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comparison tools/filters/cutWrapper.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="Cut1" name="Cut" version="1.0.1">
2 <description>columns from a table</description>
3 <command interpreter="perl">cutWrapper.pl $input "$columnList" $delimiter $out_file1</command>
4 <inputs>
5 <param name="columnList" size="10" type="text" value="c1,c2" label="Cut columns"/>
6 <param name="delimiter" type="select" label="Delimited by">
7 <option value="T">Tab</option>
8 <option value="Sp">Whitespace</option>
9 <option value="Dt">Dot</option>
10 <option value="C">Comma</option>
11 <option value="D">Dash</option>
12 <option value="U">Underscore</option>
13 <option value="P">Pipe</option>
14 </param>
15 <param format="txt" name="input" type="data" label="From"/>
16 </inputs>
17 <outputs>
18 <data format="tabular" name="out_file1" >
19 <actions>
20 <conditional name="delimiter">
21 <when value="T">
22 <conditional name="input">
23 <when datatype_isinstance="interval">
24 <action type="format" default="tabular">
25 <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 1-->
26
27 <filter type="insert_column" column="0" value="interval"/>
28
29 <filter type="insert_column" ref="columnList" /> <!-- startCol -->
30
31 <filter type="insert_column" ref="columnList" /> <!-- endCol -->
32
33 <filter type="multiple_splitter" column="1" separator=","/>
34 <filter type="column_strip" column="1"/> <!-- get rid of all external whitespace -->
35 <filter type="string_function" column="1" name="lower" />
36 <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/>
37 <filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's -->
38 <filter type="boolean" column="1" cast="int" />
39
40 <filter type="multiple_splitter" column="2" separator=","/>
41 <filter type="column_strip" column="2"/> <!-- get rid of all external whitespace -->
42 <filter type="string_function" column="2" name="lower" />
43 <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/>
44 <filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's -->
45 <filter type="boolean" column="2" cast="int" />
46
47 <filter type="multiple_splitter" column="3" separator=","/>
48 <filter type="column_strip" column="3"/> <!-- get rid of all external whitespace -->
49 <filter type="string_function" column="3" name="lower" />
50 <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/>
51 <filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's -->
52 <filter type="boolean" column="3" cast="int" />
53
54 <filter type="metadata_value" ref="input" name="chromCol" column="1" />
55 <filter type="metadata_value" ref="input" name="startCol" column="2" />
56 <filter type="metadata_value" ref="input" name="endCol" column="3" />
57
58 </option>
59 </action>
60
61 <conditional name="out_file1">
62 <when datatype_isinstance="interval">
63 <action type="metadata" name="chromCol">
64 <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 0-->
65 <filter type="multiple_splitter" column="0" separator=","/>
66 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
67 <filter type="string_function" column="0" name="lower" />
68 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
69 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
70 <filter type="insert_column" value="1" iterate="True" column="0"/>
71 <filter type="boolean" column="1" cast="int" />
72 <filter type="metadata_value" ref="input" name="chromCol" column="1" />
73 </option>
74 </action>
75
76 <action type="metadata" name="startCol">
77 <option type="from_param" name="columnList" column="0" offset="0"> <!-- startCol is 0-->
78 <filter type="multiple_splitter" column="0" separator=","/>
79 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
80 <filter type="string_function" column="0" name="lower" />
81 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
82 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
83 <filter type="insert_column" value="1" iterate="True" column="0"/>
84 <filter type="boolean" column="1" cast="int" />
85 <filter type="metadata_value" ref="input" name="startCol" column="1" />
86 </option>
87 </action>
88
89 <action type="metadata" name="endCol">
90 <option type="from_param" name="columnList" column="0" offset="0"> <!-- endCol is 0-->
91 <filter type="multiple_splitter" column="0" separator=","/>
92 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
93 <filter type="string_function" column="0" name="lower" />
94 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
95 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
96 <filter type="insert_column" value="1" iterate="True" column="0"/>
97 <filter type="boolean" column="1" cast="int" />
98 <filter type="metadata_value" ref="input" name="endCol" column="1" />
99 </option>
100 </action>
101
102 <action type="metadata" name="nameCol" default="0">
103 <option type="from_param" name="columnList" column="0" offset="0"> <!-- nameCol is 0-->
104 <filter type="multiple_splitter" column="0" separator=","/>
105 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
106 <filter type="string_function" column="0" name="lower" />
107 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
108 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
109 <filter type="insert_column" value="1" iterate="True" column="0"/>
110 <filter type="boolean" column="1" cast="int" />
111 <filter type="metadata_value" ref="input" name="nameCol" column="1" />
112 </option>
113 </action>
114
115 <action type="metadata" name="strandCol" default="0">
116 <option type="from_param" name="columnList" column="0" offset="0"> <!-- strandCol is 0-->
117 <filter type="multiple_splitter" column="0" separator=","/>
118 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
119 <filter type="string_function" column="0" name="lower" />
120 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
121 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
122 <filter type="insert_column" value="1" iterate="True" column="0"/>
123 <filter type="boolean" column="1" cast="int" />
124 <filter type="metadata_value" ref="input" name="strandCol" column="1" />
125 </option>
126 </action>
127 </when>
128 </conditional>
129
130 </when>
131 </conditional>
132 </when>
133 </conditional>
134 </actions>
135 </data>
136 </outputs>
137 <tests>
138 <test>
139 <param name="columnList" value="c1,c4,c2,c3"/>
140 <param name="delimiter" value="T"/>
141 <param name="input" value="1.bed"/>
142 <output name="out_file1" file="eq-cut.dat"/>
143 </test>
144 </tests>
145 <help>
146
147 .. class:: warningmark
148
149 **WARNING: This tool breaks column assignments.** To re-establish column assignments run the tools and click on the pencil icon in the latest history item.
150
151 .. class:: infomark
152
153 The output of this tool is always in tabular format (e.g., if your original delimiters are commas, they will be replaced with tabs). For example:
154
155 Cutting columns 1 and 3 from::
156
157 apple,is,good
158 windows,is,bad
159
160 will give::
161
162 apple good
163 windows bad
164
165 -----
166
167 **What it does**
168
169 This tool selects (cuts out) specified columns from the dataset.
170
171 - Columns are specified as **c1**, **c2**, and so on. Column count begins with **1**
172 - Columns can be specified in any order (e.g., **c2,c1,c6**)
173 - If you specify more columns than actually present - empty spaces will be filled with dots
174
175 -----
176
177 **Example**
178
179 Input dataset (six columns: c1, c2, c3, c4, c5, and c6)::
180
181 chr1 10 1000 gene1 0 +
182 chr2 100 1500 gene2 0 +
183
184 **cut** on columns "**c1,c4,c6**" will return::
185
186 chr1 gene1 +
187 chr2 gene2 +
188
189 **cut** on columns "**c6,c5,c4,c1**" will return::
190
191 + 0 gene1 chr1
192 + 0 gene2 chr2
193
194
195 **cut** on columns "**c8,c7,c4**" will return::
196
197 . . gene1
198 . . gene2
199
200
201 </help>
202 </tool>