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comparison sort.xml @ 0:ec66f9d90ef0 draft

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author bgruening
date Thu, 05 Sep 2013 04:58:21 -0400
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1 <tool id="unixtools_sort_header_tool" name="Sort" version="0.1.1">
2 <requirements>
3 <requirement type="package" version="8.21">gnu_coreutils</requirement>
4 <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement>
5 </requirements>
6 <command interpreter="sh">
7 #if int($header) > 0:
8 (sed -u '${header}'q &amp;&amp; sort $unique $ignore_case --stable -t ' '
9
10 #for $key in $sortkeys
11 '-k ${key.column}${key.order}${key.style},${key.column}'
12 #end for
13
14 ) &lt; '${infile}' &gt; '${outfile}'
15 #else:
16 (sort $unique $ignore_case --stable -t ' '
17
18 #for $key in $sortkeys
19 '-k ${key.column}${key.order}${key.style},${key.column}'
20 #end for
21
22 ) &lt; '${infile}' &gt; '${outfile}'
23 #end if
24 </command>
25
26 <inputs>
27 <param format="txt" name="infile" type="data" label="Sort Query" />
28 <param name="header" type="integer" size="5" value="1" label="Number of header lines" help="These will be ignored during sort.">
29 <validator type="in_range" message="Negative values are not allowed." min="0"/>
30 </param>
31
32 <param name="unique" type="boolean" checked="false" truevalue="--unique" falsevalue=""
33 label="Output unique values" help="Print only unique values (based on sorted key columns. See help section for details." />
34
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." />
36
37 <repeat name="sortkeys" title="sort key">
38 <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" />
39 <param name="order" type="select" display="radio" label="in">
40 <option value="">Ascending order</option>
41 <option value="r">Descending order</option>
42 </param>
43 <param name="style" type="select" display="radio" label="Flavor">
44 <option value="n">Fast numeric sort ([-n])</option>
45 <option value="g">General numeric sort ( scientific notation [-g])</option>
46 <option value="V">Natural/Version sort ([-V]) </option>
47 <option value="">Alphabetical sort</option>
48 <option value="h">Human-readable numbers (-h)</option>
49 <option value="R">Random order</option>
50 </param>
51 </repeat>
52 </inputs>
53 <tests>
54 </tests>
55 <outputs>
56 <data format="input" name="outfile" metadata_source="infile"/>
57 </outputs>
58 <help>
59
60 **What it does**
61
62 This tool sorts an input file.
63
64 -----
65
66 **Sorting Styles**
67
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).
69 * **General Numeric**: sort by numeric values. Handles all numeric notations (including scientific notation). Slower than *fast numeric*, so use only when necessary.
70 * **Natural Sort**: Sort in 'natural' order (natural to humans, not to computers). See example below.
71 * **Alphabetical sort**: Sort in strict alphabetical order. See example below.
72 * **Human-readable numbers**: Sort human readble numbers (e.g. 1G > 2M > 3K > 400)
73 * **Random order**: return lines in random order.
74
75 ------
76
77 **Example - Header line**
78
79 **Input file** (note first line is a header line, should not be sorted)::
80
81 Fruit Color Price
82 Banana Yellow 4.1
83 Avocado Green 8.0
84 Apple Red 3.0
85 Melon Green 6.1
86
87 **Sorting** by **numeric order** on column **3**, with **header**, will return::
88
89 Fruit Color Price
90 Apple Red 3.0
91 Banana Yellow 4.1
92 Melon Green 6.1
93 Avocado Green 8.0
94
95
96 -----
97
98 **Example - Natural vs. Alphabetical sorting**
99
100 Given the following list::
101
102 chr4
103 chr13
104 chr1
105 chr10
106 chr20
107 chr2
108
109 **Alphabetical sort** would produce the following sorted list::
110
111 chr1
112 chr10
113 chr13
114 chr2
115 chr20
116 chr4
117
118 **Natural Sort** would produce the following sorted list::
119
120 chr1
121 chr2
122 chr4
123 chr10
124 chr13
125 chr20
126
127
128 .. class:: infomark
129
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.
131
132 -----
133
134 *sort-header* is was written by A. Gordon ( gordon at cshl dot edu )
135
136 </help>
137 </tool>