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1 <tool id="unixtools_sort_header_tool" name="Sort" version="0.1.1">
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2 <requirements>
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3 <requirement type="package" version="8.21">gnu_coreutils</requirement>
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4 <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement>
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5 </requirements>
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6 <command interpreter="sh">
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7 #if int($header) > 0:
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8 (sed -u '${header}'q && sort $unique $ignore_case --stable -t ' '
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9
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10 #for $key in $sortkeys
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11 '-k ${key.column}${key.order}${key.style},${key.column}'
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12 #end for
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13
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14 ) < '${infile}' > '${outfile}'
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15 #else:
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16 (sort $unique $ignore_case --stable -t ' '
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17
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18 #for $key in $sortkeys
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19 '-k ${key.column}${key.order}${key.style},${key.column}'
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20 #end for
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21
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22 ) < '${infile}' > '${outfile}'
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23 #end if
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24 </command>
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25
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26 <inputs>
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27 <param format="txt" name="infile" type="data" label="Sort Query" />
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28 <param name="header" type="integer" size="5" value="1" label="Number of header lines" help="These will be ignored during sort.">
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29 <validator type="in_range" message="Negative values are not allowed." min="0"/>
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30 </param>
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31
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32 <param name="unique" type="boolean" checked="false" truevalue="--unique" falsevalue=""
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33 label="Output unique values" help="Print only unique values (based on sorted key columns. See help section for details." />
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34
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35 <param name="ignore_case" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Ignore case" help="Sort and Join key column values regardless of upper/lower case letters." />
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36
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37 <repeat name="sortkeys" title="sort key">
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38 <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" />
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39 <param name="order" type="select" display="radio" label="in">
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40 <option value="">Ascending order</option>
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41 <option value="r">Descending order</option>
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42 </param>
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43 <param name="style" type="select" display="radio" label="Flavor">
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44 <option value="n">Fast numeric sort ([-n])</option>
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45 <option value="g">General numeric sort ( scientific notation [-g])</option>
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46 <option value="V">Natural/Version sort ([-V]) </option>
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47 <option value="">Alphabetical sort</option>
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48 <option value="h">Human-readable numbers (-h)</option>
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49 <option value="R">Random order</option>
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50 </param>
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51 </repeat>
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52 </inputs>
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53 <tests>
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54 </tests>
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55 <outputs>
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56 <data format="input" name="outfile" metadata_source="infile"/>
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57 </outputs>
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58 <help>
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59
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60 **What it does**
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61
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62 This tool sorts an input file.
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63
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64 -----
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65
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66 **Sorting Styles**
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67
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68 * **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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69 * **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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70 * **Natural Sort**: Sort in 'natural' order (natural to humans, not to computers). See example below.
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71 * **Alphabetical sort**: Sort in strict alphabetical order. See example below.
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72 * **Human-readable numbers**: Sort human readble numbers (e.g. 1G > 2M > 3K > 400)
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73 * **Random order**: return lines in random order.
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74
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75 ------
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76
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77 **Example - Header line**
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78
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79 **Input file** (note first line is a header line, should not be sorted)::
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80
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81 Fruit Color Price
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82 Banana Yellow 4.1
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83 Avocado Green 8.0
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84 Apple Red 3.0
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85 Melon Green 6.1
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86
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87 **Sorting** by **numeric order** on column **3**, with **header**, will return::
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88
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89 Fruit Color Price
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90 Apple Red 3.0
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91 Banana Yellow 4.1
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92 Melon Green 6.1
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93 Avocado Green 8.0
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94
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95
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96 -----
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97
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98 **Example - Natural vs. Alphabetical sorting**
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99
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100 Given the following list::
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101
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102 chr4
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103 chr13
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104 chr1
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105 chr10
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106 chr20
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107 chr2
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108
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109 **Alphabetical sort** would produce the following sorted list::
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110
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111 chr1
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112 chr10
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113 chr13
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114 chr2
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115 chr20
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116 chr4
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117
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118 **Natural Sort** would produce the following sorted list::
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119
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120 chr1
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121 chr2
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122 chr4
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123 chr10
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124 chr13
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125 chr20
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126
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127
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128 .. class:: infomark
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129
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130 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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131
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132 -----
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133
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134 *sort-header* is was written by A. Gordon ( gordon at cshl dot edu )
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135
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136 </help>
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137 </tool>
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