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comparison tools/unix_tools/sort_tool.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="cshl_sort_tool" name="Sort">
2 <!--
3 note 1:
4 the 'version' sort (or natual order sort)
5 requires GNU Coreutils 7.1 or later
6
7 note 2:
8 for greater efficiency, sort buffer size is very large.
9 If your Galaxy server doesn't have so much memory (or the
10 sorts you use don't require it) - you can decrease the memory size.
11 (argument is "-S 2G")
12 -->
13 <command>sort -S 2G $unique
14 #for $key in $sortkeys
15 '-k ${key.column},${key.column}${key.order}${key.style}'
16 #end for
17 $input > $out_file1
18 </command>
19
20 <inputs>
21 <param format="txt" name="input" type="data" label="Sort Query" />
22
23 <param name="unique" type="select" label="Output only unique values?">
24 <option value="">No</option>
25 <option value="-u">Yes</option>
26 </param>
27
28 <repeat name="sortkeys" title="sort key">
29 <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true" />
30 <param name="order" type="select" display="radio" label="in">
31 <option value="r">Descending order</option>
32 <option value="">Ascending order</option>
33 </param>
34 <param name="style" type="select" display="radio" label="Flavor">
35 <option value="n">Fast numeric sort ([-n])</option>
36 <option value="g">General numeric sort ( scientific notation [-g])</option>
37 <option value="V">Natural/Version sort ([-V]) </option>
38 <option value="">Alphabetical sort</option>
39 </param>
40 </repeat>
41 </inputs>
42 <tests>
43 <test>
44 <!-- Sort Descending numerical order,
45 with scientific notation -->
46 <param name="input" value="unix_sort_input1.txt" />
47 <output name="output" file="unix_sort_output1.txt" />
48 <param name="unique" value="No" />
49 <param name="column" value="2" />
50 <param name="order" value="r" />
51 <param name="style" value="g" />
52 </test>
53 <test>
54 <!-- Sort Ascending numerical order,
55 with scientific notation - outputing unique values only
56
57 The catch:
58 chr15 appears twice, with the same value (0.0314 and 3.14e-2).
59 In the output, it should appear only once because of the unique flag
60 -->
61 <param name="input" value="unix_sort_input1.txt" />
62 <output name="output" file="unix_sort_output2.txt" />
63 <param name="unique" value="Yes" />
64 <param name="column" value="2" />
65 <param name="order" value="" />
66 <param name="style" value="g" />
67 </test>
68 <test>
69 <!-- Sort Ascending 'natural' order -->
70 <param name="input" value="unix_sort_input1.txt" />
71 <output name="output" file="unix_sort_output3.txt" />
72 <param name="unique" value="No" />
73 <param name="column" value="1" />
74 <param name="order" value="" />
75 <param name="style" value="V" />
76 </test>
77 </tests>
78 <outputs>
79 <data format="input" name="out_file1" metadata_source="input"/>
80 </outputs>
81 <help>
82
83 **What it does**
84
85 This tool runs the unix **sort** command on the selected data file.
86
87 -----
88
89 **Sorting Styles**
90
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).
92 * **General Numeric**: sort by numeric values. Handles all numeric notations (including scientific notation). Slower than *fast numeric*, so use only when necessary.
93 * **Natural Sort**: Sort in 'natural' order (natural to humans, not to computers). See example below.
94 * **Alphabetical sort**: Sort in strict alphabetical order. See example below.
95
96
97
98
99 **Sorting Examples**
100
101 Given the following list::
102
103 chr4
104 chr13
105 chr1
106 chr10
107 chr20
108 chr2
109
110 **Alphabetical sort** would produce the following sorted list::
111
112 chr1
113 chr10
114 chr13
115 chr2
116 chr20
117 chr4
118
119 **Natural Sort** would produce the following sorted list::
120
121 chr1
122 chr2
123 chr4
124 chr10
125 chr13
126 chr20
127
128
129 .. class:: infomark
130
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.
132
133 </help>
134 </tool>