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comparison awklike-filter.xml @ 0:20e8be1464f5 draft default tip

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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:14:07 -0400
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1 <tool id="csvtk_awklike_filter" name="csvtk-advanced-filter" version="@VERSION@+@GALAXY_VERSION@">
2 <description> rows by awk-like artithmetic/string expressions</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_cmd" />
8 <command detect_errors="exit_code"><![CDATA[
9
10 ###################
11 ## Start Command ##
12 ###################
13 csvtk filter2 --num-cpus "\${GALAXY_SLOTS:-1}"
14
15 ## Add additional flags as specified ##
16 #######################################
17 $global_param.illegal_rows
18 $global_param.empty_rows
19 $global_param.header
20 $global_param.lazy_quotes
21
22 ## Set Tabular input/output flag if first input is tabular ##
23 #############################################################
24 #if $in_1.is_of_type("tabular"):
25 -t -T
26 #end if
27
28 ## Set input files ##
29 #####################
30 $in_1
31
32 ## Specify fields to filter ##
33 ##############################
34 -f '$in_text'
35
36 ## Specific inputs ##
37 #####################
38 $line_number
39
40 ## To output ##
41 ###############
42 > filtered
43
44 ]]></command>
45 <inputs>
46 <expand macro="singular_input"/>
47 <param name="in_text" type="text"
48 optional="false"
49 argument="-f"
50 label="Awk-like artithmetic/string expression">
51 <help>
52 <![CDATA[
53 Examples:
54 - '$age>12'
55 - '$1 > $3'
56 - '$name=="abc"'
57 - '$1 % 2 == 0'
58 More info is available in the help section below. The ' character is invalid and will be replaced, thus you must
59 surround strings with double quotes ("string") instead.
60 ]]>
61 </help>
62 <expand macro="text_sanitizer" />
63 </param>
64 <param name="line_number" type="boolean"
65 checked="false"
66 truevalue="-n"
67 falsevalue=""
68 argument="-n"
69 label="Print initial line number as the first column"
70 />
71 <expand macro="global_parameters" />
72 </inputs>
73 <outputs>
74 <data format_source="in_1" from_work_dir="filtered" name="filtered" label="${in_1.name} filtered by ${in_text}" />
75 </outputs>
76 <tests>
77 <test>
78 <param name="in_1" value="frequency.tsv" />
79 <param name="in_text" value="$3>1" />
80 <output name="filtered" file="filtered.tsv" ftype="tabular" />
81 </test>
82 </tests>
83 <help><![CDATA[
84
85 Csvtk - Filter2 Help
86 --------------------
87
88 Info
89 ####
90
91 Csvtk advanced filter (also called filter2) outputs rows that satisfy the input awk-like artithmetic/string expressions. Please see the
92 `documentation <https://github.com/Knetic/govaluate/blob/master/MANUAL.md>`_ for further details and examples on how to write expressions.
93
94 .. class:: warningmark
95
96 Single quotes are not allowed in text inputs!
97
98 .. class:: note
99
100 If your wanted column header has a space in it, use the column number. Example: Use $1 if column #1 is called "Colony Counts"
101
102 Supported operators and types:
103
104 - Modifiers: + - / * & | ^ ** % >> <<
105 - Comparators: > >= < <= == != =~ !~
106 - Logical ops: || &&
107 - Numeric constants, as 64-bit floating point (12345.678)
108 - String constants (double quotes: "foobar")
109 - Date constants (double quotes)
110 - Boolean constants: true false
111 - Parenthesis to control order of evaluation ( )
112 - Arrays (anything separated by , within parenthesis: (1, 2, "foo"))
113 - Prefixes: ! - ~
114 - Ternary conditional: ? :
115 - Null coalescence: ??
116
117 ----
118
119 @HELP_INPUT_DATA@
120
121
122 Usage
123 #####
124
125 **Ex. Filter2 on one column:**
126
127 Suppose we had the following table:
128
129 +---------------+------------+----------+
130 | Culture Label | Cell Count | Dilution |
131 +===============+============+==========+
132 | ECo-1 | 2523 | 1000 |
133 +---------------+------------+----------+
134 | LPn-1 | 100 | 1000000 |
135 +---------------+------------+----------+
136 | LPn-2 | 4 | 1000 |
137 +---------------+------------+----------+
138
139 If we wanted to find all samples with the label LPn, we could use the filter expression '$1 =~ "LPn*"' to get the following output:
140
141 +---------------+------------+----------+
142 | Culture Label | Cell Count | Dilution |
143 +===============+============+==========+
144 | LPn-1 | 100 | 1000000 |
145 +---------------+------------+----------+
146 | LPn-2 | 4 | 1000 |
147 +---------------+------------+----------+
148
149 Note how $1 was used to get column 1 due to it containing a space
150
151 ----
152
153 **Ex2. Filter2 with multiple inputs:**
154
155 Same input table
156
157 +---------------+------------+----------+
158 | Culture Label | Cell Count | Dilution |
159 +===============+============+==========+
160 | ECo-1 | 2523 | 1000 |
161 +---------------+------------+----------+
162 | LPn-1 | 100 | 1000000 |
163 +---------------+------------+----------+
164 | LPn-2 | 4 | 1000 |
165 +---------------+------------+----------+
166
167 Now if we use the expression '$1 =~ "LPn*" && $Dilution > 1000' to filter on, we would pull out the only row that satisfies both conditions:
168
169 +---------------+------------+----------+
170 | Culture Label | Cell Count | Dilution |
171 +===============+============+==========+
172 | LPn-1 | 100 | 1000000 |
173 +---------------+------------+----------+
174
175 ----
176
177 @HELP_COLUMNS@
178
179
180 @HELP_END_STATEMENT@
181
182
183 ]]></help>
184 <expand macro="citations" />
185 </tool>