[3] | 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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