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comparison cut.xml @ 26:f22a309187a3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
author bgruening
date Fri, 16 Aug 2024 10:41:17 +0000
parents 28b4fd1b0e9a
children 08cdbfffce67
comparison
equal deleted inserted replaced
25:cd83b5644eab 26:f22a309187a3
1 <tool id="tp_cut_tool" name="Advanced Cut" version="@BASE_VERSION@.0"> 1 <tool id="tp_cut_tool" name="Advanced Cut" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
2 <description>columns from a table (cut)</description> 2 <description>columns from a table (cut)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <version_command>cut --version | head -n 1</version_command> 7 <version_command>cut --version | head -n 1</version_command>
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 cut 10 cut
11 #if str($delimiter) != '': 11 $complement
12 -d"${delimiter}" 12 $cut_type_options.cut_element
13 #if $cut_type_options.cut_element != '-f'
14 '$cut_type_options.list'
15 #else
16 '$cut_type_options.colnames_option.list'
17 #if str($cut_type_options.delimiter) != '':
18 -d"$cut_type_options.delimiter"
19 #end if
13 #end if 20 #end if
14 ${complement} 21 '$input'
15 ${cut_type_options.cut_element} 22 > '$output'
16 '${cut_type_options.list}'
17 '${input}'
18 > '${output}'
19 ]]> 23 ]]>
20 </command> 24 </command>
21 <inputs> 25 <inputs>
22 <param name="input" format="txt" type="data" label="File to cut" /> 26 <param name="input" format="txt" type="data" label="File to cut" />
23 <param name="complement" type="select" label="Operation"> 27 <param name="complement" type="select" label="Operation">
24 <option value="">Keep</option> 28 <option value="">Keep</option>
25 <option value="--complement">Discard</option> 29 <option value="--complement">Discard</option>
26 </param> 30 </param>
27 <param name="delimiter" type="select" label="Delimited by">
28 <option value="">Tab</option>
29 <option value=" ">Whitespace</option>
30 <option value=".">Dot</option>
31 <option value=",">Comma</option>
32 <option value="-">Dash</option>
33 <option value="_">Underscore</option>
34 <option value="|">Pipe</option>
35 </param>
36 <conditional name="cut_type_options"> 31 <conditional name="cut_type_options">
37 <param name="cut_element" type="select" label="Cut by"> 32 <param name="cut_element" type="select" label="Cut by">
38 <option value="-f">fields</option> 33 <option value="-f">fields</option>
39 <option value="-c">characters</option> 34 <option value="-c">characters</option>
40 <option value="-b">bytes</option>
41 </param> 35 </param>
42 <when value="-f"> 36 <when value="-f">
43 <param name="list" type="data_column" data_ref="input" multiple="true" label="List of Fields" help="(-f)" /> 37 <param name="delimiter" type="select" label="Delimited by">
38 <option value="">Tab</option>
39 <option value=" ">Whitespace</option>
40 <option value=".">Dot</option>
41 <option value=",">Comma</option>
42 <option value="-">Dash</option>
43 <option value="_">Underscore</option>
44 <option value="|">Pipe</option>
45 </param>
46 <conditional name="colnames_option">
47 <param name="header" type="select" label="Is there a header for the data's columns ?">
48 <option value="Y">Yes</option>
49 <option value="N" selected="true">No</option>
50 </param>
51 <when value="Y">
52 <param name="list" type="data_column" data_ref="input" use_header_names="true" multiple="true" label="List of Fields" help="(-f)" />
53 </when>
54 <when value="N">
55 <param name="list" type="data_column" data_ref="input" multiple="true" label="List of Fields" help="(-f)" />
56 </when>
57 </conditional>
44 </when> 58 </when>
45 <when value="-c"> 59 <when value="-c">
46 <param name="list" type="text" value="" label="List of characters" help="These will be kept/discarded (depending on 'operation'). &lt;BR /&gt; Examples: 1,3,4 or 2-5"> 60 <param name="list" type="text" value="" label="List of characters" help="These will be kept/discarded (depending on 'operation'). &lt;BR /&gt; Examples: 1,3,4 or 2-5">
47 <sanitizer>
48 <valid initial="string.printable">
49 <remove value="&apos;"/>
50 </valid>
51 </sanitizer>
52 </param>
53 </when>
54 <when value="-b">
55 <param name="list" type="text" value="" label="List of Bytes" help="These will be kept/discarded (depending on 'operation'). &lt;BR /&gt; Examples: 1,3,4 or 2-5">
56 <sanitizer> 61 <sanitizer>
57 <valid initial="string.printable"> 62 <valid initial="string.printable">
58 <remove value="&apos;"/> 63 <remove value="&apos;"/>
59 </valid> 64 </valid>
60 </sanitizer> 65 </sanitizer>
68 <data format="tabular" name="output"> 73 <data format="tabular" name="output">
69 <actions> 74 <actions>
70 <conditional name="cut_type_options.cut_element"> 75 <conditional name="cut_type_options.cut_element">
71 <!-- fields --> 76 <!-- fields -->
72 <when value="-f"> 77 <when value="-f">
73 <conditional name="delimiter"> 78 <conditional name="cut_type_options.delimiter">
74 <when value="T"> 79 <when value="T">
75 <conditional name="input"> 80 <conditional name="input">
76 <when datatype_isinstance="interval"> 81 <when datatype_isinstance="interval">
77 <action type="format" default="tabular"> 82 <action type="format" default="tabular">
78 <option type="from_param" name="list" column="0" offset="0"> <!-- chromCol is 1--> 83 <option type="from_param" name="list" column="0" offset="0"> <!-- chromCol is 1-->
182 </conditional> 187 </conditional>
183 </actions> 188 </actions>
184 </data> 189 </data>
185 </outputs> 190 </outputs>
186 <tests> 191 <tests>
187 <test> 192 <test expect_num_outputs="1">
188 <param name="input" value="cut1.txt"/> 193 <param name="input" value="cut1.txt"/>
189 <param name="list" value="1,3,4"/> 194 <param name="list" value="1,3,4"/>
190 <param name="delimiter" value=""/> 195 <param name="delimiter" value=""/>
191 <output name="output" file="cut_results1.txt"/> 196 <output name="output" file="cut_results1.txt"/>
197 <assert_command>
198 <has_text text="-f '1,3,4'"/>
199 </assert_command>
192 </test> 200 </test>
193 <test> 201
202 <test expect_num_outputs="1">
194 <param name="input" value="cut1.txt"/> 203 <param name="input" value="cut1.txt"/>
195 <param name="list" value="2" /> 204 <conditional name="cut_type_options">
196 <param name="delimiter" value="" /> 205 <param name="delimiter" value="" />
206 <conditional name="colnames_option">
207 <param name="header" value="Y"/>
208 <!-- in the test we can (apparently) not select by header name -->
209 <param name="list" value="2" />
210 </conditional>
211 </conditional>
197 <param name="complement" value="--complement" /> 212 <param name="complement" value="--complement" />
198 <output name="output" file="cut_results2.txt"/> 213 <output name="output" file="cut_results2.txt"/>
214 <assert_command>
215 <has_text text="-f '2'"/>
216 </assert_command>
199 </test> 217 </test>
200 <test> 218 <test expect_num_outputs="1">
201 <param name="input" value="cut1.txt"/> 219 <param name="input" value="cut1.txt"/>
202 <param name="list" value="-3" /> 220 <param name="list" value="-3" />
203 <param name="delimiter" value="" /> 221 <param name="delimiter" value="" />
204 <param name="cut_element" value="-c" /> 222 <param name="cut_element" value="-c" />
205 <output name="output" file="cut_results3.txt"/> 223 <output name="output" file="cut_results3.txt"/>