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comparison subtract_query.xml @ 3:f58ba0382c26 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:51:44 -0400
parents 8a3448727cec
children
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2:659a1c095357 3:f58ba0382c26
1 <tool id="subtract_query1" name="Subtract Whole Dataset" version="0.1"> 1 <tool id="subtract_query1" name="Subtract Whole Dataset" version="0.1">
2 <description>from another dataset</description> 2 <description>from another dataset</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.7.1">bx-python</requirement> 4 <import>macros.xml</import>
5 <requirement type="package" version="1.0.0">galaxy-ops</requirement> 5 </macros>
6 </requirements> 6 <expand macro="requirements" />
7 <command interpreter="python"> 7 <command><![CDATA[
8 subtract_query.py $input1 $input2 $begin_col $end_col $output 8 python '$__tool_directory__/subtract_query.py'
9 #if str($ignore_empty_end_cols) == 'true': 9 '$input1'
10 --ignore-empty-end-cols 10 '$input2'
11 #end if 11 $begin_col
12 12 $end_col
13 </command> 13 '$output'
14 <inputs> 14 #if str($ignore_empty_end_cols) == 'true':
15 <param format="txt" name="input2" type="data" label="Subtract" help="Second dataset" /> 15 --ignore-empty-end-cols
16 <param format="txt" name="input1" type="data" label="from" help="First dataset" /> 16 #end if
17 <param name="begin_col" type="data_column" data_ref="input1" force_select="False" label="Restrict subtraction between 'begin column'" /> 17 ]]></command>
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" /> 18 <inputs>
19 <param name="ignore_empty_end_cols" type="boolean" label="Ignore empty columns and whitespace at end of line when subtracting"/> 19 <param name="input2" type="data" format="txt" label="Subtract" help="Second dataset" />
20 </inputs> 20 <param name="input1" type="data" format="txt" label="from" help="First dataset" />
21 <outputs> 21 <param name="begin_col" type="data_column" data_ref="input1" force_select="False" label="Restrict subtraction between 'begin column'" />
22 <data format="input" name="output" metadata_source="input1" /> 22 <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" />
23 </outputs> 23 <param name="ignore_empty_end_cols" type="boolean" label="Ignore empty columns and whitespace at end of line when subtracting"/>
24 <tests> 24 </inputs>
25 <!-- Subtract 2 non-tabular files with no column restrictions. --> 25 <outputs>
26 <!-- Cannot figure out why this test won't pass, it works in real time... --> 26 <data name="output" format_source="input1" metadata_source="input1" />
27 <!-- 27 </outputs>
28 <test> 28 <tests>
29 <param name="input1" value="1.txt" /> 29 <!-- Subtract 2 non-tabular files with no column restrictions. -->
30 <param name="input2" value="2.txt" /> 30 <!-- Cannot figure out why this test won't pass, it works in real time... -->
31 <param name="begin_col" value="None" /> 31 <!--
32 <param name="end_col" value="None" /> 32 <test>
33 <output name="output" file="subtract-query-1.dat" /> 33 <param name="input1" value="1.txt" />
34 </test> 34 <param name="input2" value="2.txt" />
35 --> 35 <param name="begin_col" value="None" />
36 <!-- Subtract 2 tabular files with no column restrictions. --> 36 <param name="end_col" value="None" />
37 <test> 37 <output name="output" file="subtract-query-1.dat" />
38 <param name="input1" value="eq-showbeginning.dat" /> 38 </test>
39 <param name="input2" value="eq-showtail.dat" /> 39 -->
40 <param name="begin_col" value="None" /> 40 <!-- Subtract 2 tabular files with no column restrictions. -->
41 <param name="end_col" value="None" /> 41 <test>
42 <output name="output" file="subtract-query-2.dat" /> 42 <param name="input1" value="eq-showbeginning.dat" />
43 </test> 43 <param name="input2" value="eq-showtail.dat" />
44 <!-- Subtract 2 tabular files with column restrictions. --> 44 <param name="begin_col" value="" />
45 <test> 45 <param name="end_col" value="" />
46 <param name="input1" value="eq-showbeginning.dat" /> 46 <output name="output" file="subtract-query-2.dat" />
47 <param name="input2" value="eq-removebeginning.dat" /> 47 </test>
48 <param name="begin_col" value="c1" /> 48 <!-- Subtract 2 tabular files with column restrictions. -->
49 <param name="end_col" value="c3" /> 49 <test>
50 <output name="output" file="subtract-query-3.dat" /> 50 <param name="input1" value="eq-showbeginning.dat" />
51 </test> 51 <param name="input2" value="eq-removebeginning.dat" />
52 <!-- Subtract a non-tabular file from a tabular file with no column restrictions. --> 52 <param name="begin_col" value="c1" />
53 <test> 53 <param name="end_col" value="c3" />
54 <param name="input1" value="eq-showbeginning.dat" /> 54 <output name="output" file="subtract-query-3.dat" />
55 <param name="input2" value="2.txt" /> 55 </test>
56 <param name="begin_col" value="None" /> 56 <!-- Subtract a non-tabular file from a tabular file with no column restrictions. -->
57 <param name="end_col" value="None" /> 57 <test>
58 <output name="output" file="subtract-query-4.dat" /> 58 <param name="input1" value="eq-showbeginning.dat" />
59 </test> 59 <param name="input2" value="2.txt" />
60 <!-- Subtract 2 tabular files with no column restrictions, ignoring empty end columns. --> 60 <param name="begin_col" value="" />
61 <test> 61 <param name="end_col" value="" />
62 <param name="input1" value="eq-showbeginning_e.dat" /> 62 <output name="output" file="subtract-query-4.dat" />
63 <param name="input2" value="eq-showtail.dat" /> 63 </test>
64 <param name="begin_col" value="None" /> 64 <!-- Subtract 2 tabular files with no column restrictions, ignoring empty end columns. -->
65 <param name="end_col" value="None" /> 65 <test>
66 <param name="ignore_empty_end_cols" value="true" /> 66 <param name="input1" value="eq-showbeginning_e.dat" />
67 <output name="output" file="subtract-query-2.dat" /> 67 <param name="input2" value="eq-showtail.dat" />
68 </test> 68 <param name="begin_col" value="" />
69 </tests> 69 <param name="end_col" value="" />
70 <help> 70 <param name="ignore_empty_end_cols" value="true" />
71 71 <output name="output" file="subtract-query-2.dat" />
72 </test>
73 </tests>
74 <help><![CDATA[
72 .. class:: infomark 75 .. class:: infomark
73 76
74 **TIP:** This tool complements the tool in the **Operate on Genomic Intervals** tool set which subtracts the intervals of two datasets. 77 **TIP:** This tool complements the tool in the **Operate on Genomic Intervals** tool set which subtracts the intervals of two datasets.
75
76 78
77 ----- 79 -----
78 80
79 **Syntax** 81 **Syntax**
80 82
81 This tool subtracts an entire dataset from another dataset. 83 This tool subtracts an entire dataset from another dataset.
82 84
83 - Any text format is valid. 85 - 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. 86 - 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. 87 - 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). 88 - 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). 89 - 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. 90 - 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 91
100 chr2 1 5 102 chr2 1 5
101 chr10 2 10 103 chr10 2 10
102 chr1 30 55 104 chr1 30 55
103 chrY 1 20 105 chrY 1 20
104 chr1 1225979 42287290 106 chr1 1225979 42287290
105 chr10 7 8 107 chr10 7 8
106 108
107 and this is the **Second dataset**:: 109 and this is the **Second dataset**::
108 110
109 chr1 4225 19670 111 chr1 4225 19670
110 chr10 6 8 112 chr10 6 8
115 chrY 1 20 117 chrY 1 20
116 chr1 1225979 42287290 118 chr1 1225979 42287290
117 119
118 Subtracting the **Second dataset** from the **First dataset** (including all columns) will yield:: 120 Subtracting the **Second dataset** from the **First dataset** (including all columns) will yield::
119 121
120 chr10 7 8 122 chr10 7 8
121 chr10 2 10 123 chr10 2 10
122 124
123 Conversely, subtracting the **First dataset** from the **Second dataset** (including all columns) will result in an empty dataset. 125 Conversely, subtracting the **First dataset** from the **Second dataset** (including all columns) will result in an empty dataset.
124 126
125 Subtracting the **Second dataset** from the **First dataset** (restricting to columns c1 and c2) will yield:: 127 Subtracting the **Second dataset** from the **First dataset** (restricting to columns c1 and c2) will yield::
126 128
127 chr10 7 129 chr10 7
128 chr10 2 130 chr10 2
129 131 ]]></help>
130 </help>
131 </tool> 132 </tool>