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1 <tool id="cshl_sort_tool" name="Sort">
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2 <!--
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3 note 1:
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4 the 'version' sort (or natual order sort)
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5 requires GNU Coreutils 7.1 or later
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6
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7 note 2:
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8 for greater efficiency, sort buffer size is very large.
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9 If your Galaxy server doesn't have so much memory (or the
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10 sorts you use don't require it) - you can decrease the memory size.
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11 (argument is "-S 2G")
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12 -->
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13 <command>sort -S 2G $unique
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14 #for $key in $sortkeys
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15 '-k ${key.column},${key.column}${key.order}${key.style}'
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16 #end for
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17 $input > $out_file1
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18 </command>
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19
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20 <inputs>
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21 <param format="txt" name="input" type="data" label="Sort Query" />
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22
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23 <param name="unique" type="select" label="Output only unique values?">
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24 <option value="">No</option>
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25 <option value="-u">Yes</option>
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26 </param>
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27
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28 <repeat name="sortkeys" title="sort key">
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29 <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true" />
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30 <param name="order" type="select" display="radio" label="in">
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31 <option value="r">Descending order</option>
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32 <option value="">Ascending order</option>
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33 </param>
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34 <param name="style" type="select" display="radio" label="Flavor">
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35 <option value="n">Fast numeric sort ([-n])</option>
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36 <option value="g">General numeric sort ( scientific notation [-g])</option>
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37 <option value="V">Natural/Version sort ([-V]) </option>
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38 <option value="">Alphabetical sort</option>
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39 </param>
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40 </repeat>
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41 </inputs>
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42 <tests>
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43 <test>
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44 <!-- Sort Descending numerical order,
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45 with scientific notation -->
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46 <param name="input" value="unix_sort_input1.txt" />
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47 <output name="output" file="unix_sort_output1.txt" />
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48 <param name="unique" value="No" />
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49 <param name="column" value="2" />
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50 <param name="order" value="r" />
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51 <param name="style" value="g" />
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52 </test>
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53 <test>
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54 <!-- Sort Ascending numerical order,
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55 with scientific notation - outputing unique values only
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56
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57 The catch:
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58 chr15 appears twice, with the same value (0.0314 and 3.14e-2).
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59 In the output, it should appear only once because of the unique flag
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60 -->
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61 <param name="input" value="unix_sort_input1.txt" />
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62 <output name="output" file="unix_sort_output2.txt" />
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63 <param name="unique" value="Yes" />
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64 <param name="column" value="2" />
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65 <param name="order" value="" />
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66 <param name="style" value="g" />
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67 </test>
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68 <test>
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69 <!-- Sort Ascending 'natural' order -->
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70 <param name="input" value="unix_sort_input1.txt" />
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71 <output name="output" file="unix_sort_output3.txt" />
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72 <param name="unique" value="No" />
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73 <param name="column" value="1" />
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74 <param name="order" value="" />
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75 <param name="style" value="V" />
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76 </test>
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77 </tests>
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78 <outputs>
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79 <data format="input" name="out_file1" metadata_source="input"/>
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80 </outputs>
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81 <help>
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82
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83 **What it does**
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84
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85 This tool runs the unix **sort** command on the selected data file.
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86
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87 -----
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88
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89 **Sorting Styles**
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90
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91 * **Fast Numeric**: sort by numeric values. Handles integer values (e.g. 43, 134) and decimal-point values (e.g. 3.14). *Does not* handle scientific notation (e.g. -2.32e2).
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92 * **General Numeric**: sort by numeric values. Handles all numeric notations (including scientific notation). Slower than *fast numeric*, so use only when necessary.
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93 * **Natural Sort**: Sort in 'natural' order (natural to humans, not to computers). See example below.
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94 * **Alphabetical sort**: Sort in strict alphabetical order. See example below.
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95
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96
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97
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98
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99 **Sorting Examples**
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100
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101 Given the following list::
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102
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103 chr4
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104 chr13
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105 chr1
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106 chr10
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107 chr20
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108 chr2
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109
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110 **Alphabetical sort** would produce the following sorted list::
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111
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112 chr1
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113 chr10
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114 chr13
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115 chr2
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116 chr20
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117 chr4
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118
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119 **Natural Sort** would produce the following sorted list::
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120
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121 chr1
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122 chr2
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123 chr4
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124 chr10
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125 chr13
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126 chr20
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127
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128
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129 .. class:: infomark
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130
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131 If you're planning to use the file with another tool that expected sorted files (such as *join*), you should use the **Alphabetical sort**, not the **Natural Sort**. Natural sort order is easier for humans, but is unnatural for computer programs.
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132
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133 </help>
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134 </tool>
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