root/galaxy-central/tools/unix_tools/sort_tool.xml

リビジョン 3, 4.0 KB (コミッタ: kohda, 14 年 前)

Install Unix tools  http://hannonlab.cshl.edu/galaxy_unix_tools/galaxy.html

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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
85This 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
101Given 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
131If 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>
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