Mercurial > repos > nml > csvtk_awklike_filter
annotate awklike-filter.xml @ 0:20e8be1464f5 draft default tip
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author | nml |
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date | Tue, 19 May 2020 17:14:07 -0400 |
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0
20e8be1464f5
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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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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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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