root/galaxy-central/tools/filters/compare.xml

リビジョン 2, 2.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="comp1" name="Compare two Queries" version="1.0.2">
2  <description>to find common or distinct rows</description>
3  <command interpreter="python">joinWrapper.py $input1 $input2 $field1 $field2 $mode $out_file1</command>
4  <inputs>
5    <param format="tabular" name="input1" type="data" label="Compare"/>
6    <param name="field1" label="Using column" type="data_column" data_ref="input1">
7        <validator type="no_options" message="Invalid column choice. Please try again after editing metadata of your input dataset by clicking on the pencil icon next to it."/>
8    </param>
9    <param format="tabular" name="input2" type="data" label="against" />
10    <param name="field2" label="and column" type="data_column" data_ref="input2">
11            <validator type="no_options" message="Invalid column choice. Please try again after editing metadata of your input dataset by clicking on the pencil icon next to it."/>
12    </param>
13    <param name="mode" type="select" label="To find" help="See examples below for explanation of these options">
14      <option value="N">Matching rows of 1st query</option>
15      <option value="V">Non Matching rows of 1st query</option>
16    </param>
17  </inputs>
18  <outputs>
19     <data format="input" name="out_file1" metadata_source="input1" />
20  </outputs>
21  <tests>
22    <test>
23      <param name="input1" value="1.bed"/>
24      <param name="input2" value="2.bed"/>
25      <param name="field1" value="2"/>
26      <param name="field2" value="2"/>
27      <param name="mode" value="N"/>
28      <output name="out_file1" file="fs-compare.dat"/>
29    </test>
30    <!--test case with duplicated key values-->
31    <test>
32      <param name="input1" value="1.bed"/>
33      <param name="input2" value="3.bed"/>
34      <param name="field1" value="1"/>
35      <param name="field2" value="1"/>
36      <param name="mode" value="V"/>
37      <output name="out_file1" file="fs-compare-2.dat"/>
38    </test>
39  </tests>
40  <help>
41
42.. class:: infomark
43
44**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
45
46-----
47
48**Syntax**
49
50This tool finds lines in one query that HAVE or DO NOT HAVE a common field with another query.
51
52-----
53
54**Example**
55
56If this is **First query**::
57
58  chr1 10 20 geneA
59  chr1 50 80 geneB
60  chr5 10 40 geneL
61
62and this is **Second query**::
63
64  geneA tumor-suppressor
65  geneB Foxp2
66  geneC Gnas1
67  geneE INK4a
68
69Finding lines of the **First query** whose 4th column matches the 1st column of the **Second query** yields::
70
71  chr1 10 20 geneA
72  chr1 50 80 geneB
73
74Conversely, using option **Non Matching rows of First query** on the same fields will yield::
75
76  chr5 10 40 geneL
77
78</help>
79</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。