Mercurial > repos > devteam > column_maker

annotate column_maker.xml @ 10:beec6ecc7d3c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
author iuc
date Thu, 22 Aug 2024 08:25:32 +0000
parents 33b81f9ea109
children
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10
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
iuc
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1 <tool id="Add_a_column1" name="Compute" version="2.1" profile="23.0">
9
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2 <description>on rows</description>
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3 <macros>
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4 <xml name="compute_repeat">
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5 <repeat name="expressions" title="Expressions" min="1" default="1">
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6 <param name="cond" type="text" value="c3-c2" label="Add expression">
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7 <sanitizer>
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8 <valid initial="default">
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9 <add value="&lt;" />
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10 <add value="&gt;" />
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11 <add value="&quot;" />
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12 <add value="&apos;" />
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13 </valid>
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14 </sanitizer>
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15 </param>
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16 <conditional name="add_column">
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17 <param name="mode" type="select" label="Mode of the operation">
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18 <option value="">Append</option>
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19 <option value="I">Insert</option>
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20 <option value="R">Replace</option>
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21 </param>
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22 <when value="">
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23 <param name="pos" type="hidden" value="" />
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24 </when>
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25 <when value="I">
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26 <param name="pos" type="integer" min="1" value="1" label="Insert new column before existing column number" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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27 </when>
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28 <when value="R">
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29 <param name="pos" type="integer" min="1" value="1" label="Use new column to replace column number" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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30 </when>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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31 </conditional>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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32 <yield />
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33 </repeat>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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34 </xml>
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35 </macros>
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36 <requirements>
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37 <requirement type="package" version="3.12">python</requirement>
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38 <requirement type="package" version="2.1.0">numpy</requirement>
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39 </requirements>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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40 <command detect_errors="aggressive"><![CDATA[
9
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41 python '$__tool_directory__/column_maker.py'
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42 #if str($error_handling.auto_col_types) == 'on':
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43 #set $col_types = $input.metadata.column_types
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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44 #else:
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45 #set $col_types = ','.join(['str' for t in $input.metadata.column_types.split(',')])
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46 #end if
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47 --column-types $col_types
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48 $avoid_scientific_notation
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49 #if str($ops.header_lines_select) == 'yes':
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50 --header
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51 #end if
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52 --file '$expressions_file'
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53 $error_handling.fail_on_non_existent_columns
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54 $error_handling.non_computable.action
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55 #if str($error_handling.non_computable.action) == '--non-computable-default':
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56 '$error_handling.non_computable.default_value'
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57 #end if
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58 '$input'
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59 '$out_file1'
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60 ]]></command>
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61 <configfiles>
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62 <configfile name="expressions_file"><![CDATA[
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63 #if str($ops.header_lines_select) == 'yes':
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64 #for $expr in $ops.expressions:
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65 ${expr.cond};${expr.add_column.pos}${expr.add_column.mode};${expr.new_column_name}
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66 #end for
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67 #else:
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68 #for $expr in $ops.expressions:
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69 ${expr.cond};${expr.add_column.pos}${expr.add_column.mode};
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70 #end for
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71 #end if
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72 ]]></configfile>
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73 </configfiles>
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74 <inputs>
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75 <param name="input" type="data" format="tabular" label="Input file" help="Dataset missing? See TIP below" />
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76 <conditional name="ops">
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77 <param name="header_lines_select" type="select"
e7c273e8d4d6 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
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78 label="Input has a header line with column names?"
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79 help="Select Yes to be able to specify names for new columns and have them added to the header line. If you select No, the first line will be treated as a regular line: If it is empty or starts with a # character it will be skipped, otherwise the tool will attempt to compute the specified expression on it." >
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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80 <option value="no">No</option>
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81 <option value="yes">Yes</option>
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82 </param>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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83 <when value="no">
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84 <expand macro="compute_repeat" />
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85 </when>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
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86 <when value="yes">
9
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87 <expand macro="compute_repeat">
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88 <param name="new_column_name" type="text" value="New Column" label="The new column name" />
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89 </expand>
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90 </when>
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91 </conditional>
9
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92 <param name="avoid_scientific_notation" type="boolean" truevalue="--avoid-scientific-notation" falsevalue=""
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93 label="Avoid scientific notation in any newly computed columns"
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94 help="If yes, use fully expanded decimal representation when writing new columns with floating point values. To prevent scientific notation in just specific new columns, you can use numpy's format_float_positional function in the corresponding expression." />
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95 <section name="error_handling" title="Error handling">
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96 <param name="auto_col_types" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Autodetect column types"
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97 help="By default, try to use the column types that Galaxy has recorded for the input. This simplifies expressions, but can occasionally cause problems on its own. If disabled all column values are assumed to be strings and you will have to handle conversions to different types explicitly in the expression." />
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98 <param argument="--fail-on-non-existent-columns" type="boolean" truevalue="--fail-on-non-existent-columns" falsevalue="" checked="true" label="Fail on references to non-existent columns"
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99 help="If any expression references a column number that does not exist when that expression gets computed, the tool run will fail. Uncheck to have such a situation handled as a case of a non-computable expression as configured below." />
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100 <conditional name="non_computable">
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101 <param name="action" type="select" label="If an expression cannot be computed for a row">
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102 <option value="--fail-on-non-computable">Fail the entire tool run</option>
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103 <option value="--skip-non-computable">Skip the row</option>
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104 <option value="--keep-non-computable">Keep the row unchanged</option>
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105 <option value="--non-computable-blank">Produce an empty column value for the row</option>
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106 <option value="--non-computable-default">Fill in a replacement value</option>
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107 </param>
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108 <when value="--fail-on-non-computable" />
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109 <when value="--skip-non-computable" />
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110 <when value="--keep-non-computable" />
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111 <when value="--non-computable-blank" />
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112 <when value="--non-computable-default">
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113 <param name="default_value" type="text" label="Replacement value" help="Pick from suggestions or enter your own.">
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114 <option value="nan">nan (not a number)</option>
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115 <option value="inf">inf (infinity)</option>
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116 <option value="-inf">-inf (negative infinity)</option>
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117 <option value="NA">NA (not available)</option>
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118 <option value=".">.</option>
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119 </param>
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120 </when>
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121 </conditional>
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122 </section>
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123 </inputs>
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124 <outputs>
9
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125 <data name="out_file1" format_source="input" metadata_source="input"/>
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126 </outputs>
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127 <tests>
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128 <test>
9
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129 <param name="cond" value="float(c3-c2)"/>
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130 <param name="input" value="1.bed" ftype="bed" />
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131 <output name="out_file1" file="column_maker_out1.interval"/>
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132 </test>
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133 <test>
9
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134 <param name="cond" value="c4*1."/>
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135 <param name="input" value="1.interval" ftype="interval" />
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136 <output name="out_file1" file="column_maker_out2.interval"/>
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137 </test>
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138 <test>
9
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139 <param name="cond" value="c4*1."/>
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140 <param name="input" value="1.header.tsv" ftype="tabular" />
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141 <param name="header_lines_select" value="yes" />
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142 <param name="new_column_name" value="value1_again" />
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143 <output name="out_file1" file="column_maker_out2.header.tsv"/>
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144 </test>
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145 <test>
9
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146 <param name="cond" value="round(c4*1)"/>
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147 <param name="input" value="1.interval"/>
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148 <output name="out_file1" file="column_maker_out3.interval"/>
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149 </test>
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150 <test>
8
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151 <!-- test that single column input works -->
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152 <param name="cond" value="c1/10"/>
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153 <param name="input" value="1.tab" ftype="tabular" />
8
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154 <output name="out_file1" file="column_maker_out4.tab"/>
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155 </test>
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156 <test>
6
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157 <param name="cond" value="float(.0000000000001)"/>
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158 <param name="input" value="1.bed"/>
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159 <output name="out_file1">
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160 <assert_contents>
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161 <has_text text="CCDS10397" />
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162 <has_text text="1e-13" />
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163 </assert_contents>
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164 </output>
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165 </test>
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166 <test>
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167 <param name="cond" value="float(.0000000000001)"/>
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168 <param name="input" value="1.bed" ftype="bed" />
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169 <param name="avoid_scientific_notation" value="true"/>
6
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170 <output name="out_file1">
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171 <assert_contents>
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172 <has_text text="CCDS10397" />
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173 <has_text text=".0000000000001" />
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174 <not_has_text text="1e-13" />
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175 </assert_contents>
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176 </output>
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177 </test>
9
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178 <test>
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179 <param name="input" value="1.tab" ftype="tabular" />
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180 <repeat name="expressions">
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181 <param name="cond" value="c1/10" />
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182 <conditional name="add_column">
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183 <param name="mode" value="R" />
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184 <param name="pos" value="1" />
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185 </conditional>
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186 </repeat>
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187 <repeat name="expressions">
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188 <param name="cond" value="round(c1*10)" />
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189 <conditional name="add_column">
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190 <param name="mode" value="I" />
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191 <param name="pos" value="1" />
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192 </conditional>
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193 </repeat>
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194 <output name="out_file1" file="column_maker_out4.tab" />
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195 </test>
10
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196 <test>
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197 <param name="cond" value="cos(pi)+sin(tau)*c2"/>
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198 <param name="input" value="1.bed" ftype="bed" />
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199 <output name="out_file1" file="column_maker_out5.interval"/>
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200 </test>
9
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201 <!-- Test list column type in input -->
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202 <test>
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203 <param name="input" value="bed12.bed" ftype="bed12" />
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204 <!-- get largest blocksize from column 11 of bed12 and use it as
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205 new score value -->
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206 <param name="cond" value="max(map(int, c11))" />
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207 <conditional name="add_column">
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208 <param name="mode" value="R" />
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209 <param name="pos" value="5" />
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210 </conditional>
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211 <output name="out_file1" file="bed12_modified.bed" />
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212 </test>
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213 <!-- Test error handling example from help section -->
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214 <test>
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215 <param name="input" value="short_line_test.tab" ftype="tabular" />
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216 <param name="cond" value="c6" />
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217 <conditional name="add_column">
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218 <param name="mode" value="R" />
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219 <param name="pos" value="6" />
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220 </conditional>
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221 <param name="fail_on_non_existent_columns" value="false" />
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222 <param name="action" value="--non-computable-default" />
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223 <param name="default_value" value="." />
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224 <output name="out_file1" file="short_line_test_out.tab" />
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225 </test>
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226 <!-- Test athletes BMI calculation in presence of NA values as in
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227 https://training.galaxyproject.org/training-material/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html#exercises-4
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228 -->
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229 <test>
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230 <param name="input" value="olympics.tsv" ftype="tabular" />
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231 <param name="header_lines_select" value="yes" />
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232 <param name="new_column_name" value="BMI" />
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233 <param name="cond" value="int(c8) / (int(c7) * int(c7)) * 10000" />
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234 <param name="auto_col_types" value="false" />
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235 <param name="action" value="--non-computable-default" />
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236 <param name="default_value" value="NA" />
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237 <output name="out_file1" file="olympics_bmi_out.tab" />
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238 </test>
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239 <!-- Test operation used by iwc SARS-CoV-2 consensus building WF that
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240 turns a 3-column CHROM POS REF tabular dataset into a 3-column BED
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241 dataset. -->
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242 <test>
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243 <param name="input" value="chrom_pos_ref.tab" ftype="tabular" />
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244 <repeat name="expressions">
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245 <param name="cond" value="int(c2) - (len(c3) == 1)" />
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246 <conditional name="add_column">
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247 <param name="mode" value="R" />
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248 <param name="pos" value="2" />
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249 </conditional>
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250 </repeat>
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251 <repeat name="expressions">
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252 <param name="cond" value="int(c2) + ((len(c3) - 1) or 1)" />
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253 <conditional name="add_column">
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254 <param name="mode" value="R" />
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255 <param name="pos" value="3" />
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256 </conditional>
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257 </repeat>
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258 <output name="out_file1" file="bed_from_chrom_pos_ref.bed" />
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259 </test>
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260 <!-- Test failure on expression syntax errors -->
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261 <test expect_failure="true">
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262 <param name="cond" value="c3- = c2"/>
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263 <param name="input" value="1.bed" ftype="bed" />
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264 <assert_stderr>
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265 <has_text text="syntax error during parsing." />
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266 </assert_stderr>
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267 </test>
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268 <!-- Test failure on expression NameErrors -->
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269 <test expect_failure="true">
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270 <param name="cond" value="floatfloat(c3-c2)"/>
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271 <param name="input" value="1.bed" ftype="bed" />
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272 <assert_stderr>
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273 <has_text text="name 'floatfloat' is not defined" />
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274 </assert_stderr>
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275 </test>
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276 <!-- Test failure on non-existent column ref -->
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277 <test expect_failure="true">
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278 <param name="cond" value="c7 - c2"/>
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279 <param name="input" value="1.bed" ftype="bed" />
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280 <assert_stderr>
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281 <has_text text="name 'c7' is not defined" />
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282 </assert_stderr>
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283 </test>
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284 <!-- Test failure on non-computable expression -->
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285 <test expect_failure="true">
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286 <param name="cond" value="c3 / 0"/>
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287 <param name="input" value="1.bed" ftype="bed" />
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288 <assert_stderr>
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289 <has_text text="division by zero" />
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290 </assert_stderr>
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291 </test>
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292 <!-- Test keep-non-computable prevents failure -->
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293 <test>
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294 <param name="cond" value="c3 / 0"/>
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295 <param name="input" value="1.bed" ftype="bed" />
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296 <param name="action" value="--keep-non-computable" />
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297 <output name="out_file1" file="1.bed" />
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298 </test>
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299 </tests>
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300 <help><![CDATA[
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301 .. class:: infomark
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302
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303 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
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304
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305 -----
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306
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307 **What it does**
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308
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309 This tool computes an expression on every row of a dataset and appends or inserts the result as a new column (field).
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310
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311 Several expressions can be specified and will be applied sequentially to each row.
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312
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313 **Expression rules**
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314
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315 - Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file
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316
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317 - The following built-in Python functions are available for use in expressions::
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318
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319 abs | all | any | ascii | bin | bool | chr | complex | divmod | float | format | hex | int | len | list
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320 map | max | min | oct | ord | pow | range | reversed | round | set | sorted | str | sum | type
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321
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322 acos | acosh | asin | asinh | atan | atan2 | atanh | cbrt | ceil | comb | copysign | cos | cosh | degrees
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323 dist | erf | erfc | exp | exp2 | expm1 | fabs | factorial | floor | fmod | frexp | fsum | gamma | gcd
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324 hypot | inf | isclose | isfinite | isinf | isnan | isqrt | ldexp | lgamma | log | log10 | log1p | log2
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325 modf | nextafter | perm | pow | prod | remainder | sin | sqrt | tan | tanh | tau | trunc | ulp
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326
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327 - In addition the numpy function ``format_float_positional`` is available to
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328 control the formatting of floating point numbers.
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329
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330 - Expressions can be chained, and the tool will keep track of newly added
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331 columns while working through the chain. This means you can reference a column
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332 that was created as the result of a previous expression in later ones.
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333
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334 -----
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335
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336 **Simple examples**
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337
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338 If this is your input::
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339
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340 chr1 151077881 151077918 2 200 -
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341 chr1 151081985 151082078 3 500 +
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342
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343 computing "c4 * c5" will produce::
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344
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345 chr1 151077881 151077918 2 200 - 400
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346 chr1 151081985 151082078 3 500 + 1500
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347
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348 You can also use this tool to evaluate expressions.
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349 For example, computing "c3 >= c2" for the input above will result in the following::
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350
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351 chr1 151077881 151077918 2 200 - True
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352 chr1 151081985 151082078 3 500 + True
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353
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354 Similarly, computing "type(c2) == type(c3) will return::
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355
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356 chr1 151077881 151077918 2 200 - True
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357 chr1 151081985 151082078 3 500 + True
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358
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359 -----
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diff changeset
360
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361 **Error handling**
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362
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363 The tool will always fail on syntax errors in and other unrecoverable parsing
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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364 errors with any of your expressions. For other problems, however, it offers
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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365 control over how they should be handled:
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366
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367 1. The default for "Autodetect column types" is "Yes", which means the tool
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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368 will evaluate each column value as the type that Galaxy assumes for the
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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369 column. This default behavior will allow you to write simpler expressions.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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370 The arithmetic expression "c4 * c5" from the first simple example,
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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diff changeset
371 for instance, works only because Galaxy realizes that c4 and c5 are integer
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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372 columns. Occasionally, this autodetection can cause issues. A common
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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373 such situation are missing values in columns that Galaxy thinks are of
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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374 numeric type. If you're getting errors like "Failed to convert some of the
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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375 columns in line #X ...", a solution might be to turn off column type
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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376 autodetection. The price you will have to pay for doing so is that now you
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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377 will have to handle type conversions yourself. In the first example you would
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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378 now have to use the epression: "int(c4) * int(c5)".
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diff changeset
379
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380 2. By default, if any expression references columns that are not existing before
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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381 that expression gets computed, the tool will fail, but you can uncheck the
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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382 "Fail on references to non-existent columns" option. If you do so, the result
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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383 will depend on your choice for "If an expression cannot be computed for a row"
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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384 (see 3.)
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385
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386 3. The default for rows, for which an expression fails to compute is, again, to
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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387 fail the tool run, but you can also choose to:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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388
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389 - skip the row on output
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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parents: 8
diff changeset
390
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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391 This is a simple way to only keep lines conforming to an expected standard.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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392 It is also easy to mask problems with your expressions with this option so
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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393 take a look at the results and try to understand what gets skipped and for
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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394 what reasons (the stdout of the tool will contain information about both).
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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395
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396 - keep the row unchanged
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397
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398 This can be a good solution if your input contains special separator lines
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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399 that don't follow the general tabular format of other lines and you would
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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400 like to keep those lines
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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401
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402 - produce an empty column value for the row
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403
9
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404 This will use the empty string as a substitute for non-computable items.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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405 Different from the "keep the row unchanged option" the problematic line will
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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406 have a column added or changed. This option is a good choice for inputs
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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407 in which all rows have the same tabular layout where you want to make sure
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
iuc
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408 that the same is true for the output, i.e. that all output lines still have
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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409 the same number of columns.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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410
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411 - fill in a replacement value
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412
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413 This option is very similar to the previous one, but lets you control the
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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414 replacement value.
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415
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416 **Example**
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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417
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418 In the following input::
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419
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420 chr1 151077881 151077918 2 200 -
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421 chr1 151081985 151082078 3 500 +
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422 chr1 151090031 151090938 4 700
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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423
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424 the last line does not have a strand column. This violates the bed file format
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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425 specification, which says that unknown strand is to be encoded as ``.`` in the
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7
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426 strand column.
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diff changeset
427
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428 You can fix the file with the following tool run:
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429
9
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430 **Add expression**: `c6`
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431
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432 **Mode of the operation**: `Replace`
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diff changeset
433
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434 **Use new column to replace column number**: `6`
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435
9
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436 **Fail on references to non-existent columns**: `No`
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diff changeset
437
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438 **If an expression cannot be computed for a row**: `Fill in a replacement value`
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439
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440 **Replacement value**: `.`
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227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e"
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441 ]]></help>
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442 <citations>
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
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443 <citation type="doi">10.1093/nar/gkae410</citation>
beec6ecc7d3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 06a92568f3409b035fd8a08725db20933d8d15e6
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444 </citations>
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445 </tool>