annotate export_to_spreadsheet.xml @ 0:10257d6d545b draft

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