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annotate table_compute.xml @ 6:56a8da1f2243 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 68bec02f3dbf1d7eaaa8d7577e361f635ba14fac
author iuc
date Fri, 14 Feb 2025 09:22:40 +0000
parents 3bf5661c0280
children
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1 <tool id="table_compute" name="Table Compute" version="@VERSION@+galaxy@WRAPPER_VERSION@">
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2 <description>computes operations on table data</description>
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3 <macros>
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4 <token name="@VERSION@">1.2.4</token>
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5 <token name="@WRAPPER_VERSION@">1</token>
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6 <token name="@COPEN@"><![CDATA[<code>]]></token>
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7 <token name="@CCLOSE@"><![CDATA[</code>]]></token>
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8 <import>allowed_functions.xml</import>
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9 <!-- text field validators -->
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10 <macro name="validator_text" >
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11 <validator type="regex" message="No special characters allowed">^(?:\w+)?$</validator>
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12 <sanitizer sanitize="false" />
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13 </macro>
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14 <macro name="validator_text_required" >
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15 <validator type="regex" message="No special characters allowed">^(?:\w+)?$</validator>
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16 <validator type="empty_field" />
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17 </macro>
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18 <macro name="validator_index_identifiers" >
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19 <validator type="regex" message="Specify a comma-separated list of index names without special characters">^(?:\w+(?:, *\w+)*)?$</validator>
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20 <sanitizer sanitize="false" />
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21 </macro>
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22 <macro name="validator_index_ranges">
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23 <validator type="regex" message="Specify a comma-separated list index numbers or ranges">^(?:-?\d+(?::-?\d+)*(?:, *-?\d+(?::-?\d+)*)*)?$</validator>
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24 <sanitizer sanitize="false" />
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25 </macro>
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26 <macro name="validator_functiondef">
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27 <validator type="regex" message="An expression is required and is allowed to contain only letters, numbers and the characters _ !-+=/*%.&lt;&gt;()">^[\w !\-+=/*%,.&lt;&gt;()]+$</validator>
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28 <sanitizer sanitize="false" />
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29 </macro>
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30 <!-- macro for main input tests -->
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31 <macro name="test_inputs_single" >
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32 <conditional name="singtabop" >
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33 <param name="use_type" value="single" />
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34 <param name="input" value="small.tsv" />
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35 <conditional name="user" >
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36 <yield />
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37 </conditional>
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38 </conditional>
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39 </macro>
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40 <macro name="test_inputs_ranges" >
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41 <conditional name="singtabop" >
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42 <param name="use_type" value="single" />
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43 <param name="input" value="examples.1.tsv" />
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44 <conditional name="user" >
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45 <param name="mode" value="select" />
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46 <yield />
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47 </conditional>
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48 </conditional>
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49 </macro>
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50 <!-- macro for umi to transcript tests -->
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51 <macro name="umi2trans" >
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52 <yield />
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53 <conditional name="user" >
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54 <param name="mode" value="element" />
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55 <conditional name="elem_val">
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56 <param name="element_op" value="None" />
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57 </conditional>
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58 <conditional name="element" >
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59 <param name="mode" value="custom" />
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60 <param name="custom_expr" value="-math.log(1 - elem/4096) * 4096 if elem != 4096 else elem - 0.5" />
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61 </conditional>
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62 </conditional>
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63 </macro>
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64 <!-- macro for file inputs -->
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65 <macro name="file_opts">
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66 <param name="input" type="data" format="tsv,tabular" label="Table" />
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67 <param name="col_row_names" type="select" display="checkboxes" multiple="true" optional="true"
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68 label="Input data has">
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69 <option value="has_col_names" selected="true">Column names on the first row</option>
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70 <option value="has_row_names" selected="true">Row names on the first column</option>
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71 </param>
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72 <section name="adv" title="Advanced File Options " expanded="false" >
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73 <param name="header" type="integer" min="0" optional="true" label="Header begins at line N" help="All lines before line N will be skipped. If a value is set, this will override the above 'Column names on the first row' parameter." />
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74 <param name="nrows" type="integer" min="0" optional="true" label="Read N lines only" help="Parses only N lines after the header line." />
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75 <param name="skipfooter" type="integer" min="0" optional="true" label="Skip N lines from bottom" help="Do not use this in conjunction with the 'Read N lines only' parameter." />
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76 <param name="skip_blank_lines" type="boolean" checked="true" falsevalue="False" truevalue="True" label="Skip blank lines" help="Otherwise it will insert NaN values for every blank line detected." />
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77 </section>
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78 </macro>
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79 <!-- element value macro -->
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80 <macro name="elem_val_macro" token_when="@WHEN@" >
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81 <when value="@WHEN@" >
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82 <param name="element_value" type="text" optional="true" label="Filter value" help="This value is converted to numeric if possible, otherwise it is treated as a string" />
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83 </when>
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84 </macro>
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85 <!-- Row/Col macro -->
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86 <macro name="select_rowcols" >
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87 <param name="select_cols_wanted" type="text" optional="true" label="List of columns to select" help="Comma separated. (e.g. @COPEN@3:5,10,-1,2:-2@CCLOSE@ will select columns @COPEN@3,4,5,10,-1,2,1,0,-1,-2@CCLOSE@, where negative indices refer to the offset from the last index). Columns can be duplicated by specifying them multiple times. Leave blank to retain all columns. See Example #1 for an example of using this mode." >
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88 <expand macro="validator_index_ranges" />
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89 </param>
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90 <param name="select_rows_wanted" type="text" optional="true" label="List of rows to select" help="The same rules apply as above" >
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91 <expand macro="validator_index_ranges" />
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92 </param>
0
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93 </macro>
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94 </macros>
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95 <requirements>
4
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96 <requirement type="package" version="1.2.4">pandas</requirement>
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97 <requirement type="package" version="1.19.2">numpy</requirement>
0
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98 </requirements>
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99
6
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100 <required_files>
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101 <include path="scripts/safety.py" />
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102 </required_files>
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103
0
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104 <version_command><![CDATA[
1
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105 python '$__tool_directory__/scripts/table_compute.py' --version
0
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106 ]]></version_command>
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107
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108 <command detect_errors="exit_code"><![CDATA[
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109 ## Can only import generated userconfig.py if calling
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110 ## script is in the same directory. Soft-linking does
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111 ## not satisfy importing, so we copy everything.
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112 cp '$userconf' ./userconfig.py &&
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113 cp '$__tool_directory__/scripts/safety.py' ./safety.py &&
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114 cp '$__tool_directory__/scripts/table_compute.py' ./table_compute.py &&
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115 python ./table_compute.py
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116 ]]></command>
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117 <configfiles>
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118 <configfile name="userconf"><![CDATA[
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119 Default = {
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120 "reader_skip": 0,
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121 "precision": $precision,
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122 #if 'ignore_nas' in str($out_opts):
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123 "narm": True,
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124 #else:
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125 "narm": False,
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126 #end if
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127 #if 'output_headers_row' in str($out_opts):
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128 "out_headers_row": True,
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129 #else:
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130 "out_headers_row": False,
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131 #end if
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132 #if 'output_headers_col' in str($out_opts):
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133 "out_headers_col": True,
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134 #else:
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135 "out_headers_col": False,
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136 #end if
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137 "user_mode": '$singtabop.use_type',
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138 "outtable": '$table'
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139 }
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140
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141 #if str($singtabop.use_type) == "single":
2
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142 #set $op_mode = str($singtabop.user.mode)
0
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143 Data = {
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144 "tables": [
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145 {
1
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146 "file": '$singtabop.input',
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147 #if $singtabop.adv.header:
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148 "header": int('$singtabop.adv.header'),
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149 #elif 'has_col_names' in str($singtabop.col_row_names):
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150 "header": 0,
0
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151 #else:
1
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152 "header": None,
0
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153 #end if
1
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154 "row_names": #if ('has_row_names' in str($singtabop.col_row_names)) then 0 else False#,
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155 "skipfooter": #if $singtabop.adv.skipfooter then int($singtabop.adv.skipfooter) else 0#,
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156 #if $singtabop.adv.skip_blank_lines
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157 "skip_blank_lines": $singtabop.adv.skip_blank_lines,
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158 #else
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159 "skip_blank_lines": None,
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160 #end if
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161 #if $singtabop.adv.nrows
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162 "nrows": int('$singtabop.adv.nrows'),
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163 #else
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164 "nrows": None,
0
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165 #end if
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166 }
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167 ],
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168 "params": {
2
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169 "user_mode_single": '$op_mode',
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170 #if $op_mode == 'precision':
0
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171 ## Literally do nothing, the user just sets the precision slider
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172 ## at the top default level
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173 }
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
174 #elif $op_mode == 'select':
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
175 "select_cols_unique": #echo 'select_cols_keepdupe' in str($singtabop.user.select_keepdupe)#,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
176 "select_rows_unique": #echo 'select_rows_keepdupe' in str($singtabop.user.select_keepdupe)#,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
177 #if $singtabop.user.select_cols_wanted:
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
178 "select_cols_wanted": '$singtabop.user.select_cols_wanted',
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
179 #else
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
180 "select_cols_wanted": None,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
181 #end if
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
182 #if $singtabop.user.select_rows_wanted:
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
183 "select_rows_wanted": '$singtabop.user.select_rows_wanted',
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
184 #else
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
185 "select_rows_wanted": None,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
186 #end if
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
187 }
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
188 #elif $op_mode == 'filtersumval':
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
189 #set $filter_type = str($singtabop.user.filtersumval_mode.use)
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
190 "filtersumval_mode": '$filter_type',
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
191 "filtersumval_axis": $singtabop.user.axis,
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
192 #if $filter_type == 'operation':
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
193 "filtersumval_compare": '$singtabop.user.filtersumval_mode.compare_op',
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
194 "filtersumval_op": '$singtabop.user.filtersumval_mode.operation',
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
195 "filtersumval_against": $singtabop.user.filtersumval_mode.against,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
196 "filtersumval_minmatch": None,
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
197 #elif $filter_type == 'element':
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
198 "filtersumval_compare": None,
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
199 "filtersumval_op": '$singtabop.user.filtersumval_mode.operation',
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
200 ## against could be string or float, so we parse this in the code
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
201 "filtersumval_against": '$singtabop.user.filtersumval_mode.against',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
202 "filtersumval_minmatch": $singtabop.user.filtersumval_mode.minmatch,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
203 #end if
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
204 }
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
205 #elif $op_mode == 'matrixapply':
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
206 "matrixapply_dimension": $singtabop.user.dimension,
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
207 #if str($singtabop.user.matrixapply_func.vector_op) == 'custom':
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
208 #set $custom_func = str($singtabop.user.matrixapply_func.custom_func).strip()
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
209 "matrixapply_custom": True,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
210 "matrixapply_custom_func": '$custom_func',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
211 "matrixapply_op": None,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
212 #else
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
213 "matrixapply_custom": False,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
214 "matrixapply_custom_func": None,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
215 "matrixapply_op": '$singtabop.user.matrixapply_func.vector_op',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
216 #end if
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
217 }
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
218 #elif $op_mode == 'element':
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
219 #set $filter_type = str($singtabop.user.elem_val.element_op)
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
220 #set $element_mode = str($singtabop.user.element.mode)
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
221 #if $filter_type == "None":
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
222 "element_op": None,
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
223 #elif $filter_type == "rowcol":
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
224 "element_op": "rowcol",
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
225 #if $singtabop.user.elem_val.select_rows_wanted
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
226 "element_rows": '$singtabop.user.elem_val.select_rows_wanted',
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
227 #end if
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
228 #if $singtabop.user.elem_val.select_cols_wanted
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
229 "element_cols": '$singtabop.user.elem_val.select_cols_wanted',
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
230 #end if
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
231 "element_inclusive": $singtabop.user.elem_val.inclusive_selection,
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
232 #else:
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
233 "element_op": '$filter_type',
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
234 ## Value is string or float, parsed in code later
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
235 "element_value" : '$singtabop.user.elem_val.element_value',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
236 #end if
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
237 "element_mode": '$element_mode',
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
238 #if $element_mode == "replace":
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
239 "element_replace": '$singtabop.user.element.replace_value',
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
240 #elif $element_mode == "modify":
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
241 "element_modify_op": '$singtabop.user.element.modify_op',
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
242 #elif $element_mode == "scale":
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
243 "element_scale_op": '$singtabop.user.element.scale_op',
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
244 "element_scale_value": $singtabop.user.element.scale_value,
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
245 #elif $element_mode == "custom":
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
246 #set $custom_func = str($singtabop.user.element.custom_expr).strip()
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
247 "element_customop": '$custom_func',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
248 #end if
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
249 }
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
250 #elif $op_mode == 'fulltable':
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
251 "mode": '$singtabop.user.general.use',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
252 #if str($singtabop.user.general.use) == 'melt':
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
253 #if str($singtabop.user.general.id_vars).strip():
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
254 #set $melt_ids = [i.strip() for i in str($singtabop.user.general.id_vars).split(',')]
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
255 #else
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
256 #set $melt_ids = 'None'
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
257 #end if
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
258 #if str($singtabop.user.general.value_vars).strip():
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
259 #set $melt_values = [i.strip() for i in str($singtabop.user.general.value_vars).split(',')]
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
260 #else
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
261 #set $melt_values = 'None'
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
262 #end if
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
263 "MELT": {
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
264 "melt_ids": $melt_ids,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
265 "melt_values": $melt_values,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
266 },
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
267 #elif str($singtabop.user.general.use) == 'pivot':
4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
268 #set $pivot_index = None
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
269 #set $pivot_columns = None
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
270 #set $pivot_values = None
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
271 #set $pivot_aggfunc = None
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
272
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
273 #if str($singtabop.user.general.index).strip()
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
274 #set $pivot_index = [i.strip() for i in str($singtabop.user.general.index).split(',')]
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
275 #if len($pivot_index)==1
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
276 #set $pivot_index = "'"+$pivot_index[0]+"'"
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
277 #end if
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
278 #else
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
279 #set $pivot_index = 'None'
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
280 #end if
4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
281 #if str($singtabop.user.general.column).strip()
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
282 #set $pivot_columns = [i.strip() for i in str($singtabop.user.general.column).split(',')]
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
283 #if len($pivot_columns)==1
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
284 #set $pivot_columns = "'"+$pivot_columns[0]+"'"
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
285 #end if
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
286 #else
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
287 #set $pivot_columns = 'None'
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
288 #end if
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
289 #if str($singtabop.user.general.values).strip()
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
290 #set $pivot_values = [i.strip() for i in str($singtabop.user.general.values).split(',')]
4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
291 #if len($pivot_values)==1
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
292 #set $pivot_values = "'"+$pivot_values[0]+"'"
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
293 #end if
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
294 #else
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
295 #set $pivot_values = 'None'
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
296 #end if
4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
297
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
298 ## The aggfunc is either a - column : [array] map
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
299 ## or just an [array]
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
300 #if str($singtabop.user.general.aggfunc).strip() == 'None'
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
301 #set $pivot_aggfunc = 'None'
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
302 #end if
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
303 #if not($pivot_aggfunc)
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
304 #set $pivot_aggfunc = [i.strip() for i in str($singtabop.user.general.aggfunc).split(',')]
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
305 #if len($pivot_aggfunc)==1
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
306 #set $pivot_aggfunc = "'"+$pivot_aggfunc[0]+"'"
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
307 #end if
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
308 #end if
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
309
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
310 "PIVOT": {
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
311 "pivot_index": $pivot_index,
4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
312 "pivot_columns": $pivot_columns,
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
313 "pivot_values": $pivot_values,
4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
314 #if $pivot_aggfunc == 'None':
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
315 "pivot_aggfunc": {
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
316 #for $i, $s in enumerate($singtabop.user.general.colfun_map)
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
317 #echo 16*' ' + "'" + str($s.column) + "'" + ' : ['
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
318 #echo ','.join([ "'%s'" % $t.aggfunc for $j, $t in enumerate($s.functions) ])
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
319 #echo '],\n'
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
320 #end for
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
321 }
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
322 #else
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
323 "pivot_aggfunc": $pivot_aggfunc
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
324 #end if
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
325 },
4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
326
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
327 #elif str($singtabop.user.general.use) == 'custom':
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
328 #set $custom_func = str($singtabop.user.general.fulltable_custom_expr).strip()
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
329 "fulltable_customop": '$custom_func',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
330 #end if
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
331 },
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
332 #end if
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
333 }
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
334
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
335 #elif str($singtabop.use_type) == "multiple":
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
336 #set $custom_func = str($singtabop.fulltable_custom_expr).strip()
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
337 Data = {
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
338 "tables": [
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
339 #for $i, $s in enumerate($singtabop.tables)
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
340 {
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
341 "file": '${s.input}',
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
342 #if $s.adv.header:
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
343 "header": int('${s.adv.header}'),
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
344 #elif 'has_col_names' in str($s.col_row_names):
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
345 "header": 0,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
346 #else:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
347 "header": None,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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348 #end if
1
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diff changeset
349 "row_names": #if ('has_row_names' in str($s.col_row_names)) then 0 else False#,
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
350 "skipfooter": #if $s.adv.skipfooter then int('$s.adv.skipfooter') else 0#,
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
351 #if $s.adv.skip_blank_lines:
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
352 "skip_blank_lines": $s.adv.skip_blank_lines,
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
353 #else
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
354 "skip_blank_lines": None,
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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355 #end if
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
356 #if $s.adv.nrows:
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
357 "nrows": int('${s.adv.nrows}'),
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
358 #else
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
359 "nrows": None,
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
360 #end if
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
361
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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diff changeset
362 },
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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diff changeset
363 #end for
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
364 ],
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
365 'params': {
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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366 "fulltable_customop" : '$custom_func',
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
367 }
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
368 }
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
369 #end if
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
370
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
371 ]]>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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diff changeset
372 </configfile>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
373 </configfiles>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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diff changeset
374 <inputs>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
375 <conditional name="singtabop" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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376 <param name="use_type" type="select" label="Input Single or Multiple Tables" help="Operations on single tables are better tailored towards more general use-cases. For multiple tables usage, all tables should ideally be of the same dimensions for simple operations, although complex operations are also supported for unequally sized tables (see Help section)." >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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377 <option value="single">Single Table</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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378 <option value="multiple">Multiple Tables</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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diff changeset
379 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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diff changeset
380 <when value="single">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
381 <expand macro="file_opts" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
382 <conditional name="user" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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diff changeset
383 <param name="mode" type="select" label="Type of table operation" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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384 <option value="precision">No operation (just reformat on output)</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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diff changeset
385 <option value="select">Drop, keep or duplicate rows and columns</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
386 <option value="filtersumval">Filter rows or columns by their properties</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
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387 <option value="matrixapply">Compute expression across rows or columns</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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diff changeset
388 <option value="element">Manipulate selected table elements</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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389 <option value="fulltable">Perform a full table operation</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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diff changeset
390 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
391 <when value="precision" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
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392 <when value="select">
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
393 <expand macro="select_rowcols" />
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
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394 <param name="select_keepdupe" type="select" display="checkboxes" multiple="true" label="Duplicate Indices" help="Keep duplicates when specifying ranges (e.g. if unset, @COPEN@1:3,2:4@CCLOSE@ will yield @COPEN@1,2,3,4@CCLOSE@ instead of @COPEN@1,2,3,2,3,4@CCLOSE@)" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
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395 <option value="select_cols_keepdupe" selected="true" >Keep duplicate columns</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
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396 <option value="select_rows_keepdupe" selected="true" >Keep duplicate rows</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
397 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
398 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
399 <when value="filtersumval" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
400 <param name="axis" type="select" display="radio"
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
401 label="Filter" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
402 <option value="1">Rows</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
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403 <option value="0">Columns</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
404 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
405 <conditional name="filtersumval_mode" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
406 <param name="use" type="select" label="Filter criterion" help="See Example #2 for an example of using this mode." >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
407 <option value="operation" >Result of function applied to columns/rows</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
408 <option value="element" >Number of column/row elements passing filter</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
409 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
410 <when value="operation">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
411 <param name="operation" type="select" label="Keep column/row if its observed" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
412 <expand macro="select_vectorops" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
413 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
414 <param name="compare_op" type="select" label="is" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
415 <expand macro="select_twovaluebooleanops" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
416 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
417 <param name="against" type="float" label="this value" value="0" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
418 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
419 <when value="element">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
420 <param name="minmatch" type="integer" min="1" value="0" label="Keep column/row if at least" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
421 <param name="operation" type="select" label="of its element are" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
422 <expand macro="select_twovaluebooleanops" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
423 <option value="str_eq" >~ (Matching)</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
424 <option value="str_ne" >!~ (not Matching)</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
425 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
426 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
427 <param name="against" type="text" label="this value">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
428 <expand macro="validator_functiondef" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
429 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
430 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
431 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
432 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
433 <when value="matrixapply" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
434 <conditional name="matrixapply_func">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
435 <param name="vector_op" type="select" label="Calculate">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
436 <option value="custom">Custom Function</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
437 <expand macro="select_vectorops" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
438 <option value="rank">Ranks</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
439 <option value="cumsum" >Cumulative Sum</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
440 <option value="cumprod" >Cumulative Product</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
441 <option value="cummin" >Cumulative Minimum</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
442 <option value="cummax" >Cumulative Maximum</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
443 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
444 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
445 <when value="custom">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
446 <param name="custom_func" type="text"
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
447 label="Custom function on 'vec'"
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
448 help="The parameter name is @COPEN@vec@CCLOSE@, referring to a vector of a specific row or column being operated on. Numpy and Pandas DataFrame operators are supported. e.g. @COPEN@np.sum(vec) + np.median(vec)@CCLOSE@, and @COPEN@vec.sum() + vec.median()@CCLOSE@ are equivalent operations." >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
449 <expand macro="validator_functiondef" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
450 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
451 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
452 <when value="min" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
453 <when value="max" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
454 <when value="sum" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
455 <when value="count" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
456 <when value="nunique" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
457 <when value="mean" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
458 <when value="median" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
459 <when value="std" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
460 <when value="sem" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
461 <when value="var" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
462 <when value="mad" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
463 <when value="product" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
464 <when value="rank" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
465 <when value="cumsum" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
466 <when value="cumprod" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
467 <when value="cummin" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
468 <when value="cummax" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
469 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
470 <param name="dimension" type="select" label="For each">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
471 <option value="0">Column</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
472 <option value="1">Row</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
473 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
474 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
475 <when value="fulltable">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
476 <conditional name="general" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
477 <param name="use" type="select" label="Operation" help="See Examples 5, 7, and 8 for usage" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
478 <option value="transpose">Transpose</option>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
479 <option value="melt">Melt</option>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
480 <option value="pivot">Pivot</option>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
481 <option value="custom">Custom</option>
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
482 </param>
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
483 <when value="transpose" />
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
484 <when value="melt" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
485 <param name="id_vars" type="text" value="" label="Variable IDs"
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
486 help="Comma-delimited list of column names to use as identifiers" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
487 <expand macro="validator_index_identifiers" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
488 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
489 <param name="value_vars" type="text" value="" label="Unpivoted IDs"
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
490 help="Comma-delimited list of column names to un-pivot. Leave blank to use all." >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
491 <expand macro="validator_index_identifiers" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
492 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
493 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
494 <when value="pivot" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
495 <param name="index" type="text" value=""
4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
496 label="Index"
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
497 help="Name of the column to use as new index" >
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
498 <expand macro="validator_text" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
499 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
500 <param name="column" type="text" value=""
4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
501 label="Column"
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
502 help="Name of the column to use to generate the columns of the new table from.
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
503 Cannot be used in conjunction with the Column-Function Mapping parameter."
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
504 optional="true">
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
505 <expand macro="validator_text_required" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
506 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
507 <param name="values" type="text" value=""
4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
508 label="Values"
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
509 help="Names of the columns to use for populating the cells of the new table. Leave blank to use all." >
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
510 <expand macro="validator_index_identifiers" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
511 </param>
4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
512 <param name="aggfunc" type="select" optional="true"
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
513 label="Aggregator Function"
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
514 help="The function used to aggregate the values for each unique index.
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
515 Cannot be used with the Column-Function Mapping parameter below.
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
516 By default this value is np.mean. Leave blank for default behaviour.
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
517 See Example 10 for more information on its usage." >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
518 <expand macro="select_vectorops">
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
519 <option value="all">All</option>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
520 <option value="any">Any</option>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
521 </expand>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
522 </param>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
523 <repeat name="colfun_map" title="Column-Function Mapping" min="0">
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
524 <param name="column" type="text" label="Value Column"
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
525 help="Either a numeric index, or a value column name." />
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parents: 3
diff changeset
526 <repeat name="functions" title="Aggregator Function" min="0" >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
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parents: 3
diff changeset
527 <!-- if zero, then this defaults to np.mean -->
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
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parents: 3
diff changeset
528 <param name="aggfunc" type="select" label="Function"
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
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parents: 3
diff changeset
529 help="The function used to aggregate the values for each unique index.
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
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parents: 3
diff changeset
530 By default this is np.mean. See Example 11 for more information on its usage." >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
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parents: 3
diff changeset
531 <expand macro="select_vectorops">
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parents: 3
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532 <option value="all">All</option>
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parents: 3
diff changeset
533 <option value="any">Any</option>
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parents: 3
diff changeset
534 </expand>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
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parents: 3
diff changeset
535 </param>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
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parents: 3
diff changeset
536 </repeat>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
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parents: 3
diff changeset
537 </repeat>
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
538 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
539 <when value="custom" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
540 <param name="fulltable_custom_expr" type="text"
4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
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parents: 3
diff changeset
541 label="Custom expression on 'table', along 'axis' (0 or 1)"
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
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parents: 3
diff changeset
542 help="The parameter name is @COPEN@table@CCLOSE@ and @COPEN@axis@CCLOSE@, referring to the table being acted on and the column (@COPEN@0@CCLOSE@) or row (@COPEN@1@CCLOSE@) to perform the operation on. Numpy, math, Pandas DataFrame operators, and inline @COPEN@if else@CCLOSE@ are supported (e.g. @COPEN@np.log(table) - table.mean(0) / table.std(1)@CCLOSE@). See Example #5 in the Help section. ">
0
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parents:
diff changeset
543 <expand macro="validator_functiondef" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
544 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
545 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
546 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
547 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
548 <when value="element">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
549 <conditional name="element" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
550 <param name="mode" type="select"
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
551 label="Operation to perform" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
552 <option value="replace">Replace values</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
553 <option value="modify">Transform</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
554 <option value="scale">Arithmetic operation</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
555 <option value="custom">Custom</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
556 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
557 <when value="replace" >
2
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parents: 1
diff changeset
558 <param name="replace_value" type="text" label="Replacement value" help="If you want to reuse the current value of each element as part of the replacement value, you can refer to it using the special @COPEN@{elem}@CCLOSE@ placeholder (see Example #9 in the Help section).">
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
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parents: 1
diff changeset
559 <sanitizer>
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parents: 1
diff changeset
560 <valid>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
561 <add value="{" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
562 <add value="}" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
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parents: 1
diff changeset
563 </valid>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
564 </sanitizer>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
565 </param>
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
566 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
567 <when value="modify" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
568 <param name="modify_op" type="select" label="Transformation function" help="Example: to transform values to their square root, select @COPEN@Square Root@CCLOSE@ here.">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
569 <expand macro="select_onevalueoperator" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
570 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
571 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
572 <when value="scale">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
573 <param name="scale_op" type="select" label="Operation" help="The selected operation will be applied to the table elements as the first operand. The value of the second operand can be provided in the next box. Example: to raise all values to the power of 5, select @COPEN@Power@CCLOSE@ here and type @COPEN@5@CCLOSE@ in the box below." >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
574 <expand macro="select_twovaluenumericoperator" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
575 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
576 <param name="scale_value" type="float" value="0" label="Second operand value" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
577 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
578 <when value="custom">
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
579 <param name="custom_expr" type="text" label="Custom expression on 'elem'"
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
580 help="The parameter name is @COPEN@elem@CCLOSE@, referring to the element being acted on. Most operators and @COPEN@if@CCLOSE@ @COPEN@else@CCLOSE@ statements are supported. See Examples #3 and #4 in the Help section.">
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
581 <expand macro="validator_functiondef" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
582 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
583 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
584 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
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585 <conditional name="elem_val" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
586 <param name="element_op" type="select" label="Operate on elements"
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
587 help="Only selected elements will be manipulated. Other elements will retain their original value." >
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
588 <expand macro="select_twovaluebooleanops" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
589 <option value="None" selected="true">All</option>
1
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iuc
parents: 0
diff changeset
590 <option value="rowcol" >Specific Rows and/or Columns</option>
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
591 </expand>
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592 </param>
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parents:
diff changeset
593 <when value="None" />
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
594 <expand macro="elem_val_macro" when="lt" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
595 <expand macro="elem_val_macro" when="le" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
596 <expand macro="elem_val_macro" when="gt" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
597 <expand macro="elem_val_macro" when="ge" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
598 <expand macro="elem_val_macro" when="eq" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
599 <expand macro="elem_val_macro" when="ne" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
600 <when value="rowcol" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
601 <expand macro="select_rowcols" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
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parents: 0
diff changeset
602 <param name="inclusive_selection" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Inclusive Selection" help="If enabled, all elements that match ANY row or column given above will be acted on. Otherwise, only the elements that match BOTH a row or column given above will be acted on." />
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
603 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
604 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
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605 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
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606 </conditional>
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parents:
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607 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
608 <when value="multiple">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
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609 <repeat name="tables" title="Tables" min="1" default="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
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610 <expand macro="file_opts" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
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parents:
diff changeset
611 </repeat>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
612 <param name="fulltable_custom_expr" type="text"
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
613 label="Custom expression on 'tableN'"
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
614 help="The parameter name is @COPEN@tableN@CCLOSE@, where @COPEN@N@CCLOSE@ refers to a specific table. e.g. @COPEN@table1 + table3 - table2@CCLOSE@, will add the first and third input tables and then subtract the second. Most operators and @COPEN@if@CCLOSE@ @COPEN@else@CCLOSE@ statements are supported. See Example #6 in the Help section for further examples.">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
615 <expand macro="validator_functiondef" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
616 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
617 </when>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
618 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
619 <param name="out_opts" type="select" display="checkboxes" multiple="true" optional="true"
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
620 label="Output formatting options">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
621 <option value="ignore_nas" selected="true">Ignore NA values</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
622 <option value="output_headers_col" selected="true">Output column headers</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
623 <option value="output_headers_row" selected="true">Output row headers</option>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
624 </param>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
625 <param name="precision" type="integer" min="0" max="20" value="6" label="Output decimal precision" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
626 </inputs>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
627 <outputs>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
628 <data name="table" format="tabular" label="${tool.name} on ${on_string}" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
629 </outputs>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
630 <tests>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
631 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
632 <!-- Test 1: Select -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
633 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
634 <param name="mode" value="select" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
635 <param name="select_cols_wanted" value="2:4,2,2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
636 <param name="select_rows_wanted" value="2:5,3,3" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
637 <param name="select_keepdupe" value="select_cols_keepdupe" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
638 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
639 <param name="precision" value="2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
640 <output name="table" value="small.select.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
641 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
642 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
643 <!-- Test 2: Select, cols only -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
644 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
645 <param name="mode" value="select" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
646 <param name="select_cols_wanted" value="2:4,2,2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
647 <param name="select_keepdupe" value="select_cols_keepdupe,select_rows_keepdupe" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
648 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
649 <param name="precision" value="2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
650 <output name="table" value="small.select.colsonly.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
651 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
652 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
653 <!-- Test 3: Select, rows only -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
654 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
655 <param name="mode" value="select" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
656 <param name="select_rows_wanted" value="2:5,3,3" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
657 <param name="select_keepdupe" value="select_cols_keepdupe" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
658 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
659 <param name="precision" value="2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
660 <output name="table" value="small.select.rowsonly.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
661 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
662 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
663 <!-- Test 4: Filtersumval, row -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
664 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
665 <param name="mode" value="filtersumval" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
666 <param name="axis" value="1" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
667 <conditional name="filtersumval_mode" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
668 <param name="use" value="operation" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
669 <param name="operation" value="sum" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
670 <param name="compare_op" value="gt" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
671 <param name="against" value="50" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
672 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
673 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
674 <param name="precision" value="2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
675 <output name="table" value="small.fs.rowsum.gt.50.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
676 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
677 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
678 <!-- Test 5: Filtersumval, col neq 0 -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
679 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
680 <param name="mode" value="filtersumval" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
681 <param name="axis" value="0" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
682 <conditional name="filtersumval_mode" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
683 <param name="use" value="operation" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
684 <param name="operation" value="sum" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
685 <param name="compare_op" value="ne" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
686 <param name="against" value="0" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
687 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
688 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
689 <param name="precision" value="2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
690 <output name="table" value="small.fs.colsum.neq0.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
691 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
692 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
693 <!-- Test 6: Filtersumval, col val gt 10 -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
694 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
695 <param name="mode" value="filtersumval" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
696 <param name="axis" value="0" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
697 <conditional name="filtersumval_mode" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
698 <param name="use" value="operation" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
699 <param name="operation" value="sum" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
700 <param name="compare_op" value="gt" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
701 <param name="against" value="10" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
702 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
703 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
704 <param name="precision" value="2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
705 <output name="table" value="small.fs.colsum.gt10.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
706 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
707 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
708 <!-- Test 7: Filtersumval, median val col >= 2 -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
709 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
710 <param name="mode" value="filtersumval" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
711 <param name="axis" value="0" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
712 <conditional name="filtersumval_mode" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
713 <param name="use" value="operation" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
714 <param name="operation" value="median" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
715 <param name="compare_op" value="ge" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
716 <param name="against" value="2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
717 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
718 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
719 <param name="precision" value="5" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
720 <output name="table" value="small.fs.medvalcol.ge2.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
721 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
722 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
723 <!-- Test 8: Filtersumval, keep rows with at least
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
724 two values > 2 -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
725 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
726 <param name="mode" value="filtersumval" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
727 <param name="axis" value="1" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
728 <conditional name="filtersumval_mode" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
729 <param name="use" value="element" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
730 <param name="operation" value="gt" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
731 <param name="against" value="2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
732 <param name="minmatch" value="2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
733 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
734 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
735 <param name="precision" value="5" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
736 <output name="table" value="small.fs.elemgt2.mm2.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
737 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
738 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
739 <!-- Test 9: Filtersumval, keep cols with at least
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
740 4 string values matching "0" -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
741 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
742 <param name="mode" value="filtersumval" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
743 <param name="axis" value="0" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
744 <conditional name="filtersumval_mode" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
745 <param name="use" value="element" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
746 <param name="operation" value="str_ne" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
747 <param name="against" value="0" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
748 <param name="minmatch" value="4" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
749 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
750 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
751 <param name="precision" value="3" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
752 <output name="table" value="small.fs.elemnmatch0.mm4.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
753 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
754 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
755 <!-- Test 10: Matrix Apply, row max -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
756 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
757 <param name="mode" value="matrixapply" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
758 <param name="dimension" value="1" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
759 <conditional name="matrixapply_func" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
760 <param name="vector_op" value="max" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
761 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
762 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
763 <param name="precision" value="0" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
764 <param name="out_opts" value="ignore_nas,output_headers_row" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
765 <output name="table" value="small.matapp.rowmax.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
766 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
767 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
768 <!-- Test 11: Element, all, scale, remainder 5 -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
769 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
770 <param name="mode" value="element" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
771 <conditional name="elem_val">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
772 <param name="element_op" value="None" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
773 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
774 <conditional name="element" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
775 <param name="mode" value="scale" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
776 <param name="scale_op" value="mod" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
777 <param name="scale_value" value="5" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
778 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
779 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
780 <param name="precision" value="2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
781 <output name="table" value="small.element.scalerem5.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
782 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
783 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
784 <!-- Test 12: Matrix Apply, column custom -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
785 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
786 <param name="mode" value="matrixapply" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
787 <param name="dimension" value="0" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
788 <conditional name="matrixapply_func" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
789 <param name="vector_op" value="custom" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
790 <param name="custom_func" value="vec.sum()+vec.median()" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
791 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
792 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
793 <param name="precision" value="2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
794 <param name="out_opts" value="ignore_nas,output_headers_row" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
795 <output name="table" value="small.matapp.colcust.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
796 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
797 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
798 <!-- Test 13: Element, non-zero, custom -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
799 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
800 <param name="mode" value="element" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
801 <conditional name="elem_val">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
802 <param name="element_op" value="gt" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
803 <param name="element_value" value="0" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
804 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
805 <conditional name="element" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
806 <param name="mode" value="custom" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
807 <!-- valid complex expression for non-zero vals -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
808 <param name="custom_expr" value="(math.log10(elem)+elem)/elem if (elem &lt; math.inf) else 1.0" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
809 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
810 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
811 <output name="table" value="small.element.custom.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
812 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
813 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
814 <!-- Test 14: umi2transcript test1 -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
815 <expand macro="umi2trans" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
816 <param name="input" value="mat1.umi.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
817 <output name="table" value="mat1.trans.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
818 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
819 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
820 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
821 <!-- Test 15: umi2transcript test2 -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
822 <expand macro="umi2trans" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
823 <param name="input" value="mat2.umi.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
824 <output name="table" value="mat2.trans.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
825 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
826 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
827 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
828 <!-- Test 16: B-test - mean and sd in custom func -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
829 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
830 <param name="mode" value="fulltable" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
831 <conditional name="general" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
832 <param name="use" value="custom" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
833 <param name="fulltable_custom_expr"
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
834 value="table - table.mean(0) / table.std(0)" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
835 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
836 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
837 <output name="table" value="small.fulltable.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
838 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
839 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
840 <!-- Test 17: Multiple table test -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
841 <conditional name="singtabop" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
842 <param name="use_type" value="multiple" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
843 <repeat name="tables">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
844 <param name="input" value="small.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
845 </repeat>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
846 <repeat name="tables">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
847 <param name="input" value="small.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
848 </repeat>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
849 <repeat name="tables">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
850 <param name="input" value="small.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
851 </repeat>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
852 <param name="fulltable_custom_expr" value="(3 * table1) + np.log(table3 + 20) - table2" /> </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
853 <output name="table" value="small.multiple.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
854 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
855 <!-- User tests that failed previously -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
856 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
857 <!-- Test 18 -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
858 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
859 <param name="mode" value="fulltable" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
860 <conditional name="general" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
861 <param name="use" value="custom" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
862 <param name="fulltable_custom_expr" value="table * 2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
863 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
864 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
865 <output name="table" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
866 <assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
867 <has_n_columns n="10" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
868 <has_line_matching expression="^gene1\s20\.000000\s0\s12\s-20\.200000\s20\s2\.200000\s0\.000000\s0\s0\.000000$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
869 <has_line_matching expression="gene5\s2\.000000\s0\s0\s-20\.000000\s880\s12\.000000\s0\.000000\s0\s3\.800000" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
870 </assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
871 </output>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
872 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
873 <test expect_num_outputs="1">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
874 <!-- Test 19 -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
875 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
876 <param name="mode" value="fulltable" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
877 <conditional name="general" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
878 <param name="use" value="custom" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
879 <param name="fulltable_custom_expr" value="table == 5" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
880 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
881 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
882 <output name="table" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
883 <assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
884 <has_n_columns n="10" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
885 <has_line_matching expression="^gene1(\sFalse)+$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
886 <has_line_matching expression="gene5(\sFalse)+$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
887 </assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
888 </output>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
889 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
890 <test expect_num_outputs="1" expect_failure="true">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
891 <!-- Test 20 -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
892 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
893 <param name="mode" value="fulltable" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
894 <conditional name="general" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
895 <param name="use" value="custom" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
896 <param name="fulltable_custom_expr" value="for n in table: n = n + 1" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
897 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
898 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
899 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
900 <test expect_num_outputs="1" expect_failure="true">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
901 <!-- Test 21 -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
902 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
903 <param name="mode" value="fulltable" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
904 <conditional name="general" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
905 <param name="use" value="custom" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
906 <param name="fulltable_custom_expr" value="table + table[0,0]" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
907 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
908 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
909 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
910 <test expect_num_outputs="1">
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
911 <!-- Test 22: Transpose -->
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
912 <expand macro="test_inputs_single" >
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
913 <param name="mode" value="fulltable" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
914 <conditional name="general" >
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
915 <param name="use" value="transpose" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
916 </conditional>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
917 </expand>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
918 <param name="out_opts" value="ignore_nas,output_headers_col" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
919 <output name="table" >
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
920 <assert_contents>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
921 <has_n_columns n="5" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
922 </assert_contents>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
923 </output>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
924 </test>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
925 <test expect_num_outputs="1">
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
926 <!-- Test 23: Melt -->
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
927 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
928 <param name="mode" value="fulltable" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
929 <conditional name="general" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
930 <param name="use" value="melt" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
931 <param name="id_vars" value="cell1,cell3" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
932 <param name="value_vars" value="cell5,cell6" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
933 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
934 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
935 <param name="out_opts" value="ignore_nas,output_headers_col" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
936 <output name="table" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
937 <assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
938 <has_n_columns n="4" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
939 <has_line_matching expression="^cell1\scell3\svariable\svalue$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
940 <has_line_matching expression="^1\.0+\s0+\scell6\s6\.0+$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
941 </assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
942 </output>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
943 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
944 <test expect_num_outputs="1">
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
945 <!-- Test 24: Pivot -->
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
946 <expand macro="test_inputs_single" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
947 <param name="mode" value="fulltable" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
948 <conditional name="general" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
949 <param name="use" value="pivot" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
950 <param name="index" value="cell1" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
951 <param name="column" value="cell2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
952 <param name="values" value="cell3,cell7,cell9" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
953 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
954 </expand>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
955 <output name="table" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
956 <assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
957 <has_n_columns n="4" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
958 <has_line_matching expression="^\scell3\scell7\scell9$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
959 <has_line_matching expression="^1\.0+\s0\.0+\s0\.0+\s1\.90+$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
960 <has_line_matching expression="^10\.0+\s6\.0+\s0\.0+\s0\.0+$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
961 </assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
962 </output>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
963 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
964 <!-- Add Example Text Tests -->
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
965 <test expect_num_outputs="1" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
966 <!-- Test 25: Ex 1 -->
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
967 <conditional name="singtabop" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
968 <param name="use_type" value="single" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
969 <param name="input" value="examples.1.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
970 <param name="col_row_names" value="has_col_names,has_row_names" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
971 <conditional name="user" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
972 <param name="mode" value="select" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
973 <param name="select_cols_wanted" value="1,1,3" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
974 <param name="select_rows_wanted" value="1:3,2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
975 <param name="select_keepdupe" value="select_cols_keepdupe,select_rows_keepdupe" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
976 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
977 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
978 <output name="table" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
979 <assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
980 <has_n_columns n="4" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
981 <has_line_matching expression="^\s+c1\s+c1\s+c3$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
982 <has_line_matching expression="^g2\s+3\s+3\s+9$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
983 </assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
984 </output>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
985 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
986 <test expect_num_outputs="1" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
987 <!-- Test 26: Ex 2 -->
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
988 <conditional name="singtabop" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
989 <param name="use_type" value="single" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
990 <param name="input" value="examples.2.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
991 <param name="col_row_names" value="has_col_names,has_row_names" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
992 <conditional name="user" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
993 <param name="mode" value="filtersumval" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
994 <param name="axis" value="1" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
995 <conditional name="filtersumval_mode" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
996 <param name="use" value="operation" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
997 <param name="operation" value="sum" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
998 <param name="compare_op" value="lt" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
999 <param name="against" value="50" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1000 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1001 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1002 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1003 <output name="table" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1004 <assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1005 <has_n_columns n="4" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1006 <has_line_matching expression="^\s+c1\s+c2\s+c3$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1007 <has_line_matching expression="^g3\s+4\s+8\s+12$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1008 </assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1009 </output>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1010 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1011 <test expect_num_outputs="1" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1012 <!-- Test 27: Ex 3_P1 -->
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1013 <conditional name="singtabop" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1014 <param name="use_type" value="single" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1015 <param name="input" value="examples.3p1.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1016 <param name="col_row_names" value="has_col_names,has_row_names" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1017 <conditional name="user" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1018 <param name="mode" value="element" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1019 <conditional name="element" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1020 <param name="mode" value="custom" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1021 <param name="custom_expr" value="elem &#60; 10" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1022 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1023 <conditional name="elem_val" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1024 <param name="element_op" value="None" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1025 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1026 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1027 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1028 <output name="table" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1029 <assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1030 <has_n_columns n="4" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1031 <has_line_matching expression="^g1\s+False\s+False\s+False$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1032 <has_line_matching expression="^g4\s+False\s+True\s+True$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1033 </assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1034 </output>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1035 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1036 <test expect_num_outputs="1" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1037 <!-- Test 28: Ex 3_P2 -->
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1038 <conditional name="singtabop" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1039 <param name="use_type" value="single" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1040 <param name="input" value="examples.3p2.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1041 <param name="col_row_names" value="has_col_names,has_row_names" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1042 <conditional name="user" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1043 <param name="mode" value="matrixapply" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1044 <param name="dimension" value="1" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1045 <conditional name="matrixapply_func" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1046 <param name="vector_op" value="sum" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1047 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1048 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1049 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1050 <output name="table" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1051 <assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1052 <has_n_columns n="2" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1053 <has_line_matching expression="^g1\s+0$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1054 <has_line_matching expression="^g4\s+2$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1055 </assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1056 </output>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1057 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1058 <test expect_num_outputs="1" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1059 <!-- Test 29: Ex 4 -->
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1060 <conditional name="singtabop" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1061 <param name="use_type" value="single" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1062 <param name="input" value="examples.4.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1063 <param name="col_row_names" value="has_col_names,has_row_names" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1064 <conditional name="user" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1065 <param name="mode" value="element" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1066 <conditional name="element" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1067 <param name="mode" value="custom" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1068 <param name="custom_expr" value="(math.log(elem) / elem) if (elem > 5) else 1" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1069 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1070 <conditional name="elem_val" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1071 <param name="element_op" value="All" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1072 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1073 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1074 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1075 <output name="table" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1076 <assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1077 <has_n_columns n="4" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1078 <has_line_matching expression="^g1\s+1\.00\d+\s+0\.149\d+\s+0\.113\d+$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1079 <has_line_matching expression="^g4\s+0\.05\d+\s+1\.000\d+\s+1\.000\d+$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1080 </assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1081 </output>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1082 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1083 <test expect_num_outputs="1" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1084 <!-- Test 30: Ex 5 -->
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1085 <conditional name="singtabop" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1086 <param name="use_type" value="single" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1087 <param name="input" value="examples.5.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1088 <param name="col_row_names" value="has_col_names,has_row_names" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1089 <conditional name="user" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1090 <param name="mode" value="fulltable" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1091 <conditional name="general" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1092 <param name="use" value="custom" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1093 <param name="fulltable_custom_expr" value="table - table.mean(0)/table.std(0)" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1094 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1095 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1096 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1097 <output name="table" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1098 <assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1099 <has_n_columns n="4" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1100 <has_line_matching expression="^g1\s+9\.\d+\s+17\.\d+\s+28\.\d+$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1101 <has_line_matching expression="^g4\s+80\.\d+\s+7\.\d+\s+8\.\d+$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1102 </assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1103 </output>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1104 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1105 <test expect_num_outputs="1" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1106 <!-- Test 31: Ex 6 -->
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1107 <conditional name="singtabop" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1108 <param name="use_type" value="multiple" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1109 <repeat name="tables" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1110 <param name="input" value="examples.6p1.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1111 <param name="col_row_names" value="has_col_names,has_row_names" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1112 </repeat>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1113 <repeat name="tables" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1114 <param name="input" value="examples.6p2.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1115 <param name="col_row_names" value="has_col_names,has_row_names" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1116 </repeat>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1117 <repeat name="tables" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1118 <param name="input" value="examples.6p3.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1119 <param name="col_row_names" value="has_col_names,has_row_names" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1120 </repeat>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1121 <param name="fulltable_custom_expr" value="table1 / min(np.max(np.max(table2)), np.max(np.max(table3)))" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1122 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1123 <output name="table" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1124 <assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1125 <has_n_columns n="4" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1126 <has_line_matching expression="^g1\s+3\.3\d+\s+6\.6\d+\s+10\.0\d+$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1127 <has_line_matching expression="^g3\s+1\.3\d+\s+2\.6\d+\s+3\.3\d+$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1128 </assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1129 </output>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1130 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1131 <test expect_num_outputs="1" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1132 <!-- Test 32: Ex 7 -->
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1133 <conditional name="singtabop" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1134 <param name="use_type" value="single" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1135 <param name="input" value="examples.7.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1136 <param name="col_row_names" value="has_col_names,has_row_names" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1137 <conditional name="user">
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1138 <param name="mode" value="fulltable" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1139 <conditional name="general" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1140 <param name="use" value="melt" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1141 <param name="id_vars" value="A" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1142 <param name="value_vars" value="B,C" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1143 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1144 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1145 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1146 <output name="table" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1147 <assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1148 <has_n_columns n="4" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1149 <has_line_matching expression="^0\s+a\s+B\s+B\s*$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1150 <has_line_matching expression="^5\s+c\s+C\s+5\s*$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1151 </assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1152 </output>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1153 </test>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1154 <test expect_num_outputs="1" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1155 <!-- Test 33: Ex 8 -->
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1156 <conditional name="singtabop" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1157 <param name="use_type" value="single" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1158 <param name="input" value="examples.8.tsv" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1159 <param name="col_row_names" value="has_col_names,has_row_names" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1160 <conditional name="user" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1161 <param name="mode" value="fulltable" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1162 <conditional name="general" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1163 <param name="use" value="pivot" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1164 <param name="index" value="foo" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1165 <param name="column" value="bar" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1166 <param name="values" value="baz" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1167 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1168 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1169 </conditional>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1170 <output name="table" >
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1171 <assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1172 <has_n_columns n="4" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1173 <has_line_matching expression="^one\s+1\s+2\s+3$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1174 <has_line_matching expression="^two\s+4\s+5\s+6$" />
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1175 </assert_contents>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1176 </output>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1177 </test>
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1178 <test expect_num_outputs="1" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1179 <!-- Test 34: Negative range test #1 -->
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1180 <expand macro="test_inputs_ranges" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1181 <param name="select_cols_wanted" value="-2:2,1,-1" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1182 <param name="select_rows_wanted" value="1,3:-3,1" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1183 </expand>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1184 <output name="table" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1185 <assert_contents>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1186 <has_n_columns n="7" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1187 <has_line_matching expression="^\s*c2\s+c3\s+c1\s+c2\s+c1\s+c3$" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1188 <has_line_matching expression="^g1\s+20\s+30\s+10\s+20\s+10\s+30$" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1189 </assert_contents>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1190 </output>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1191 </test>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1192 <test expect_num_outputs="1" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1193 <!-- Test 35: Negative range test #2 -->
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1194 <expand macro="test_inputs_ranges" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1195 <param name="select_cols_wanted" value="-1,-3,3:-3,2" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1196 <param name="select_rows_wanted" value="3:-1" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1197 <param name="select_keepdupe" value="" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1198 </expand>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1199 <output name="table" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1200 <assert_contents>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1201 <has_n_columns n="7" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1202 <has_line_matching expression="^\s*c3\s+c1\s+c3\s+c2\s+c1\s+c2$" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1203 <has_line_matching expression="^g4\s+3\s+81\s+3\s+6\s+81\s+6$" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1204 </assert_contents>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1205 </output>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1206 </test>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1207 <test expect_num_outputs="1">
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1208 <!-- Test 36: Skip first 3 lines -->
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1209 <conditional name="singtabop" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1210 <param name="use_type" value="single" />
5
3bf5661c0280 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit f0fd699a4e713c57ab7d3d9d8cbb18b41aa6c7cd
iuc
parents: 4
diff changeset
1211 <param name="input" value="skiplines.tsv" ftype="tabular" />
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1212 <section name="adv" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1213 <param name="header" value="2" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1214 <param name="nrows" value="4" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1215 <param name="skip_blank_lines" value="true" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1216 </section>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1217 <conditional name="user" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1218 <param name="mode" value="precision" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1219 </conditional>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1220 </conditional>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1221 <param name="precision" value="2" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1222 <output name="table" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1223 <assert_contents>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1224 <has_n_columns n="4" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1225 <has_line_matching expression="^\s+c1\s+c2\s+c3$" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1226 <has_line_matching expression="^g4\s+81\s+6\s+3$" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1227 </assert_contents>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1228 </output>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1229 </test>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1230 <test expect_num_outputs="1">
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1231 <!-- Test 37: Skip first 3 lines -->
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1232 <conditional name="singtabop" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1233 <param name="use_type" value="single" />
5
3bf5661c0280 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit f0fd699a4e713c57ab7d3d9d8cbb18b41aa6c7cd
iuc
parents: 4
diff changeset
1234 <param name="input" value="skiplines.tsv" ftype="tabular" />
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1235 <section name="adv" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1236 <param name="header" value="2" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1237 <param name="skipfooter" value="2" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1238 <param name="skip_blank_lines" value="false" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1239 </section>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1240 <conditional name="user" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1241 <param name="mode" value="precision" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1242 </conditional>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1243 </conditional>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1244 <param name="precision" value="2" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1245 <param name="out_opts" value="" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1246 <output name="table" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1247 <assert_contents>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1248 <has_n_columns n="3" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1249 <has_line_matching expression="^10.00\s+20.00\s+30.00$" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1250 <has_line_matching expression="^\s+$" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1251 </assert_contents>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1252 </output>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1253 </test>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1254 <test expect_num_outputs="1" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1255 <!-- Test 38: Row Col replace with format spec #1 -->
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1256 <conditional name="singtabop" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1257 <param name="use_type" value="single" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1258 <param name="input" value="examples.1.tsv" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1259 <param name="col_row_names" value="has_col_names,has_row_names" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1260 <conditional name="user" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1261 <param name="mode" value="element" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1262 <conditional name="element" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1263 <param name="mode" value="replace" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1264 <param name="replace_value" value="chr{elem:.0f}" />
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1265 </conditional>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1266 <conditional name="elem_val" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1267 <param name="element_op" value="rowcol" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1268 <param name="select_cols_wanted" value="2" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1269 <param name="select_rows_wanted" value="2,4" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1270 <param name="inclusive_selection" value="True" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1271 </conditional>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1272 </conditional>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1273 </conditional>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1274 <output name="table" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1275 <assert_contents>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1276 <has_n_columns n="4" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1277 <has_line_matching expression="^g2\s+chr3\s+chr6\s+chr9$" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1278 <has_line_matching expression="^g4\s+chr81\s+chr6\s+chr3$" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1279 </assert_contents>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1280 </output>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1281 </test>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1282 <test expect_num_outputs="1" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1283 <!-- Test 39: Row Col replace with format spec #2 -->
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1284 <conditional name="singtabop" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1285 <param name="use_type" value="single" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1286 <param name="input" value="examples.1.tsv" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1287 <param name="col_row_names" value="has_col_names,has_row_names" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1288 <conditional name="user" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1289 <param name="mode" value="element" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1290 <conditional name="element" >
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1291 <param name="mode" value="replace" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1292 <param name="replace_value" value="chr{elem:.0f}" />
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1293 </conditional>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1294 <conditional name="elem_val" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1295 <param name="element_op" value="rowcol" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1296 <param name="select_cols_wanted" value="2" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1297 <param name="select_rows_wanted" value="2,4" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1298 <param name="inclusive_selection" value="False" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1299 </conditional>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1300 </conditional>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1301 </conditional>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1302 <output name="table" >
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1303 <assert_contents>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1304 <has_n_columns n="4" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1305 <has_line_matching expression="^g2\s+3\s+chr6\s+9$" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1306 <has_line_matching expression="^g4\s+81\s+chr6\s+3$" />
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1307 </assert_contents>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1308 </output>
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1309 </test>
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1310 <test expect_num_outputs="1">
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1311 <!-- Test 40: Test safety of Replacement value free text
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1312 Tries to escape/reenter config file quoting.
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1313 If the test fails, this shows that Python has performed
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1314 string concatenation upon importing the config file. -->
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1315 <conditional name="singtabop" >
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1316 <param name="use_type" value="single" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1317 <param name="input" value="examples.1.tsv" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1318 <param name="col_row_names" value="has_col_names,has_row_names" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1319 <conditional name="user" >
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1320 <param name="mode" value="element" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1321 <conditional name="elem_val">
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1322 <param name="element_op" value="None" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1323 </conditional>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1324 <conditional name="element" >
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1325 <param name="mode" value="replace" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1326 <param name="scale_op" value="mod" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1327 <param name="replace_value" value="a'+'b" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1328 </conditional>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1329 </conditional>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1330 </conditional>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1331 <output name="table" >
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1332 <assert_contents>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1333 <has_n_columns n="4" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1334 <not_has_text text="g1&#009;ab" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1335 <not_has_text text="g2&#009;ab" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1336 <not_has_text text="g3&#009;ab" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1337 <not_has_text text="g4&#009;ab" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1338 </assert_contents>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1339 </output>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1340 </test>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1341 <test expect_num_outputs="1" expect_failure="true">
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1342 <!-- Test 41: Test safety of custom expression free text
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1343 Tries to escape/reenter config file quoting.
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1344
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1345 This test is expected to fail if either
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1346 - a validator disallows the use of single quotes or
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1347 - the single quotes get sanitized (which is unlikely to result in a
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1348 valid expression); note that in this situation, it cannot be
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1349 guaranteed that the single quote sanitization is safe with
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1350 *every* input
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1351
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1352 If the test succeeds unexpectedly, this shows that Python
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1353 has performed string concatenation upon importing the config file
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1354 resulting in each element of the test table being retained.
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1355 -->
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1356 <conditional name="singtabop" >
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1357 <param name="use_type" value="single" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1358 <param name="input" value="examples.4.tsv" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1359 <param name="col_row_names" value="has_col_names,has_row_names" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1360 <conditional name="user" >
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1361 <param name="mode" value="element" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1362 <conditional name="element" >
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1363 <param name="mode" value="custom" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1364 <param name="custom_expr" value="el'+'em" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1365 </conditional>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1366 <conditional name="elem_val" >
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1367 <param name="element_op" value="All" />
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1368 </conditional>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1369 </conditional>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1370 </conditional>
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1371 </test>
4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1372 <test expect_num_outputs="1" >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1373 <!-- Pivot aggregator operations -->
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1374 <conditional name="singtabop" >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1375 <param name="use_type" value="single" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1376 <param name="input" value="pivot.tsv" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1377 <param name="col_row_names" value="has_col_names,has_row_names" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1378 <conditional name="user" >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1379 <param name="mode" value="fulltable" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1380 <conditional name="general" >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1381 <param name="use" value="pivot" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1382 <param name="index" value="Position" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1383 <repeat name="colfun_map" >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1384 <param name="column" value="Age" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1385 <repeat name="functions"><param name="aggfunc" value="mean" /></repeat>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1386 </repeat>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1387 <repeat name="colfun_map" >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1388 <param name="column" value="Random" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1389 <repeat name="functions"><param name="aggfunc" value="mean" /></repeat>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1390 <repeat name="functions"><param name="aggfunc" value="std" /></repeat>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1391 </repeat>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1392 </conditional>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1393 </conditional>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1394 </conditional>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1395 <output name="table" >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1396 <assert_contents>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1397 <has_n_columns n="4" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1398 <has_line_matching expression="^Manager\s+34.3\d+\s+0.325\d+\s+0.306\d+" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1399 <has_line_matching expression="^Programmer\s+32.3\d+\s+0.423\d+\s+0.477\d+" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1400 </assert_contents>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1401 </output>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1402 </test>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1403 <test expect_num_outputs="1" >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1404 <!-- Pivot table operations from PR 3480 -->
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1405 <conditional name="singtabop" >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1406 <param name="use_type" value="single" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1407 <param name="input" value="table1.tsv" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1408 <param name="col_row_names" value="has_col_names" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1409 <conditional name="user" >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1410 <param name="mode" value="fulltable" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1411 <conditional name="general" >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1412 <param name="use" value="pivot" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1413 <param name="index" value="A" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1414 <param name="column" value="C" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1415 <param name="values" value="D" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1416 <param name="aggfunc" value="max" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1417 </conditional>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1418 </conditional>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1419 </conditional>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1420 <output name="table" >
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1421 <assert_contents>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1422 <has_text_matching expression="bar\t7\t6" />
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1423 </assert_contents>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1424 </output>
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1425 </test>
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1426 </tests>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1427 <help><![CDATA[
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1428 Table Compute
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1429 -------------
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1430
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1431 This tool is a Galaxy wrapper for the `Pandas Data Analysis Library <https://pandas.pydata.org/>`_ in Python,
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1432 for manipulating and computing expressions upon tabular data and matrices. It can perform functions on the
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1433 element, row, and column basis, as well as sub-select, duplicate, replace, and perform general and custom
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1434 expressions on rows, columns, and elements.
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1435
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1436
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1437 .. class:: infomark
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1438
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1439 Only a single operation can be performed on the data. Multiple operations
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1440 can be performed by chaining successive runs of this tool. This is to
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1441 provide a more transparent workflow for complex operations.
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1442
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1443
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1444 Many of the examples given below relate to common research use-cases such as filtering large matrices for
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1445 specific values, counting unique instances of elements, conditionally manipulating the data, and replacing
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1446 unwanted values. Full table operations such as normalisation can be easily performed by scaling the data via
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1447 mean/median/min/max (and many other) metrics, and general expressions can even be computed across multiple
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1448 tables.
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1449
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1450
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1451 Examples
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1452 ========
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1453
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1454 Example 1: Sub-selecting from a table
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1455 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1456
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1457 We have the following table:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1458
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1459 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1460 . c1 c2 c3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1461 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1462 g1 10 20 30
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1463 g2 3 6 9
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1464 g3 4 8 12
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1465 g4 81 6 3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1466 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1467
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1468 and we want to duplicate c1 and remove c2. Also select g1 to g3 and add g2 at the end as well. This
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1469 would result in the output table:
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1470
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1471 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1472 . c1 c1 c3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1473 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1474 g1 10 10 30
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1475 g2 3 3 9
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1476 g3 4 4 12
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1477 g2 3 3 9
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1478 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1479
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1480 In Galaxy we would select the following:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1481
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1482 * *Input Single or Multiple Tables* → **Single Table**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1483 * *Column names on first row?* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1484 * *Row names on first column?* → **Yes**
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1485 * *Type of table operation* → **Drop, keep or duplicate rows and columns**
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1486
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1487 * *List of columns to select* → ``1,1,3``
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1488 * *List of rows to select* → ``1:3,2``
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1489 * *Keep duplicate columns* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1490 * *Keep duplicate rows* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1491
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1492 Example 2: Filter for rows with row sums less than 50
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1493 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1494
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1495 We have the following table:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1496
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1497 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1498 . c1 c2 c3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1499 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1500 g1 10 20 30
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1501 g2 3 6 9
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1502 g3 4 8 12
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1503 g4 81 6 3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1504 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1505
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1506 and we want:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1507
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1508 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1509 . c1 c2 c3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1510 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1511 g2 3 6 9
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1512 g3 4 8 12
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1513 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1514
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1515 In Galaxy we would select the following:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1516
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1517 * *Input Single or Multiple Tables* → **Single Table**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1518 * *Column names on first row?* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1519 * *Row names on first column?* → **Yes**
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1520 * *Type of table operation* → **Filter rows or columns by their properties**
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1521
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1522 * *Filter* → **Rows**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1523 * *Filter Criterion* → **Result of function applied to columns/rows**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1524
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1525 * *Keep column/row if its observed* → **Sum**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1526 * *is* → **< (Less Than)**
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1527 * *this value* → ``50``
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1528
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1529
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1530 Example 3: Count the number of values per row smaller than a specified value
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1531 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1532
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1533 We have the following table:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1534
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1535 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1536 . c1 c2 c3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1537 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1538 g1 10 20 30
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1539 g2 3 6 9
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1540 g3 4 8 12
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1541 g4 81 6 3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1542 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1543
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1544 and we want to count how many elements in each row are smaller than 10, i.e.,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1545 we want to obtain the following results table:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1546
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1547 === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1548 . vec
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1549 === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1550 g1 0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1551 g2 3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1552 g3 2
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1553 g4 2
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1554 === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1555
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1556 In Galaxy we would select the following:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1557
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1558 * *Input Single or Multiple Tables* → **Single Table**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1559 * *Column names on first row?* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1560 * *Row names on first column?* → **Yes**
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1561 * *Type of table operation* → **Manipulate selected table elements**
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1562
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1563 * *Operation to perform* → **Custom**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1564
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1565 * *Custom Expression on 'elem'* → ``elem < 10``
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1566
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1567 * *Operate on elements* → **All**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1568
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1569 **Note:** *There are actually simpler ways to achieve our purpose, but here we are demonstrating
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1570 the use of a custom expression.*
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1571
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1572 After executing, we would then be presented with a table like so:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1573
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1574 === ===== ===== =====
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1575 . c1 c2 c3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1576 === ===== ===== =====
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1577 g1 False False False
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1578 g2 True True True
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1579 g3 True True False
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1580 g4 False True True
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1581 === ===== ===== =====
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1582
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1583 To get to our desired table, we would then process this table with the tool again:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1584
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1585 * *Input Single or Multiple Tables* → **Single Table**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1586 * *Column names on first row?* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1587 * *Row names on first column?* → **Yes**
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1588 * *Type of table operation* → **Compute Expression across Rows or Columns**
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1589
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1590 * *Calculate* → **Sum**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1591 * *For each* → **Row**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1592
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1593 Executing this will sum all the 'True' values in each row. Note that the values must have no
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1594 extra whitespace in them for this to work (e.g. 'True ' or ' True' will not be parsed correctly).
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1595
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1596
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1597 Example 4: Perform a scaled log-transformation conditionally
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1598 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1599
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1600 We want to perform a scaled log transformation on all values greater than 5, and set all
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1601 other values to 1.
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1602
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1603 We have the following table:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1604
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1605 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1606 . c1 c2 c3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1607 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1608 g1 0 20 30
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1609 g2 3 0 9
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1610 g3 4 8 0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1611 g4 81 0 0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1612 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1613
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1614 and we want:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1615
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1616 === ========== ========= =========
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1617 . c1 c2 c3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1618 === ========== ========= =========
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1619 g1 1.00000000 0.1497866 0.1133732
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1620 g2 1.00000000 1.0000000 0.2441361
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1621 g3 1.00000000 0.2599302 1.0000000
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1622 g4 0.05425246 1.0000000 1.0000000
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1623 === ========== ========= =========
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1624
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1625 In Galaxy we would select the following:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1626
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1627 * *Input Single or Multiple Tables* → **Single Table**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1628 * *Column names on first row?* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1629 * *Row names on first column?* → **Yes**
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1630 * *Type of table operation* → **Manipulate selected table elements**
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1631
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1632 * *Operation to perform* → **Custom**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1633
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1634 * *Custom Expression* → ``(math.log(elem) / elem) if (elem > 5) else 1``
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1635
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1636 * *Operate on elements* → **All**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1637
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1638
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1639 Example 5: Perform a Full table operation
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1640 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1641
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1642 We have the following table:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1643
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1644 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1645 . c1 c2 c3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1646 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1647 g1 10 20 30
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1648 g2 3 10 9
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1649 g3 4 8 10
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1650 g4 81 10 10
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1651 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1652
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1653 and we want to subtract from each column the mean of that column divided by the standard
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1654 deviation of it to yield:
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1655
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1656
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1657 === ========= ========= =========
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1658 . c1 c2 c3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1659 === ========= ========= =========
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1660 g1 9.351737 17.784353 28.550737
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1661 g2 2.351737 7.784353 7.550737
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1662 g3 3.351737 5.784353 8.550737
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1663 g4 80.351737 7.784353 8.550737
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1664 === ========= ========= =========
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1665
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1666 In Galaxy we would select the following:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1667
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1668 * *Input Single or Multiple Tables* → **Single Table**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1669 * *Column names on first row?* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1670 * *Row names on first column?* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1671 * *Type of table operation* → **Perform a Full Table Operation**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1672
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1673 * *Operation* → **Custom**
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1674 * *Custom Expression on 'table' along axis (0 or 1)* → ``table - table.mean(0)/table.std(0)``
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1675
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1676
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1677 Example 6: Perform operations on multiple tables
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1678 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1679
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1680 We have the following three input tables:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1681
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1682 Table 1
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1683
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1684 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1685 . c1 c2 c3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1686 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1687 g1 10 20 30
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1688 g2 3 10 9
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1689 g3 4 8 10
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1690 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1691
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1692 Table 2
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1693
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1694 === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1695 . c1 c2
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1696 === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1697 g1 1 2
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1698 g2 3 4
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1699 g3 6 5
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1700 === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1701
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1702 Table 3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1703
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1704 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1705 . c1 c2 c3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1706 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1707 g1 1 2 3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1708 g2 1 2 3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1709 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1710
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1711
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1712 *Note that the dimensions of these tables do not match.*
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1713
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1714 Dimensions:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1715 * Table1 [3,3]
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1716 * Table2 [3,2]
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1717 * Table3 [2,3]
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1718
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1719 In order to perform simple operations between Tables, they must be of the same dimensions.
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1720
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1721 To add Table2 to Table3 we would have to transpose one of the tables using the in-built `T` method::
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1722
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1723 table2 + table3.T
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1724
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1725 or::
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1726
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1727 table2.T + table3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1728
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1729 We can also perform more general operations using all 3 tables, such as taking the minimum value of
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1730 the maximum values of Table2 and Table3, and dividing the Table1 values by it::
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1731
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1732 table1 / min(table2.values.max(), table3.values.max())
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1733
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1734
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1735 To perform these types of operations in Galaxy we would select the following:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1736
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1737 * *Input Single or Multiple Tables* → **Multiple Tables**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1738 * *(For each inserted table)*
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1739 * *Column names on first row?* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1740 * *Row names on first column?* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1741 * *Custom Expression* → ::
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1742
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1743 <insert your desired function>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1744
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1745 Please note that the last example shown above was chosen to illustrate the
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1746 limitations of the tool. Nested attributes like `table2.values.max` are
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1747 disallowed in expressions in the tool so the above would have to be replaced
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1748 with the harder to read workaround::
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1749
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1750 table1 / min(np.max(np.max(table2)), np.max(np.max(table3)))
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1751
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1752 .. class:: infomark
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1753
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1754 Complex operations (like ones that would benefit from specifying nested
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1755 attributes) can often be broken into subsequent runs ot the tool, in
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1756 which the first run generates an intermediate table representing the result
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1757 of the "inner" operation that the second run can then use as input to
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1758 perform the "outer" operation.
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1759
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1760 Also note that, currently `min()`, `max()` and `sum()` are the only built-in
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1761 Python functions that can be used inside expressions. If you want to use
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1762 additional functions, these have to be qualified functions from the `math`,
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1763 `np` or `pd` libraries.
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1764
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1765
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1766 Example 7: Melt
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1767 ~~~~~~~~~~~~~~~
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1768
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1769 We have the following table
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1770
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1771 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1772 . A B C
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1773 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1774 0 a B 1
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1775 1 b B 3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1776 2 c B 5
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1777 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1778
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1779 and we want:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1780
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1781 === === ======== =====
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1782 . A variable value
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1783 === === ======== =====
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1784 0 a B B
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1785 1 b B B
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1786 2 c B B
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1787 3 a C 1
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1788 4 b C 3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1789 5 c C 5
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1790 === === ======== =====
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1791
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1792
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1793 In Galaxy we would select the following:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1794
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1795 * *Input Single or Multiple Tables* → **Single Table**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1796 * *Column names on first row?* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1797 * *Row names on first column?* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1798 * *Type of table operation* → **Perform a Full Table Operation**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1799
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1800 * *Operation* → **Melt**
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1801 * *Variable IDs* → ``A``
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1802 * *Unpivoted IDs* → ``B,C``
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1803
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1804 This converts the "B" and "C" columns into variables.
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1805
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1806
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1807 Example 8: Pivot
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1808 ~~~~~~~~~~~~~~~~
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1809
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1810 We have the following table
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1811
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1812 === === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1813 . foo bar baz zoo
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1814 === === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1815 0 one A 1 x
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1816 1 one B 2 y
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1817 2 one C 3 z
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1818 3 two A 4 q
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1819 4 two B 5 w
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1820 5 two C 6 t
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1821 === === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1822
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1823 and we want:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1824
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1825 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1826 . A B C
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1827 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1828 one 1 2 3
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1829 two 4 5 6
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1830 === === === ===
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1831
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1832 In Galaxy we would select the following:
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1833
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1834 * *Input Single or Multiple Tables* → **Single Table**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1835 * *Column names on first row?* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1836 * *Row names on first column?* → **Yes**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1837 * *Type of table operation* → **Perform a Full Table Operation**
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1838
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1839 * *Operation* → **Pivot**
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1840 * *Index* → ``foo``
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1841 * *Column* → ``bar``
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1842 * *Values* → ``baz``
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1843
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1844 This splits the matrix using "foo" and "bar" using only the values from "baz". Header values
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1845 may contain extra information.
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
1846
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1847
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1848 Example 9: Replacing text in specific rows or columns
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1849 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1850
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1851 We have the following table
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1852
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1853 === === === ===
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1854 . c1 c2 c3
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1855 === === === ===
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1856 g1 10 20 30
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1857 g2 3 3 9
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1858 g3 4 8 12
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1859 g4 81 6 3
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1860 === === === ===
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1861
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1862 and we want to add "chr" to the elements in column 2 AND rows 2 and 4:
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1863
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1864 === === ==== ===
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1865 . c1 c2 c3
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1866 === === ==== ===
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1867 g1 10 20 30
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1868 g2 3 chr3 9
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1869 g3 4 8 12
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1870 g4 81 chr6 3
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1871 === === ==== ===
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1872
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1873 In Galaxy we would select the following:
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1874
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1875 * *Input Single or Multiple Tables* → **Single Table**
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1876 * *Column names on first row?* → **Yes**
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1877 * *Row names on first column?* → **Yes**
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1878
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1879 * *Type of table operation* → **Manipulate selected table elements**
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1880
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1881 * *Operation to perform* → **Replace values**
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1882
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1883 * *Replacement value* → ``chr{elem:.0f}``
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1884
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1885 Here, the placeholder ``{elem}`` lets us refer to each element's current value,
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1886 while the ``:.0f`` part is a format specifier that makes sure numbers are printed
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1887 without decimals (for a complete description of the available syntax see the
2
02c3e335a695 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"
iuc
parents: 1
diff changeset
1888 `Python Format Specification Mini-Language <https://docs.python.org/3/library/string.html#formatspec>`_).
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1889
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1890 * *Operate on elements* → **Specific Rows and/or Columns**
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1891 * *List of columns to select* → ``2``
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1892 * *List of rows to select* → ``2,4``
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1893 * *Inclusive Selection* → ``No``
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1894
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1895
3
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1896 If we wanted to instead add "chr" to the ALL elements in column 2 and rows 2 and 4, we
60ff16842fcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"
iuc
parents: 2
diff changeset
1897 would repeat the steps above but set the *Inclusive Selection* to "Yes", to give:
1
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1898
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1899 === ===== ===== =====
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1900 . c1 c2 c3
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1901 === ===== ===== =====
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1902 g1 10 chr20 30
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1903 g2 chr3 chr3 chr9
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1904 g3 4 8 12
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1905 g4 chr81 chr6 chr3
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1906 === ===== ===== =====
dddadbbac949 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"
iuc
parents: 0
diff changeset
1907
4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1908
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1909 Example 10: Pivot Table with unified Aggregator
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1910 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1911
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1912 For an input table of:
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1913
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1914 === === ===== === ===
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1915 A B C D E
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1916 === === ===== === ===
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1917 foo one small 1 2
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1918 foo one large 2 4
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1919 foo one large 2 5
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1920 foo two small 3 5
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1921 foo two small 3 6
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1922 bar one large 4 6
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1923 bar one small 5 8
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1924 bar two small 6 9
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1925 bar two large 7 9
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1926 === === ===== === ===
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1927
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1928 we wish to pivot the table with the 'A' column as the new row index and use the values of the column 'C' as the new column indexes, based on the aggregated values of 'D'. By default the aggregator function is the mean, but here we will instead pick the max, to yield:
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1929
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1930 === == ==
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1931 C l s
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1932 A
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1933 === == ==
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1934 bar 7 6
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1935 foo 2 3
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1936 === == ==
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1937
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1938 In Galaxy we would select the following:
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1939
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1940 * *Input Single or Multiple Tables* → **Single Table**
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1941 * *Column names on first row?* → **Yes**
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1942 * *Row names on first column?* → **Yes**
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1943 * *Type of table operation* → **Perform a Full Table Operation**
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1944
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1945 * *Operation* → **Pivot**
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1946 * *Index* → ``A``
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1947 * *Column* → ``C``
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1948 * *Values* → ``D``
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1949 * *Aggregator Function* → ``max``
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1950
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1951
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1952 Example 11: Pivot Table with custom Aggregrator
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1953 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1954
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1955 For an input table of:
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1956
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1957
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1958 ==== ========== =========== === ========
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1959 Name Position City Age Random
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1960 ==== ========== =========== === ========
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1961 Mary Manager Boston 34 0.678577
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1962 Josh Programmer New York 37 0.973168
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1963 Jon Manager Chicago 29 0.146668
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1964 Lucy Manager Los Angeles 40 0.150120
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1965 Jane Programmer Chicago 29 0.112769
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1966 Sue Programmer Boston 31 0.185198
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1967 ==== ========== =========== === ========
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1968
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1969 we wish to pivot the table with the 'Position' column as the new index and transform the 'Age' and 'Random' columns to have mean and standard deviation values
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1970
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1971 ========== ========= ======== ========
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1972 Position Age Random Random
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1973 . mean mean std
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1974 ========== ========= ======== ========
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1975 Manager 34.333333 0.325122 0.306106
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1976 Programmer 32.333333 0.423712 0.477219
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1977 ========== ========= ======== ========
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1978
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1979 In Galaxy we would select the following:
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1980
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1981 * *Input Single or Multiple Tables* → **Single Table**
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1982 * *Column names on first row?* → **Yes**
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1983 * *Row names on first column?* → **Yes**
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1984 * *Type of table operation* → **Perform a Full Table Operation**
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1985
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1986 * *Operation* → **Pivot**
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1987 * *Index* → ``Position``
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1988 * *Column-Function Mapping*
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1989
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1990 * *Value Column* → ``Age``
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1991
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1992 * *Function* → ``mean``
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1993
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1994 * *Value Column* → ``Random``
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1995
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1996 * *Function* → ``mean``
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1997 * *Function* → ``std``
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1998
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
1999
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
2000 This splits the matrix using "foo" and "bar" using only the values from "baz". Header values
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
2001 may contain extra information.
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
2002
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
2003
93a3ce78ce55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d741508e5ed912cdeee4f67ec8451b6e6865363c"
iuc
parents: 3
diff changeset
2004
0
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
2005 ]]></help>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
2006 <citations></citations>
1b0f96ed73f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
iuc
parents:
diff changeset
2007 </tool>