Mercurial > repos > nml > csvtk_awklike_filter

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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:14:07 -0400
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0
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1 <tool id="csvtk_awklike_filter" name="csvtk-advanced-filter" version="@VERSION@+@GALAXY_VERSION@">
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2 <description> rows 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 filter2 --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 $in_1
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31
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32 ## Specify fields to filter ##
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33 ##############################
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34 -f '$in_text'
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35
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36 ## Specific inputs ##
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37 #####################
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38 $line_number
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39
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40 ## To output ##
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41 ###############
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42 > filtered
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43
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44 ]]></command>
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45 <inputs>
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46 <expand macro="singular_input"/>
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47 <param name="in_text" type="text"
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48 optional="false"
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49 argument="-f"
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50 label="Awk-like artithmetic/string expression">
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51 <help>
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52 <![CDATA[
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53 Examples:
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54 - '$age>12'
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55 - '$1 > $3'
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56 - '$name=="abc"'
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57 - '$1 % 2 == 0'
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58 More info is available in the help section below. The ' character is invalid and will be replaced, thus you must
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59 surround strings with double quotes ("string") instead.
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60 ]]>
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61 </help>
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62 <expand macro="text_sanitizer" />
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63 </param>
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64 <param name="line_number" type="boolean"
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65 checked="false"
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66 truevalue="-n"
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67 falsevalue=""
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68 argument="-n"
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69 label="Print initial line number as the first column"
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70 />
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71 <expand macro="global_parameters" />
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72 </inputs>
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73 <outputs>
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74 <data format_source="in_1" from_work_dir="filtered" name="filtered" label="${in_1.name} filtered by ${in_text}" />
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75 </outputs>
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76 <tests>
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77 <test>
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78 <param name="in_1" value="frequency.tsv" />
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79 <param name="in_text" value="$3>1" />
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80 <output name="filtered" file="filtered.tsv" ftype="tabular" />
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81 </test>
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82 </tests>
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83 <help><![CDATA[
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84
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85 Csvtk - Filter2 Help
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86 --------------------
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87
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88 Info
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89 ####
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90
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91 Csvtk advanced filter (also called filter2) outputs rows that satisfy the input awk-like artithmetic/string expressions. Please see the
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92 `documentation <https://github.com/Knetic/govaluate/blob/master/MANUAL.md>`_ for further details and examples on how to write expressions.
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93
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94 .. class:: warningmark
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95
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96 Single quotes are not allowed in text inputs!
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97
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98 .. class:: note
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99
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100 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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101
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102 Supported operators and types:
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103
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104 - Modifiers: + - / * & | ^ ** % >> <<
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105 - Comparators: > >= < <= == != =~ !~
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106 - Logical ops: || &&
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107 - Numeric constants, as 64-bit floating point (12345.678)
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108 - String constants (double quotes: "foobar")
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109 - Date constants (double quotes)
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110 - Boolean constants: true false
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111 - Parenthesis to control order of evaluation ( )
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112 - Arrays (anything separated by , within parenthesis: (1, 2, "foo"))
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113 - Prefixes: ! - ~
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114 - Ternary conditional: ? :
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115 - Null coalescence: ??
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116
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117 ----
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118
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119 @HELP_INPUT_DATA@
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120
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121
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122 Usage
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123 #####
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124
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125 **Ex. Filter2 on one column:**
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126
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127 Suppose we had the following table:
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128
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129 +---------------+------------+----------+
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130 | Culture Label | Cell Count | Dilution |
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131 +===============+============+==========+
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132 | ECo-1 | 2523 | 1000 |
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133 +---------------+------------+----------+
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134 | LPn-1 | 100 | 1000000 |
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135 +---------------+------------+----------+
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136 | LPn-2 | 4 | 1000 |
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137 +---------------+------------+----------+
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138
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139 If we wanted to find all samples with the label LPn, we could use the filter expression '$1 =~ "LPn*"' to get the following output:
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140
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141 +---------------+------------+----------+
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142 | Culture Label | Cell Count | Dilution |
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143 +===============+============+==========+
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144 | LPn-1 | 100 | 1000000 |
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145 +---------------+------------+----------+
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146 | LPn-2 | 4 | 1000 |
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147 +---------------+------------+----------+
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148
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149 Note how $1 was used to get column 1 due to it containing a space
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150
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151 ----
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152
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153 **Ex2. Filter2 with multiple inputs:**
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154
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155 Same input table
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156
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157 +---------------+------------+----------+
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158 | Culture Label | Cell Count | Dilution |
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159 +===============+============+==========+
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160 | ECo-1 | 2523 | 1000 |
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161 +---------------+------------+----------+
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162 | LPn-1 | 100 | 1000000 |
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163 +---------------+------------+----------+
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164 | LPn-2 | 4 | 1000 |
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165 +---------------+------------+----------+
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166
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167 Now if we use the expression '$1 =~ "LPn*" && $Dilution > 1000' to filter on, we would pull out the only row that satisfies both conditions:
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168
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169 +---------------+------------+----------+
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170 | Culture Label | Cell Count | Dilution |
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171 +===============+============+==========+
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172 | LPn-1 | 100 | 1000000 |
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173 +---------------+------------+----------+
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174
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175 ----
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176
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177 @HELP_COLUMNS@
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178
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179
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180 @HELP_END_STATEMENT@
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181
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182
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183 ]]></help>
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184 <expand macro="citations" />
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185 </tool>