Mercurial > repos > devteam > subtract_query
comparison subtract_query.xml @ 0:8a3448727cec draft
Imported from capsule None
author | devteam |
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date | Tue, 01 Apr 2014 09:12:49 -0400 |
parents | |
children | f58ba0382c26 |
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-1:000000000000 | 0:8a3448727cec |
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1 <tool id="subtract_query1" name="Subtract Whole Dataset" version="0.1"> | |
2 <description>from another dataset</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.7.1">bx-python</requirement> | |
5 <requirement type="package" version="1.0.0">galaxy-ops</requirement> | |
6 </requirements> | |
7 <command interpreter="python"> | |
8 subtract_query.py $input1 $input2 $begin_col $end_col $output | |
9 #if str($ignore_empty_end_cols) == 'true': | |
10 --ignore-empty-end-cols | |
11 #end if | |
12 | |
13 </command> | |
14 <inputs> | |
15 <param format="txt" name="input2" type="data" label="Subtract" help="Second dataset" /> | |
16 <param format="txt" name="input1" type="data" label="from" help="First dataset" /> | |
17 <param name="begin_col" type="data_column" data_ref="input1" force_select="False" label="Restrict subtraction between 'begin column'" /> | |
18 <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 datasets" /> | |
19 <param name="ignore_empty_end_cols" type="boolean" label="Ignore empty columns and whitespace at end of line when subtracting"/> | |
20 </inputs> | |
21 <outputs> | |
22 <data format="input" name="output" metadata_source="input1" /> | |
23 </outputs> | |
24 <tests> | |
25 <!-- Subtract 2 non-tabular files with no column restrictions. --> | |
26 <!-- Cannot figure out why this test won't pass, it works in real time... --> | |
27 <!-- | |
28 <test> | |
29 <param name="input1" value="1.txt" /> | |
30 <param name="input2" value="2.txt" /> | |
31 <param name="begin_col" value="None" /> | |
32 <param name="end_col" value="None" /> | |
33 <output name="output" file="subtract-query-1.dat" /> | |
34 </test> | |
35 --> | |
36 <!-- Subtract 2 tabular files with no column restrictions. --> | |
37 <test> | |
38 <param name="input1" value="eq-showbeginning.dat" /> | |
39 <param name="input2" value="eq-showtail.dat" /> | |
40 <param name="begin_col" value="None" /> | |
41 <param name="end_col" value="None" /> | |
42 <output name="output" file="subtract-query-2.dat" /> | |
43 </test> | |
44 <!-- Subtract 2 tabular files with column restrictions. --> | |
45 <test> | |
46 <param name="input1" value="eq-showbeginning.dat" /> | |
47 <param name="input2" value="eq-removebeginning.dat" /> | |
48 <param name="begin_col" value="c1" /> | |
49 <param name="end_col" value="c3" /> | |
50 <output name="output" file="subtract-query-3.dat" /> | |
51 </test> | |
52 <!-- Subtract a non-tabular file from a tabular file with no column restrictions. --> | |
53 <test> | |
54 <param name="input1" value="eq-showbeginning.dat" /> | |
55 <param name="input2" value="2.txt" /> | |
56 <param name="begin_col" value="None" /> | |
57 <param name="end_col" value="None" /> | |
58 <output name="output" file="subtract-query-4.dat" /> | |
59 </test> | |
60 <!-- Subtract 2 tabular files with no column restrictions, ignoring empty end columns. --> | |
61 <test> | |
62 <param name="input1" value="eq-showbeginning_e.dat" /> | |
63 <param name="input2" value="eq-showtail.dat" /> | |
64 <param name="begin_col" value="None" /> | |
65 <param name="end_col" value="None" /> | |
66 <param name="ignore_empty_end_cols" value="true" /> | |
67 <output name="output" file="subtract-query-2.dat" /> | |
68 </test> | |
69 </tests> | |
70 <help> | |
71 | |
72 .. class:: infomark | |
73 | |
74 **TIP:** This tool complements the tool in the **Operate on Genomic Intervals** tool set which subtracts the intervals of two datasets. | |
75 | |
76 | |
77 ----- | |
78 | |
79 **Syntax** | |
80 | |
81 This tool subtracts an entire dataset from another dataset. | |
82 | |
83 - Any text format is valid. | |
84 - If both dataset formats are tabular, you may restrict the subtraction to specific columns **contained in both datasets** and the resulting dataset will include only the columns specified. | |
85 - The begin column must be less than or equal to the end column. If it is not, begin column is switched with end column. | |
86 - If begin column is specified but end column is not, end column will default to begin_column (and vice versa). | |
87 - All blank and comment lines are skipped and not included in the resulting dataset (comment lines are lines beginning with a # character). | |
88 - Duplicate lines are eliminated from both dataset prior to subtraction. If any duplicate lines were eliminated from the first dataset, the number is displayed in the resulting history item. | |
89 | |
90 ----- | |
91 | |
92 **Example** | |
93 | |
94 If this is the **First dataset**:: | |
95 | |
96 chr1 4225 19670 | |
97 chr10 6 8 | |
98 chr1 24417 24420 | |
99 chr6_hla_hap2 0 150 | |
100 chr2 1 5 | |
101 chr10 2 10 | |
102 chr1 30 55 | |
103 chrY 1 20 | |
104 chr1 1225979 42287290 | |
105 chr10 7 8 | |
106 | |
107 and this is the **Second dataset**:: | |
108 | |
109 chr1 4225 19670 | |
110 chr10 6 8 | |
111 chr1 24417 24420 | |
112 chr6_hla_hap2 0 150 | |
113 chr2 1 5 | |
114 chr1 30 55 | |
115 chrY 1 20 | |
116 chr1 1225979 42287290 | |
117 | |
118 Subtracting the **Second dataset** from the **First dataset** (including all columns) will yield:: | |
119 | |
120 chr10 7 8 | |
121 chr10 2 10 | |
122 | |
123 Conversely, subtracting the **First dataset** from the **Second dataset** (including all columns) will result in an empty dataset. | |
124 | |
125 Subtracting the **Second dataset** from the **First dataset** (restricting to columns c1 and c2) will yield:: | |
126 | |
127 chr10 7 | |
128 chr10 2 | |
129 | |
130 </help> | |
131 </tool> |