Mercurial > repos > nml > csvtk_filter

annotate filter.xml @ 0:58ed60d20336 draft default tip

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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:23:16 -0400
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1 <tool id="csvtk_filter" name="csvtk-filter" version="@VERSION@+@GALAXY_VERSION@">
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2 <description> rows through arithmetic expression(s)</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 filter --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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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 $in_1
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31
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32 ## Specify fields to filter ##
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33 ##############################
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34 -F -f '$in_text'
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35
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36 ## Specific inputs ##
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37 #####################
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38 $any
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39 $line_number
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40
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41 ## To output ##
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42 ###############
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43 > filtered
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44
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45 ]]></command>
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46 <inputs>
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47 <expand macro="singular_input"/>
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48 <param name="in_text" type="text"
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49 optional="false"
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50 argument="-F -f"
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51 label="Specify column(s) and numeric expression to filter for"
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52 help="Give column name/number and the numeric expression that you want to evaluate. Example: 'frequency>4'. See help below for more examples">
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53 <expand macro="text_sanitizer" />
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54 </param>
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55 <param name="line_number" type="boolean"
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56 checked="false"
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57 truevalue="-n"
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58 falsevalue=""
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59 argument="-n"
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60 label="Print initial line number as the first column"
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61 />
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62 <param name="any" type="boolean"
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63 checked="false"
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64 truevalue="--any"
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65 falsevalue=""
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66 argument="--any"
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67 label="Return row if any row value satisfies the condition"
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68 help="For multiple column filters only"
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69 />
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70 <expand macro="global_parameters" />
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71 </inputs>
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72 <outputs>
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73 <data format_source="in_1" from_work_dir="filtered" name="filtered" label="${in_1.name} filtered with ${in_text}" />
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="in_1" value="frequency.tsv" />
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78 <param name="in_text" value="frequency>1" />
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79 <output name="filtered" file="filtered.tsv" ftype="tabular" />
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80 </test>
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81 </tests>
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82 <help><![CDATA[
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83
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84 Csvtk - Filter Help
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85 -------------------
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86
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87 Info
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88 ####
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89
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90 Csvtk filter outputs rows that satisfy an input numerical expression on the specified column(s).
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91
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92 .. class:: warningmark
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93
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94 Single quotes are not allowed in text inputs!
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95
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96 @HELP_INPUT_DATA@
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97
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98
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99 Usage
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100 #####
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101
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102 **Ex. Filter on one column:**
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103
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104 Suppose we had the following table:
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105
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106 +---------------+------------+----------+
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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107 | Culture Label | Cell Count | Dilution |
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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108 +===============+============+==========+
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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109 | ECo-1 | 2523 | 1000 |
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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110 +---------------+------------+----------+
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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111 | LPn-1 | 100 | 1000000 |
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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112 +---------------+------------+----------+
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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113 | LPn-2 | 4 | 1000 |
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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114 +---------------+------------+----------+
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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115
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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116 If we used the filter expression "Cell Count>100", we would get the following output column:
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117
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118 +---------------+------------+----------+
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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119 | Culture Label | Cell Count | Dilution |
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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120 +===============+============+==========+
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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121 | ECo-1 | 2523 | 1000 |
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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122 +---------------+------------+----------+
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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123
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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124 ----
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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125
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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126 **Ex2. Filter on two columns:**
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127
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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128 Same input table
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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129
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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130 +---------------+------------+----------+
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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131 | Culture Label | Cell Count | Dilution |
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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132 +===============+============+==========+
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133 | ECo-1 | 2523 | 1000 |
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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134 +---------------+------------+----------+
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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135 | LPn-1 | 100 | 1000000 |
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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136 +---------------+------------+----------+
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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137 | LPn-2 | 4 | 1000 |
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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138 +---------------+------------+----------+
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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139
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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140 Now if we use the expression "2-3>50" to filter on, we would pull out:
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141
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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142 +---------------+------------+----------+
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143 | Culture Label | Cell Count | Dilution |
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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144 +===============+============+==========+
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145 | ECo-1 | 2523 | 1000 |
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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146 +---------------+------------+----------+
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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147 | LPn-1 | 100 | 1000000 |
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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148 +---------------+------------+----------+
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149
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150 Row 3 is not returned back as its column 2 is not greater than 50.
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151
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152 However, if **Any** is set to Yes, then Row 3 would be returned as its column 3 is greater than 50
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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153 making it satisfy one part of the expression.
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154
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155
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156 **Note:** - Multiple columns can only be specified with a "-"
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157
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158 ----
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159
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160 @HELP_COLUMNS@
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161
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162
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163 @HELP_END_STATEMENT@
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164
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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165
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166 ]]></help>
58ed60d20336 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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167 <expand macro="citations" />
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168 </tool>