root/galaxy-central/tools/filters/cutWrapper.xml

リビジョン 2, 10.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
153The 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
169This 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
179Input 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>
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。