root/galaxy-central/tools/new_operations/subtract_query.xml

リビジョン 2, 4.4 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="subtract_query1" name="Subtract Whole Query">
2  <description>from another query</description>
3  <command interpreter="python">subtract_query.py $input1 $input2 $begin_col $end_col $output</command>
4  <inputs>
5    <param format="txt" name="input2" type="data" label="Subtract" help="Second query" />
6    <param format="txt" name="input1" type="data" label="from" help="First query" />
7    <param name="begin_col" type="data_column" data_ref="input1" force_select="False" label="Restrict subtraction between 'begin column'" />
8    <param name="end_col" type="data_column" data_ref="input1" force_select="False" label="and 'end column'" help="Specifying columns for restricting subtraction is available only for tabular formatted queries" />
9  </inputs>
10  <outputs>
11    <data format="input" name="output" metadata_source="input1" />
12  </outputs>
13  <tests>
14        <!-- Subtract 2 non-tabular files with no column restrictions. -->
15        <!-- Cannot figure out why this test won't pass, it works in real time...
16    <test>
17      <param name="input1" value="1.txt" />
18      <param name="input2" value="2.txt" />
19      <param name="begin_col" value="None" />
20      <param name="end_col" value="None" />
21      <output name="output" file="subtract-query-1.dat" />
22    </test>
23    -->
24        <!-- Subtract 2 tabular files with no column restrictions. -->
25    <test>
26      <param name="input1" value="eq-showbeginning.dat" />
27      <param name="input2" value="eq-showtail.dat" />
28      <param name="begin_col" value="None" />
29      <param name="end_col" value="None" />
30      <output name="output" file="subtract-query-2.dat" />
31    </test>
32        <!-- Subtract 2 tabular files with column restrictions. -->
33    <test>
34      <param name="input1" value="eq-showbeginning.dat" />
35      <param name="input2" value="eq-removebeginning.dat" />
36      <param name="begin_col" value="c1" />
37      <param name="end_col" value="c3" />
38      <output name="output" file="subtract-query-3.dat" />
39    </test>
40        <!-- Subtract a non-tabular file from a tabular file with no column restrictions. -->
41    <test>
42      <param name="input1" value="eq-showbeginning.dat" />
43      <param name="input2" value="2.txt" />
44      <param name="begin_col" value="None" />
45      <param name="end_col" value="None" />
46      <output name="output" file="subtract-query-4.dat" />
47    </test>
48  </tests>
49  <help>
50
51.. class:: infomark
52
53**TIP:** This tool complements the tool in the **Operate on Genomic Intervals** tool set which subtracts the intervals of two queries.
54
55
56-----
57
58**Syntax**
59
60This tool subtracts an entire query from another query. 
61
62- Any text format is valid.
63- If both query formats are tabular, you may restrict the subtraction to specific columns **contained in both queries** and the resulting query will include only the columns specified.
64- The begin column must be less than or equal to the end column.  If it is not, begin column is switched with end column.
65- If begin column is specified but end column is not, end column will default to begin_column (and vice versa).
66- All blank and comment lines are skipped and not included in the resulting query (comment lines are lines beginning with a # character).
67- Duplicate lines are eliminated from both queries prior to subtraction.  If any duplicate lines were eliminated from the first query, the number is displayed in the resulting history item.
68
69-----
70
71**Example**
72
73If this is the **First query**::
74
75  chr1            4225    19670
76  chr10           6       8
77  chr1            24417   24420
78  chr6_hla_hap2   0       150
79  chr2            1       5
80  chr10           2       10
81  chr1            30      55
82  chrY            1       20
83  chr1            1225979 42287290
84  chr10           7       8
85
86and this is the **Second query**::
87
88  chr1            4225    19670
89  chr10           6       8
90  chr1            24417   24420
91  chr6_hla_hap2   0       150
92  chr2            1       5
93  chr1            30      55
94  chrY            1       20
95  chr1            1225979 42287290
96
97Subtracting the **Second query** from the **First query** (including all columns) will yield::
98
99  chr10           7       8
100  chr10           2       10
101
102Conversely, subtracting the **First query** from the **Second query** (including all columns) will result in an empty dataset.
103
104Subtracting the **Second query** from the **First query** (restricting to columns c1 and c2) will yield::
105
106  chr10           7
107  chr10           2
108
109  </help>
110</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。