/tools/filters/sorter.xml
XML | 188 lines | 160 code | 28 blank | 0 comment | 0 complexity | ac85880aac664e6a7a2a50b9e4479db7 MD5 | raw file
1<tool id="sort1" name="Sort" version="1.0.3"> 2 <description>data in ascending or descending order</description> 3 <command interpreter="python"> 4 sorter.py 5 6 --input=${input} 7 --output=${out_file1} 8 9 #if (str($style) == 'num'): 10 #set $style = 'n' 11 #elif (str($style) == 'gennum'): 12 #set $style = 'g' 13 #else: 14 #set $style = '' 15 #end if 16 17 #set $order = '' if (str($order) == 'ASC') else 'r' 18 19 --key=${column},${column}${style}${order} 20 21 22 #for $col in $column_set: 23 #set $other_column = str($col.other_column) 24 25 #if (str($col.other_style) == 'num'): 26 #set $other_style = 'n' 27 #elif (str($col.other_style) == 'gennum'): 28 #set $other_style = 'g' 29 #else: 30 #set $other_style = '' 31 #end if 32 33 #set $other_order = '' if (str($col.other_order) == "ASC") else 'r' 34 --key=${other_column},${other_column}${other_style}${other_order} 35 #end for 36 </command> 37 <inputs> 38 <param format="tabular" name="input" type="data" label="Sort Dataset" /> 39 <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true"/> 40 <param name="style" type="select" label="with flavor"> 41 <option value="num">Numerical sort</option> 42 <option value="gennum">General numeric sort</option> 43 <option value="alpha">Alphabetical sort</option> 44 </param> 45 <param name="order" type="select" label="everything in"> 46 <option value="DESC">Descending order</option> 47 <option value="ASC">Ascending order</option> 48 </param> 49 <repeat name="column_set" title="Column selection"> 50 <param name="other_column" label="on column" type="data_column" data_ref="input" accept_default="true" /> 51 <param name="other_style" type="select" label="with flavor"> 52 <option value="num">Numerical sort</option> 53 <option value="gennum">General numeric sort</option> 54 <option value="alpha">Alphabetical sort</option> 55 </param> 56 <param name="other_order" type="select" label="everything in"> 57 <option value="DESC">Descending order</option> 58 <option value="ASC">Ascending order</option> 59 </param> 60 </repeat> 61 </inputs> 62 <outputs> 63 <data format="input" name="out_file1" metadata_source="input"/> 64 </outputs> 65 <tests> 66 <test> 67 <param name="input" value="sort_in1.bed"/> 68 <param name="column" value="1"/> 69 <param name="style" value="alpha"/> 70 <param name="order" value="ASC"/> 71 <param name="other_column" value="3"/> 72 <param name="other_style" value="num"/> 73 <param name="other_order" value="DESC"/> 74 <output name="out_file1" file="sort_out1.bed"/> 75 </test> 76 <test> 77 <param name="input" value="sort_in1.bed"/> 78 <param name="column" value="1"/> 79 <param name="style" value="alpha"/> 80 <param name="order" value="ASC"/> 81 <param name="other_column" value="3"/> 82 <param name="other_style" value="num"/> 83 <param name="other_order" value="ASC"/> 84 <output name="out_file1" file="sort_out2.bed"/> 85 </test> 86 <test> 87 <param name="input" value="sort_in2.bed"/> 88 <param name="column" value="5"/> 89 <param name="style" value="gennum"/> 90 <param name="order" value="ASC"/> 91 <output name="out_file1" file="sort_out3.bed"/> 92 </test> 93 </tests> 94 <help> 95.. class:: infomark 96 97**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* 98 99----- 100 101**Syntax** 102 103This tool sorts the dataset on any number of columns in either ascending or descending order. 104 105* **Numerical sort** orders numbers by their magnitude, ignores all characters besides numbers, and evaluates a string of numbers to the value they signify. 106* **General numeric sort** orders numbers by their general numerical value. Unlike the numerical sort option, it can handle numbers in scientific notation too. 107* **Alphabetical sort** is a phonebook type sort based on the conventional order of letters in an alphabet. Each nth letter is compared with the nth letter of other words in the list, starting at the first letter of each word and advancing to the second, third, fourth, and so on, until the order is established. Therefore, in an alphabetical sort, 2 comes after 100 (1 < 2). 108 109----- 110 111**Examples** 112 113The list of numbers 4,17,3,5 collates to 3,4,5,17 by numerical sorting, while it collates to 17,3,4,5 by alphabetical sorting. 114 115Sorting the following:: 116 117 Q d 7 II jhu 45 118 A kk 4 I h 111 119 Pd p 1 ktY WS 113 120 A g 10 H ZZ 856 121 A edf 4 tw b 234 122 BBB rt 10 H ZZ 100 123 A rew 10 d b 1111 124 C sd 19 YH aa 10 125 Hah c 23 ver bb 467 126 MN gtr 1 a X 32 127 N j 9 a T 205 128 BBB rrf 10 b Z 134 129 odfr ws 6 Weg dew 201 130 C f 3 WW SW 34 131 A jhg 4 I b 345 132 Pd gf 7 Gthe de 567 133 rS hty 90 YY LOp 89 134 A g 10 H h 43 135 A g 4 I h 500 136 137on columns 1 (alphabetical), 3 (numerical), and 6 (numerical) in ascending order will yield:: 138 139 A kk 4 I h 111 140 A edf 4 tw b 234 141 A jhg 4 I b 345 142 A g 4 I h 500 143 A g 10 H h 43 144 A g 10 H ZZ 856 145 A rew 10 d b 1111 146 BBB rt 10 H ZZ 100 147 BBB rrf 10 b Z 134 148 C f 3 WW SW 34 149 C sd 19 YH aa 10 150 Hah c 23 ver bb 467 151 MN gtr 1 a X 32 152 N j 9 a T 205 153 odfr ws 6 Weg dew 201 154 Pd p 1 ktY WS 113 155 Pd gf 7 Gthe de 567 156 Q d 7 II jhu 45 157 rS hty 90 YY LOp 89 158 159 160Sorting the following:: 161 162 chr10 100 200 feature1 100.01 + 163 chr20 800 900 feature2 1.1 + 164 chr2 500 600 feature3 1000.1 + 165 chr1 300 400 feature4 1.1e-05 + 166 chr21 300 500 feature5 1.1e2 + 167 chr15 700 800 feature6 1.1e4 + 168 169on column 5 (numerical) in ascending order will yield:: 170 171 chr1 300 400 feature4 1.1e-05 + 172 chr15 700 800 feature6 1.1e4 + 173 chr20 800 900 feature2 1.1 + 174 chr21 300 500 feature5 1.1e2 + 175 chr10 100 200 feature1 100.01 + 176 chr2 500 600 feature3 1000.1 + 177 178on column 5 (general numeric) in ascending order will yield:: 179 180 chr1 300 400 feature4 1.1e-05 + 181 chr20 800 900 feature2 1.1 + 182 chr10 100 200 feature1 100.01 + 183 chr21 300 500 feature5 1.1e2 + 184 chr2 500 600 feature3 1000.1 + 185 chr15 700 800 feature6 1.1e4 + 186 187 </help> 188</tool>