Mercurial > repos > nml > csvtk_awklike_mutate

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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:15:08 -0400
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0
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1 <tool id="csvtk_awklike_mutate" name="csvtk-advanced-mutate" version="@VERSION@+@GALAXY_VERSION@">
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2 <description> new column by awk-like artithmetic/string expressions</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_cmd" />
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8 <command detect_errors="exit_code"><![CDATA[
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9
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10 ###################
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11 ## Start Command ##
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12 ###################
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13 csvtk mutate2 --num-cpus "\${GALAXY_SLOTS:-1}"
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14
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15 ## Add additional flags as specified ##
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16 #######################################
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17 $global_param.illegal_rows
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18 $global_param.empty_rows
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19 $global_param.header
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20 $global_param.lazy_quotes
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21
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22 ## Set Tabular input/output flag if first input is tabular ##
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23 #############################################################
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24 #if $in_1.is_of_type("tabular"):
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25 -t -T
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26 #end if
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27
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28 ## Set input files ##
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29 #####################
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30 $in_1
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31
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32 ## Specific inputs ##
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33 #####################
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34 -e '$in_text'
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35 -n '$column_name'
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36 -L '$additional.digit_number'
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37 $additional.digit_strings
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38
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39 ## To output ##
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40 ###############
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41 > mutated
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42
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43 ]]></command>
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44 <inputs>
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45 <expand macro="singular_input"/>
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46 <param name="in_text" type="text" argument="-e" label="Awk-like artithmetic/string expression" >
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47 <help>
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48 <![CDATA[
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49 Examples:
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50 - '$age>12'
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51 - '$1 > $3'
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52 - '$name=="abc"'
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53 - '$1 % 2 == 0'
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54 More info is available in the help section below. The ' character is invalid and will be replaced, thus you must
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55 surround strings with double quotes ("string") instead.
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56 ]]>
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57 </help>
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58 <expand macro="text_sanitizer" />
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59 </param>
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60 <param name="column_name" type="text" argument="-n" value="New_Column"
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61 label="New column name"
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62 help="Specify what the new column should be called">
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63 <expand macro="text_sanitizer" />
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64 </param>
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65 <section name="additional" title="Additional Parameters" expanded="true">
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66 <param name="digit_number" type="integer" value="2" argument="-L"
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67 label="Number of digits after the decimal to keep"
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68 help="Keep input integer number of decimal places"
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69 />
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70 <param name="digit_strings" type="boolean" checked="false" argument="-s"
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71 truevalue="-s"
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72 falsevalue=""
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73 label="Input digits as strings"
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74 help="Treat digits as string to avoid converting big digits into scientific notation. No longer supports mathematical operations if set to yes"
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75 />
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76 </section>
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77 <expand macro="global_parameters" />
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78 </inputs>
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79 <outputs>
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80 <data format_source="in_1" from_work_dir="mutated" name="mutated" label="${in_1.name} mutated by ${in_text}" />
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81 </outputs>
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82 <tests>
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83 <test>
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84 <param name="in_1" value="awk_mutate_input.csv" />
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85 <param name="in_text" value="$2*$3" />
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86 <param name="column_name" value="CFU/ml" />
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87 <section name="additional">
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88 <param name="digit_number" value="0" />
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89 </section>
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90 <output name="mutated" file="awk_mutate_output.csv" ftype="csv" />
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91 </test>
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92 </tests>
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93 <help><![CDATA[
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94
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95 Csvtk - Mutate2 Help
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96 --------------------
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97
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98 Info
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99 ####
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100
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101 Csvtk advanced mutate (also called mutate2) outputs a column that evaluates the input expression. Please see the
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102 `documentation <https://github.com/Knetic/govaluate/blob/master/MANUAL.md>`_ for further details and examples on how to write expressions.
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103
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104 Also checkout the tools `website <https://bioinf.shenwei.me/csvtk/usage/#mutate2>`_ for additional ideas on how to structure expressions!
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105
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106 .. class:: warningmark
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107
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108 Single quotes are not allowed in text inputs!
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109
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110 .. class:: note
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111
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112 If your wanted column header has a space in it, use the column number. Example: Use $1 if column #1 is called "Colony Counts"
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113
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114 Supported operators and types:
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115
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116 - Modifiers: + - / * & | ^ ** % >> <<
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117 - Comparators: > >= < <= == != =~ !~
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118 - Logical ops: || &&
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119 - Numeric constants, as 64-bit floating point (12345.678)
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120 - String constants (double quotes only: "foobar")
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121 - Date constants (double quotes)
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122 - Boolean constants: true false
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123 - Parenthesis to control order of evaluation ( )
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124 - Arrays (anything separated by , within parenthesis: (1, 2, "foo"))
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125 - Prefixes: ! - ~
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126 - Ternary conditional: ? :
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127 - Null coalescence: ??
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128
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129 ----
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130
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131 @HELP_INPUT_DATA@
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132
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133
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134 Usage
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135 #####
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136
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137 Some quick and simple examples:
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138
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139 **Ex. Mutate2 with Numbers:**
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140
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141 Suppose we had the following table:
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142
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143 +---------------+------------+----------+
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144 | Culture Label | Cell Count | Dilution |
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145 +===============+============+==========+
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146 | ECo-1 | 2523 | 1000 |
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147 +---------------+------------+----------+
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148 | LPn-1 | 100 | 1000000 |
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149 +---------------+------------+----------+
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150 | LPn-2 | 4 | 1000 |
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151 +---------------+------------+----------+
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152
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153 If we wanted to evaluate the CFU/ml of these samples (supposing a 1ml volume plated) with this tool,
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154 we could create give our new column a name like "CFU/ml" and then use the expression "$2*$3" to get:
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155
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156 +---------------+------------+----------+-----------+
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157 | Culture Label | Cell Count | Dilution | CFU/ml |
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158 +===============+============+==========+===========+
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159 | ECo-1 | 2523 | 1000 | 2523000 |
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160 +---------------+------------+----------+-----------+
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161 | LPn-1 | 100 | 1000000 | 100000000 |
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162 +---------------+------------+----------+-----------+
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163 | LPn-2 | 4 | 1000 | 4000 |
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164 +---------------+------------+----------+-----------+
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165
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166 Note how $2 was used to get column 2 due to it containing a space in its name
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167
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168 ----
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169
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170 @HELP_COLUMNS@
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171
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172
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173 @HELP_END_STATEMENT@
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174
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175
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176 ]]></help>
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177 <expand macro="citations" />
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178 </tool>