Mercurial > repos > bgruening > cp_export_to_spreadsheet
comparison export_to_spreadsheet.xml @ 0:10257d6d545b draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
author | bgruening |
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date | Thu, 26 Mar 2020 16:38:48 -0400 |
parents | |
children | c956182d4e2c |
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-1:000000000000 | 0:10257d6d545b |
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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 (",")">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> |