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1 <tool id="cshl_sort_header" name="Sort" version="0.1.1">
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2 <command interpreter="perl">sort-header
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3 --header $header
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4 $unique
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5 $ignore_case
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6 --stable
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7 -t ' '
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8 #for $key in $sortkeys
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9 '-k ${key.column}${key.order}${key.style},${key.column}'
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10 #end for
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11 --output '$out_file1'
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12 '$input1'
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13 </command>
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14
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15 <inputs>
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16 <param format="txt" name="input1" type="data" label="Sort Query" />
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17
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18 <!-- header line is boolean for now, but the values are 1 or 0.
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19 in the future, we can use Galaxy's number-of-comment-lines variable -->
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20 <param name="header" type="boolean" checked="false" truevalue="1" falsevalue="0"
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21 label="First line is a header line" help="Use if first line contains column headers. It will not be sorted." />
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22
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23 <param name="unique" type="boolean" checked="false" truevalue="--unique" falsevalue=""
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24 label="Output unique values" help="Print only unique values (based on sorted key columns. See help section for details." />
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25
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26 <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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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="input1" accept_default="true" />
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30 <param name="order" type="select" display="radio" label="in">
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31 <option value="">Ascending order</option>
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32 <option value="r">Descending 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 <option value="h">Human-readable numbers (-h)</option>
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40 <option value="R">Random order</option>
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41 </param>
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42 </repeat>
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43 </inputs>
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44 <tests>
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45 </tests>
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46 <outputs>
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47 <data format="input" name="out_file1" metadata_source="input1"
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48 />
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49 </outputs>
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50 <help>
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51
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52 **What it does**
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53
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54 This tool sorts an input file.
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55
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56 -----
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57
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58 **Sorting Styles**
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59
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60 * **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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61 * **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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62 * **Natural Sort**: Sort in 'natural' order (natural to humans, not to computers). See example below.
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63 * **Alphabetical sort**: Sort in strict alphabetical order. See example below.
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64 * **Human-readable numbers**: Sort human readble numbers (e.g. 1G > 2M > 3K > 400)
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65 * **Random order**: return lines in random order.
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66
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67 ------
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68
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69 **Example - Header line**
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70
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71 **Input file** (note first line is a header line, should not be sorted)::
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72
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73 Fruit Color Price
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74 Banana Yellow 4.1
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75 Avocado Green 8.0
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76 Apple Red 3.0
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77 Melon Green 6.1
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78
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79 **Sorting** by **numeric order** on column **3**, with **header**, will return::
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80
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81 Fruit Color Price
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82 Apple Red 3.0
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83 Banana Yellow 4.1
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84 Melon Green 6.1
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85 Avocado Green 8.0
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86
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87
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88 -----
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89
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90 **Example - Natural vs. Alphabetical sorting**
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91
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92 Given the following list::
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93
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94 chr4
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95 chr13
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96 chr1
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97 chr10
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98 chr20
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99 chr2
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100
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101 **Alphabetical sort** would produce the following sorted list::
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102
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103 chr1
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104 chr10
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105 chr13
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106 chr2
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107 chr20
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108 chr4
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109
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110 **Natural Sort** would produce the following sorted list::
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111
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112 chr1
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113 chr2
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114 chr4
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115 chr10
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116 chr13
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117 chr20
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118
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119
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120 .. class:: infomark
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121
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122 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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123
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124 -----
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125
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126 *sort-header* is was written by A. Gordon ( gordon at cshl dot edu )
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127
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128 </help>
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129 </tool>
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