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comparison cutWrapper.xml @ 1:f848742a0c1a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
author devteam
date Fri, 05 Aug 2016 16:37:57 -0400
parents aa367513335f
children
comparison
equal deleted inserted replaced
0:aa367513335f 1:f848742a0c1a
1 <tool id="Cut1" name="Cut" version="1.0.1"> 1 <tool id="Cut1" name="Cut" version="1.0.2">
2 <description>columns from a table</description> 2 <description>columns from a table</description>
3 <command interpreter="perl">cutWrapper.pl "${input}" "${columnList}" "${delimiter}" "${out_file1}"</command> 3 <command>
4 perl $__tool_directory__/cutWrapper.pl
5 "${input}"
6 "${columnList}"
7 "${delimiter}"
8 "${out_file1}"
9 </command>
4 <inputs> 10 <inputs>
5 <param name="columnList" type="text" value="c1,c2" label="Cut columns"/> 11 <param name="columnList" type="text" value="c1,c2" label="Cut columns"/>
6 <param name="delimiter" type="select" label="Delimited by"> 12 <param name="delimiter" type="select" label="Delimited by">
7 <option value="T">Tab</option> 13 <option value="T">Tab</option>
8 <option value="Sp">Whitespace</option> 14 <option value="Sp">Whitespace</option>
21 <when value="T"> 27 <when value="T">
22 <conditional name="input"> 28 <conditional name="input">
23 <when datatype_isinstance="interval"> 29 <when datatype_isinstance="interval">
24 <action type="format" default="tabular"> 30 <action type="format" default="tabular">
25 <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 1--> 31 <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 1-->
26 32
27 <filter type="insert_column" column="0" value="interval"/> 33 <filter type="insert_column" column="0" value="interval"/>
28 34
29 <filter type="insert_column" ref="columnList" /> <!-- startCol --> 35 <filter type="insert_column" ref="columnList" /> <!-- startCol -->
30 36
31 <filter type="insert_column" ref="columnList" /> <!-- endCol --> 37 <filter type="insert_column" ref="columnList" /> <!-- endCol -->
32 38
33 <filter type="multiple_splitter" column="1" separator=","/> 39 <filter type="multiple_splitter" column="1" separator=","/>
34 <filter type="column_strip" column="1"/> <!-- get rid of all external whitespace --> 40 <filter type="column_strip" column="1"/> <!-- get rid of all external whitespace -->
35 <filter type="string_function" column="1" name="lower" /> 41 <filter type="string_function" column="1" name="lower" />
36 <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/> 42 <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/>
37 <filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's --> 43 <filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's -->
38 <filter type="boolean" column="1" cast="int" /> 44 <filter type="boolean" column="1" cast="int" />
39 45
40 <filter type="multiple_splitter" column="2" separator=","/> 46 <filter type="multiple_splitter" column="2" separator=","/>
41 <filter type="column_strip" column="2"/> <!-- get rid of all external whitespace --> 47 <filter type="column_strip" column="2"/> <!-- get rid of all external whitespace -->
42 <filter type="string_function" column="2" name="lower" /> 48 <filter type="string_function" column="2" name="lower" />
43 <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/> 49 <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/>
44 <filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's --> 50 <filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's -->
45 <filter type="boolean" column="2" cast="int" /> 51 <filter type="boolean" column="2" cast="int" />
46 52
47 <filter type="multiple_splitter" column="3" separator=","/> 53 <filter type="multiple_splitter" column="3" separator=","/>
48 <filter type="column_strip" column="3"/> <!-- get rid of all external whitespace --> 54 <filter type="column_strip" column="3"/> <!-- get rid of all external whitespace -->
49 <filter type="string_function" column="3" name="lower" /> 55 <filter type="string_function" column="3" name="lower" />
50 <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/> 56 <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/>
51 <filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's --> 57 <filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's -->
52 <filter type="boolean" column="3" cast="int" /> 58 <filter type="boolean" column="3" cast="int" />
53 59
54 <filter type="metadata_value" ref="input" name="chromCol" column="1" /> 60 <filter type="metadata_value" ref="input" name="chromCol" column="1" />
55 <filter type="metadata_value" ref="input" name="startCol" column="2" /> 61 <filter type="metadata_value" ref="input" name="startCol" column="2" />
56 <filter type="metadata_value" ref="input" name="endCol" column="3" /> 62 <filter type="metadata_value" ref="input" name="endCol" column="3" />
57 63
58 </option> 64 </option>
59 </action> 65 </action>
60 66
61 <conditional name="out_file1"> 67 <conditional name="out_file1">
62 <when datatype_isinstance="interval"> 68 <when datatype_isinstance="interval">
63 <action type="metadata" name="chromCol"> 69 <action type="metadata" name="chromCol">
64 <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 0--> 70 <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 0-->
65 <filter type="multiple_splitter" column="0" separator=","/> 71 <filter type="multiple_splitter" column="0" separator=","/>
66 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> 72 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
67 <filter type="string_function" column="0" name="lower" /> 73 <filter type="string_function" column="0" name="lower" />
68 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> 74 <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 --> 75 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
70 <filter type="insert_column" value="1" iterate="True" column="0"/> 76 <filter type="insert_column" value="1" iterate="True" column="0"/>
71 <filter type="boolean" column="1" cast="int" /> 77 <filter type="boolean" column="1" cast="int" />
72 <filter type="metadata_value" ref="input" name="chromCol" column="1" /> 78 <filter type="metadata_value" ref="input" name="chromCol" column="1" />
73 </option> 79 </option>
74 </action> 80 </action>
75 81
76 <action type="metadata" name="startCol"> 82 <action type="metadata" name="startCol">
77 <option type="from_param" name="columnList" column="0" offset="0"> <!-- startCol is 0--> 83 <option type="from_param" name="columnList" column="0" offset="0"> <!-- startCol is 0-->
78 <filter type="multiple_splitter" column="0" separator=","/> 84 <filter type="multiple_splitter" column="0" separator=","/>
79 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> 85 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
80 <filter type="string_function" column="0" name="lower" /> 86 <filter type="string_function" column="0" name="lower" />
83 <filter type="insert_column" value="1" iterate="True" column="0"/> 89 <filter type="insert_column" value="1" iterate="True" column="0"/>
84 <filter type="boolean" column="1" cast="int" /> 90 <filter type="boolean" column="1" cast="int" />
85 <filter type="metadata_value" ref="input" name="startCol" column="1" /> 91 <filter type="metadata_value" ref="input" name="startCol" column="1" />
86 </option> 92 </option>
87 </action> 93 </action>
88 94
89 <action type="metadata" name="endCol"> 95 <action type="metadata" name="endCol">
90 <option type="from_param" name="columnList" column="0" offset="0"> <!-- endCol is 0--> 96 <option type="from_param" name="columnList" column="0" offset="0"> <!-- endCol is 0-->
91 <filter type="multiple_splitter" column="0" separator=","/> 97 <filter type="multiple_splitter" column="0" separator=","/>
92 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> 98 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
93 <filter type="string_function" column="0" name="lower" /> 99 <filter type="string_function" column="0" name="lower" />
96 <filter type="insert_column" value="1" iterate="True" column="0"/> 102 <filter type="insert_column" value="1" iterate="True" column="0"/>
97 <filter type="boolean" column="1" cast="int" /> 103 <filter type="boolean" column="1" cast="int" />
98 <filter type="metadata_value" ref="input" name="endCol" column="1" /> 104 <filter type="metadata_value" ref="input" name="endCol" column="1" />
99 </option> 105 </option>
100 </action> 106 </action>
101 107
102 <action type="metadata" name="nameCol" default="0"> 108 <action type="metadata" name="nameCol" default="0">
103 <option type="from_param" name="columnList" column="0" offset="0"> <!-- nameCol is 0--> 109 <option type="from_param" name="columnList" column="0" offset="0"> <!-- nameCol is 0-->
104 <filter type="multiple_splitter" column="0" separator=","/> 110 <filter type="multiple_splitter" column="0" separator=","/>
105 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> 111 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
106 <filter type="string_function" column="0" name="lower" /> 112 <filter type="string_function" column="0" name="lower" />
109 <filter type="insert_column" value="1" iterate="True" column="0"/> 115 <filter type="insert_column" value="1" iterate="True" column="0"/>
110 <filter type="boolean" column="1" cast="int" /> 116 <filter type="boolean" column="1" cast="int" />
111 <filter type="metadata_value" ref="input" name="nameCol" column="1" /> 117 <filter type="metadata_value" ref="input" name="nameCol" column="1" />
112 </option> 118 </option>
113 </action> 119 </action>
114 120
115 <action type="metadata" name="strandCol" default="0"> 121 <action type="metadata" name="strandCol" default="0">
116 <option type="from_param" name="columnList" column="0" offset="0"> <!-- strandCol is 0--> 122 <option type="from_param" name="columnList" column="0" offset="0"> <!-- strandCol is 0-->
117 <filter type="multiple_splitter" column="0" separator=","/> 123 <filter type="multiple_splitter" column="0" separator=","/>
118 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> 124 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
119 <filter type="string_function" column="0" name="lower" /> 125 <filter type="string_function" column="0" name="lower" />
121 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> 127 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
122 <filter type="insert_column" value="1" iterate="True" column="0"/> 128 <filter type="insert_column" value="1" iterate="True" column="0"/>
123 <filter type="boolean" column="1" cast="int" /> 129 <filter type="boolean" column="1" cast="int" />
124 <filter type="metadata_value" ref="input" name="strandCol" column="1" /> 130 <filter type="metadata_value" ref="input" name="strandCol" column="1" />
125 </option> 131 </option>
126 </action> 132 </action>
127 </when> 133 </when>
128 </conditional> 134 </conditional>
129 135
130 </when> 136 </when>
131 </conditional> 137 </conditional>
132 </when> 138 </when>
133 </conditional> 139 </conditional>
134 </actions> 140 </actions>
139 <param name="columnList" value="c1,c4,c2,c3"/> 145 <param name="columnList" value="c1,c4,c2,c3"/>
140 <param name="delimiter" value="T"/> 146 <param name="delimiter" value="T"/>
141 <param name="input" value="1.bed"/> 147 <param name="input" value="1.bed"/>
142 <output name="out_file1" file="eq-cut.dat"/> 148 <output name="out_file1" file="eq-cut.dat"/>
143 </test> 149 </test>
150 <test>
151 <param name="columnList" value="c1,c4,c2-c3" />
152 <param name="delimiter" value="T" />
153 <param name="input" value="1.bed" />
154 <output name="out_file1" file="eq-cut.dat" />
155 </test>
144 </tests> 156 </tests>
145 <help> 157 <help>
146 158
147 .. class:: warningmark 159 .. class:: warningmark
148 160
154 166
155 Cutting columns 1 and 3 from:: 167 Cutting columns 1 and 3 from::
156 168
157 apple,is,good 169 apple,is,good
158 windows,is,bad 170 windows,is,bad
171 linux,is,best
159 172
160 will give:: 173 will give::
161 174
162 apple good 175 apple good
163 windows bad 176 windows bad
177 linux best
164 178
165 ----- 179 -----
166 180
167 **What it does** 181 **What it does**
168 182
186 chr1 gene1 + 200 chr1 gene1 +
187 chr2 gene2 + 201 chr2 gene2 +
188 202
189 **cut** on columns "**c6,c5,c4,c1**" will return:: 203 **cut** on columns "**c6,c5,c4,c1**" will return::
190 204
191 + 0 gene1 chr1 205 + 0 gene1 chr1
192 + 0 gene2 chr2 206 + 0 gene2 chr2
193 207
208 **cut** on columns "**c1-c3**" will return::
209
210 chr1 10 1000
211 chr2 100 1500
212
194 213
195 **cut** on columns "**c8,c7,c4**" will return:: 214 **cut** on columns "**c8,c7,c4**" will return::
196 215
197 . . gene1 216 . . gene1
198 . . gene2 217 . . gene2
199
200
201 </help> 218 </help>
202 </tool> 219 </tool>