes":
53 _str += FOURSPACES + "Export all measurement types?:%s\n" % export_all_measurements
54
55 if 'select_measurements' in params['con_measurement_export']:
56 _str += FOURSPACES + "Press button to select measurements:%s\n" % params['con_measurement_export']['select_measurements']
57 else:
58 _str += FOURSPACES + "Press button to select measurements:\n"
59
60 _str += FOURSPACES + "Representation of Nan/Inf:%s\n" % params["represent_nan"]
61 _str += FOURSPACES + "Add a prefix to file names?:%s\n" % params["con_prefix"]["add_prefix"]
62
63 if "filename_prefix" in params["con_prefix"]:
64 _str += FOURSPACES + "Filename prefix:%s\n" % params["con_prefix"]["filename_prefix"]
65 else:
66 _str += FOURSPACES + "Filename prefix:MyPrefix_\n"
67
68 _str += FOURSPACES + "Overwrite existing files without warning?:%s\n" % params["overwrite_existing_file"]
69
70 if export_all_measurements == "Yes":
71 _str += FOURSPACES + "Data to export:Do not use\n"
72 _str += FOURSPACES + "Combine these object measurements with those of the previous object?:No\n"
73 _str += FOURSPACES + "File name:DATA.csv\n"
74 _str += FOURSPACES + "Use the object name for the file name?:Yes\n"
75 else:
76 _str += FOURSPACES + "Data to export:%s\n" % params["con_export_all_measurements"]["data_to_export"]
77
78 return _str
79
80 with open(input_pipeline) as fin:
81 lines = fin.readlines()
82
83 k, v = lines[4].strip().split(':')
84
85 module_count = int(v)
86 new_count = module_count + 1
87 lines[4] = k + ":%d\n" % new_count
88 with open("output", "w") as f:
89 f.writelines(lines)
90 f.write(write_etss())
91
92 f.close()
93 </configfile>
94 </configfiles>
95
96 <inputs>
97 <expand macro="input_pipeline_macro" />
98 <param name="delimiter" type="select" label="Select the column delimiter">
99 <option value="Comma (&quot;,&quot;)">Comma (",")</option>
100 <option value="Tab">Tab</option>
101 <sanitizer sanitize="false"/>
102 </param>
103 <param name="output_file_location" type="select" label="Output file location">
104 <option value="Default Output Folder"/>
105 </param>
106 <conditional name="con_prefix">
107 <param name="add_prefix" type="select" display="radio" label="Add a prefix to file names?">
108 <option value="Yes">Yes</option>
109 <option value="No">No</option>
110 </param>
111 <when value="Yes">
112 <param name="filename_prefix" type="text" label="Filename prefix"/>
113 </when>
114 <when value="No" />
115 </conditional>
116 <param name="overwrite_existing_file" display="radio" type="select" label="Overwrite existing files without warning?">
117 <option value="Yes">Yes</option>
118 <option value="No">No</option>
119 </param>
120 <param name="add_metadata_column_to_object" display="radio" type="select" label="Add image metadata columns to your object data file?">
121 <option value="Yes">Yes</option>
122 <option value="No">No</option>
123 </param>
124 <param name="represent_nan" type="select" label="Representation of Nan/Inf">
125 <option value="NaN">NaN</option>
126 <option value="Null">Null</option>
127 </param>
128 <conditional name="con_measurement_export">
129 <param name="export_measurement" type="select" display="radio" label="Select the measurements to export">
130 <option value="Yes">Yes</option>
131 <option value="No">No</option>
132 </param>
133 <when value="Yes">
134 <param name="select_measurement" type="text" label="Select measurements"/>
135 </when>
136 <when value="No" />
137 </conditional>
138 <param name="calc_mean" type="select" display="radio" label="Calculate the per-image mean values for object measurments">
139 <option value="Yes">Yes</option>
140 <option value="No">No</option>
141 </param>
142 <param name="calc_median" type="select" display="radio" label="Calculate the per-image median values for object measurments">
143 <option value="Yes">Yes</option>
144 <option value="No">No</option>
145 </param>
146 <param name="calc_standard_deviation" type="select" display="radio" label="Calculate the per-image standard deviation values for object measurments">
147 <option value="Yes">Yes</option>
148 <option value="No">No</option>
149 </param>
150 <conditional name="con_create_gene_pattern">
151 <param name="create_gene_pattern" type="select" display="radio" label="Create a GenePattern GCT file?">
152 <option value="Yes">Yes</option>
153 <option value="No">No</option>
154 </param>
155 <when value="Yes">
156 <conditional name="con_source_sample_row">
157 <param name="select_source_sample_row_name" type="select" label="Select source of sample row name">
158 <option value="Metadata">Metadata</option>
159 <option value="Image filename">Image filename</option>
160 </param>
161 <when value="Metadata">
162 <param name="metadata_cat" type="select" label="Select the metadata to use as the indentifier">
163 <option value="AreaOccupied">AreaOccupied</option>
164 </param>
165 </when>
166 <when value="Image filename">
167 <param name="image_filename_cat" type="select" label="Select the image to use as the indentifier">
168 <option value="None">None</option>
169 </param>
170 </when>
171 </conditional>
172 </when>
173 <when value="No" />
174 </conditional>
175 <conditional name="con_export_all_measurements">
176 <param name="export_all_measurements" type="select" display="radio" label="Export all measuremnt types?">
177 <option value="Yes">Yes</option>
178 <option value="No">No</option>
179 </param>
180 <when value="No">
181 <repeat name="r_data_to_export" title="Add another data set">
182 <param name="data_to_export" type="select" label="Data to export">
183 <option value="Image">Image</option>
184 <option value="Experiment">Experiement</option>
185 <option value="Object relationship">Object relationship</option>
186 </param>
187 <param name="use_as_filename" type="select" display="radio" label="Use the object name for the file name?">
188 <option value="Yes">Yes</option>
189 <option value="No">No</option>
190 </param>
191 </repeat>
192 </when>
193 <when value="Yes" />
194 </conditional>
195 </inputs>
196
197 <outputs>
198 <expand macro="output_pipeline_macro" />
199 </outputs>
200
201 <tests>
202 <test>
203 <expand macro="test_input_pipeline_param" />
204 <param name="delimiter" value="Tab" />
205 <param name="output_file_location" value="Default Output Folder" />
206 <conditional name="con_prefix">
207 <param name="add_prefix" value="No"/>
208 </conditional>
209 <param name="overwrite_existing_file" value="Yes" />
210 <param name="add_metadata_column_to_object" value="Yes" />
211 <param name="represent_nan" value="NaN" />
212 <conditional name="con_measurement_export">
213 <param name="export_measurement" value="No" />
214 </conditional>
215 <param name="calc_mean" value="Yes" />
216 <param name="calc_median" value="Yes" />
217 <param name="calc_standard_deviation" value="Yes" />
218 <conditional name="con_create_gene_pattern">
219 <param name="create_gene_pattern" value="No" />
220 </conditional>
221 <conditional name="con_export_all_measurements" >
222 <param name="export_all_measurements" value="Yes" />
223 </conditional>
224 <expand macro="test_out_file" file="export_to_spreadsheet.txt" />
225 </test>
226 </tests>
227
228 <expand macro="help" module="ExportToSpreadsheet" />
229 <expand macro="citations" />
230
231 </tool>