annotate export_to_spreadsheet.xml @ 5:d0178bdcd00e draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author bgruening
date Fri, 26 Feb 2021 14:12:26 +0000
parents 72a7f23f3a79
children
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1 <tool id="cp_export_to_spreadsheet" name="ExportToSpreadsheet" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
2
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2 <description>export measurements into one or more files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@VERSION_SUFFIX@">1</token>
3
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6 <xml name="metadata_sample_row" >
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7 <param name="metadata_category" type="select" label="Select the metadata to use as the identifier">
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8 <option value="FileName">File name</option>
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10 <option value="Frame">Frame</option>
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11 <option value="Height">Height</option>
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12 <option value="MD5Digest">MD5Digest</option>
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13 <option value="PathName">Path name</option>
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15 <option value="Scaling">Scaling</option>
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16 <option value="Series">Series</option>
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17 <option value="URL">URL</option>
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18 <option value="Width">Width</option>
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19 </param>
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20 <param name="metadata_measurement" type="text" label="Measurements" >
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21 <help>
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22 Choose the measurement that corresponds to the identifier, such as metadata from the Metadata tool. Please see the Metadata tool for more details on metadata collection and usage.
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24 </help>
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25 </param>
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26 </xml>
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27 </macros>
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29 <expand macro="py_requirements"/>
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30 <expand macro="cmd_modules" />
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32 <configfiles>
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33 <inputs name="inputs"/>
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34 <configfile name="script_file">
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35 import json
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36 import sys
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37 import os
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39 FOURSPACES=@SPACES@
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41 input_json_path = sys.argv[1]
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42 input_pipeline= sys.argv[2]
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44 params = json.load(open(input_json_path, "r"))
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47 def write_etss():
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48 _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
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49 _str += FOURSPACES + "Select the column delimiter:%s\n" % params["delimiter"]
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50 _str += FOURSPACES + "Add image metadata columns to your object data file?:%s\n" % params["add_metadata_column_to_object"]
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51
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52
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53 _str += FOURSPACES + "Select the measurements to export:No\n"
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54 _str += FOURSPACES + "Calculate the per-image mean values for object measurements?:%s\n" % params['calc_mean']
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55 _str += FOURSPACES + "Calculate the per-image median values for object measurements?:%s\n" % params['calc_median']
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56 _str += FOURSPACES + "Calculate the per-image standard deviation values for object measurements?:%s\n" % params['calc_standard_deviation']
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57 _str += FOURSPACES + "Output file location:Default Output Folder\\x7C\n"
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58
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59 create_gene = params["con_create_gene_pattern"]["create_gene_pattern"]
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60 _str += FOURSPACES + "Create a GenePattern GCT file?:%s\n" % create_gene
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61
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62
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63 #default values when create gene is no
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64 source_sample_row = "Metadata"
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65 image_as_id = "None"
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66 metadata_as_id = "None"
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67
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68 if create_gene == "Yes":
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69 source_sample_row = params["con_create_gene_pattern"]["con_source_sample_row"]["select_source_sample_row_name"]
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70 if source_sample_row == "Metadata":
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71 metadata_as_id = params["con_create_gene_pattern"]["con_source_sample_row"]["metadata_category"] + "_" + params["con_create_gene_pattern"]["con_source_sample_row"]["metadata_measurement"]
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72 else:
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73 image_as_id = params["con_create_gene_pattern"]["con_source_sample_row"]["image_filename_cat"]
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74
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75 _str += FOURSPACES + "Select source of sample row name:%s\n" % source_sample_row
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76 _str += FOURSPACES + "Select the image to use as the identifier:%s\n" % image_as_id
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77 _str += FOURSPACES + "Select the metadata to use as the identifier:%s\n" % metadata_as_id
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78
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79
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80 export_all_measurements = "Yes" # always export all
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82 _str += FOURSPACES + "Export all measurement types?:%s\n" % export_all_measurements
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84 _str += FOURSPACES + "Press button to select measurements:\n"
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85
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86 _str += FOURSPACES + "Representation of Nan/Inf:%s\n" % params["represent_nan"]
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87 _str += FOURSPACES + "Add a prefix to file names?:%s\n" % params["con_prefix"]["add_prefix"]
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88
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89 if "filename_prefix" in params["con_prefix"]:
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diff changeset
90 _str += FOURSPACES + "Filename prefix:%s\n" % params["con_prefix"]["filename_prefix"]
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diff changeset
91 else:
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92 _str += FOURSPACES + "Filename prefix:MyPrefix_\n"
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diff changeset
93
10257d6d545b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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94 _str += FOURSPACES + "Overwrite existing files without warning?:%s\n" % params["overwrite_existing_file"]
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95
3
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parents: 2
diff changeset
96
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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97 use_as_filename = "Yes"
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98
5
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99 _str += FOURSPACES + "Data to export:Do not use\n"
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100 _str += FOURSPACES + "Combine these object measurements with those of the previous object?:No\n"
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101 _str += FOURSPACES + "File name:DATA.csv\n"
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102 _str += FOURSPACES + "Use the object name for the file name?:Yes\n"
0
10257d6d545b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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103
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104 return _str
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105
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106 with open(input_pipeline) as fin:
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107 lines = fin.readlines()
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108
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109 k, v = lines[4].strip().split(':')
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110
10257d6d545b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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111 module_count = int(v)
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112 new_count = module_count + 1
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113 lines[4] = k + ":%d\n" % new_count
3
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114 with open("output.cppipe", "w") as f:
0
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115 f.writelines(lines)
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116 f.write(write_etss())
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117
3
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118 f.close()
0
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119 </configfile>
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120 </configfiles>
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121
10257d6d545b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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122 <inputs>
3
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123 <expand macro="input_pipeline_param" />
0
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124 <param name="delimiter" type="select" label="Select the column delimiter">
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125 <option value="Comma (&quot;,&quot;)">Comma (",")</option>
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126 <option value="Tab">Tab</option>
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127 <sanitizer sanitize="false"/>
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128 </param>
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129 <conditional name="con_prefix">
3
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130 <param name="add_prefix" type="select" label="Add a prefix to file names?">
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131 <option value="Yes">Add prefix to the file name</option>
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132 <option value="No">Do not add prefix to the file name</option>
0
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133 </param>
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134 <when value="Yes">
3
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135 <param name="filename_prefix" type="text" value="MyExpt_" label="Enter the prefix to be added to the file names"/>
0
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diff changeset
136 </when>
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137 <when value="No" />
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138 </conditional>
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139 <param name="overwrite_existing_file" display="radio" type="select" label="Overwrite existing files without warning?">
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140 <option value="Yes">Yes</option>
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141 <option value="No">No</option>
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142 </param>
3
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143 <param name="add_metadata_column_to_object" display="radio" type="select" label="Add image metadata columns to your object data file?" help="'Image_Metadata_' columns are normally exported in the Image data file, but if you select 'Yes', they will also be exported with the Object data file(s).">
0
10257d6d545b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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144 <option value="Yes">Yes</option>
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145 <option value="No">No</option>
3
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146 </param>
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147 <param name="represent_nan" type="select" label="Representation of Nan/Inf" help="CellProfiler will produce Inf or NaN values under certain rare circumstances, for instance when calculating the mean intensity of an object within a masked region of an image.">
0
10257d6d545b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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148 <option value="NaN">NaN</option>
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149 <option value="Null">Null</option>
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150 </param>
3
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151 <param name="calc_mean" type="select" display="radio" label="Calculate the per-image mean values for object measurements?" help="Select 'Yes' to calculate the population mean over all the objects in each image and save that value as an aggregate measurement in the image file.">
0
10257d6d545b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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152 <option value="Yes">Yes</option>
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153 <option value="No">No</option>
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154 </param>
3
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155 <param name="calc_median" type="select" display="radio" label="Calculate the per-image median values for object measurements?" help="Select 'Yes' to calculate the population median over all the objects in each image and save that value as an aggregate measurement in the image file.">
0
10257d6d545b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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156 <option value="Yes">Yes</option>
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157 <option value="No">No</option>
3
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158 </param>
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159 <param name="calc_standard_deviation" type="select" display="radio" label="Calculate the per-image standard deviation values for object measurements?" help="Select 'Yes' to calculate the population standard deviation over all the objects in each image and save that value as an aggregate measurement in the image file.">
0
10257d6d545b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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160 <option value="Yes">Yes</option>
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161 <option value="No">No</option>
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162 </param>
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163 <conditional name="con_create_gene_pattern">
3
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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164 <param name="create_gene_pattern" type="select" display="radio" label="Create a GenePattern GCT file?" help="Select 'Yes' to create a GCT file compatible with GenePattern. The GCT file format is a tab-delimited text file format designed for gene expression datasets; the specifics of the format are described here. By converting your measurements into a GCT file, you can make use of GenePattern’s data visualization and clustering methods.">
0
10257d6d545b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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165 <option value="Yes">Yes</option>
3
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166 <option value="No" selected="true">No</option>
0
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167 </param>
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168 <when value="Yes">
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169 <conditional name="con_source_sample_row">
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170 <param name="select_source_sample_row_name" type="select" label="Select source of sample row name">
3
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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diff changeset
171 <help>
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172 <![CDATA[
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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173 The first column of the GCT file is the unique identifier for each sample, which is ordinarily the gene name. This information may be specified in one of two ways:
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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174 <br> - Metadata: If you used the Metadata modules to add metadata to your images, you may specify a metadata tag that corresponds to the identifier for this column.
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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175 <br> - Image filename: If the gene name is not available, the image filename can be used as a surrogate identifier.
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176 ]]>
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177 </help>
0
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178 <option value="Metadata">Metadata</option>
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179 <option value="Image filename">Image filename</option>
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180 </param>
3
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181
0
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182 <when value="Metadata">
3
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183 <expand macro="metadata_sample_row" />
0
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184 </when>
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185 <when value="Image filename">
3
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186 <param name="image_filename_cat" type="text" value="None" label="Enter the name of the image to use as the identifier" help="Enter the name of the image image whose filename will be used to identify each sample row. " />
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187
0
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188 </when>
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189 </conditional>
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190 </when>
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191 <when value="No" />
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192 </conditional>
5
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193
0
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194 </inputs>
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195
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196 <outputs>
3
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197 <expand macro="output_pipeline_param" />
0
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198 </outputs>
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199
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200 <tests>
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201 <test>
3
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202 <!-- create gene pattern =no-->
0
10257d6d545b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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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">
10257d6d545b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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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 <param name="calc_mean" value="Yes" />
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213 <param name="calc_median" value="Yes" />
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214 <param name="calc_standard_deviation" value="Yes" />
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215 <conditional name="con_create_gene_pattern">
10257d6d545b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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216 <param name="create_gene_pattern" value="No" />
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217 </conditional>
3
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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218 <expand macro="test_out_file" file="export_to_spreadsheet.cppipe" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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219 </test>
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220
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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221 <test>
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222 <!-- create gene=yes , source of sampe row name= metadata-->
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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223 <expand macro="test_input_pipeline_param" />
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224 <param name="delimiter" value="Tab" />
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225 <param name="output_file_location" value="Default Output Folder" />
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226 <conditional name="con_prefix">
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227 <param name="add_prefix" value="No"/>
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228 </conditional>
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229 <param name="overwrite_existing_file" value="Yes" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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230 <param name="add_metadata_column_to_object" value="Yes" />
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231 <param name="represent_nan" value="NaN" />
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232 <param name="calc_mean" value="Yes" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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233 <param name="calc_median" value="Yes" />
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234 <param name="calc_standard_deviation" value="Yes" />
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235 <conditional name="con_create_gene_pattern">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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236 <param name="create_gene_pattern" value="Yes" />
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237 <conditional name="con_source_sample_row">
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238 <param name="select_source_sample_row_name" value="Metadata" />
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239 <param name="metadata_category" value="FileName" />
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240 <param name="metadata_measurement" value="DNA" />
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241 </conditional>
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242 </conditional>
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243 <expand macro="test_out_file" file="export_to_spreadsheet_create_gene_metadata.cppipe" />
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244 </test>
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245 <test>
5
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246 <!-- create gene=yes , source of sampe row name= image filename-->
3
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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247 <expand macro="test_input_pipeline_param" />
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248 <param name="delimiter" value="Tab" />
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249 <param name="output_file_location" value="Default Output Folder" />
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250 <conditional name="con_prefix">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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251 <param name="add_prefix" value="Yes"/>
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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252 <param name="filename_prefix" value="MyExpt_" />
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253 </conditional>
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254 <param name="overwrite_existing_file" value="Yes" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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255 <param name="add_metadata_column_to_object" value="Yes" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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256 <param name="represent_nan" value="NaN" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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257 <param name="calc_mean" value="Yes" />
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258 <param name="calc_median" value="Yes" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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259 <param name="calc_standard_deviation" value="Yes" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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260 <conditional name="con_create_gene_pattern">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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261 <param name="create_gene_pattern" value="Yes" />
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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262 <conditional name="con_source_sample_row">
72a7f23f3a79 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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diff changeset
263 <param name="select_source_sample_row_name" value="Image filename" />
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264 <param name="image_filename_cat" value="DNA" />
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265 </conditional>
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266 </conditional>
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267 <expand macro="test_out_file" file="export_to_spreadsheet_create_gene_image_filename.cppipe" />
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268 </test>
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269
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270 <test>
5
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271 <!--repeat test for multiple data export. create gene=yes , source of sampe row name= image filename-->
3
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272 <expand macro="test_input_pipeline_param" />
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273 <param name="delimiter" value="Tab" />
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274 <param name="output_file_location" value="Default Output Folder" />
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275 <conditional name="con_prefix">
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276 <param name="add_prefix" value="Yes"/>
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277 <param name="filename_prefix" value="MyExpt_" />
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278 </conditional>
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279 <param name="overwrite_existing_file" value="Yes" />
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280 <param name="add_metadata_column_to_object" value="Yes" />
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281 <param name="represent_nan" value="NaN" />
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282 <param name="calc_mean" value="Yes" />
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283 <param name="calc_median" value="Yes" />
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284 <param name="calc_standard_deviation" value="Yes" />
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285 <conditional name="con_create_gene_pattern">
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286 <param name="create_gene_pattern" value="Yes" />
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287 <conditional name="con_source_sample_row">
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288 <param name="select_source_sample_row_name" value="Image filename" />
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289 <param name="image_filename_cat" value="DNA" />
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290 </conditional>
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291 </conditional>
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292 <expand macro="test_out_file" file="export_to_spreadsheet_multi.cppipe" />
0
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293 </test>
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294 </tests>
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295
3
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296 <help>
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297 <![CDATA[
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298 .. class:: infomark
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299
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300 **What it does**
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301
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302 This tool will convert the measurements to a comma-, tab-, or other character-delimited text format and save them in one or several files, as requested.
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303
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304 @COMMON_HELP@
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305 ]]>
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306 </help>
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307
0
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308 <expand macro="citations" />
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309
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310 </tool>