Mercurial > repos > bgruening > text_processing
diff cut.xml @ 26:f22a309187a3 draft
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 |
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--- a/cut.xml Sat Oct 08 20:59:15 2022 +0000 +++ b/cut.xml Fri Aug 16 10:41:17 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="tp_cut_tool" name="Advanced Cut" version="@BASE_VERSION@.0"> +<tool id="tp_cut_tool" name="Advanced Cut" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>columns from a table (cut)</description> <macros> <import>macros.xml</import> @@ -8,14 +8,18 @@ <command> <![CDATA[ cut - #if str($delimiter) != '': - -d"${delimiter}" + $complement + $cut_type_options.cut_element + #if $cut_type_options.cut_element != '-f' + '$cut_type_options.list' + #else + '$cut_type_options.colnames_option.list' + #if str($cut_type_options.delimiter) != '': + -d"$cut_type_options.delimiter" + #end if #end if - ${complement} - ${cut_type_options.cut_element} - '${cut_type_options.list}' - '${input}' - > '${output}' + '$input' + > '$output' ]]> </command> <inputs> @@ -24,23 +28,33 @@ <option value="">Keep</option> <option value="--complement">Discard</option> </param> - <param name="delimiter" type="select" label="Delimited by"> - <option value="">Tab</option> - <option value=" ">Whitespace</option> - <option value=".">Dot</option> - <option value=",">Comma</option> - <option value="-">Dash</option> - <option value="_">Underscore</option> - <option value="|">Pipe</option> - </param> <conditional name="cut_type_options"> <param name="cut_element" type="select" label="Cut by"> <option value="-f">fields</option> <option value="-c">characters</option> - <option value="-b">bytes</option> </param> <when value="-f"> - <param name="list" type="data_column" data_ref="input" multiple="true" label="List of Fields" help="(-f)" /> + <param name="delimiter" type="select" label="Delimited by"> + <option value="">Tab</option> + <option value=" ">Whitespace</option> + <option value=".">Dot</option> + <option value=",">Comma</option> + <option value="-">Dash</option> + <option value="_">Underscore</option> + <option value="|">Pipe</option> + </param> + <conditional name="colnames_option"> + <param name="header" type="select" label="Is there a header for the data's columns ?"> + <option value="Y">Yes</option> + <option value="N" selected="true">No</option> + </param> + <when value="Y"> + <param name="list" type="data_column" data_ref="input" use_header_names="true" multiple="true" label="List of Fields" help="(-f)" /> + </when> + <when value="N"> + <param name="list" type="data_column" data_ref="input" multiple="true" label="List of Fields" help="(-f)" /> + </when> + </conditional> </when> <when value="-c"> <param name="list" type="text" value="" label="List of characters" help="These will be kept/discarded (depending on 'operation'). <BR /> Examples: 1,3,4 or 2-5"> @@ -51,15 +65,6 @@ </sanitizer> </param> </when> - <when value="-b"> - <param name="list" type="text" value="" label="List of Bytes" help="These will be kept/discarded (depending on 'operation'). <BR /> Examples: 1,3,4 or 2-5"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - </valid> - </sanitizer> - </param> - </when> </conditional> </inputs> <outputs> @@ -70,7 +75,7 @@ <conditional name="cut_type_options.cut_element"> <!-- fields --> <when value="-f"> - <conditional name="delimiter"> + <conditional name="cut_type_options.delimiter"> <when value="T"> <conditional name="input"> <when datatype_isinstance="interval"> @@ -184,20 +189,33 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="input" value="cut1.txt"/> <param name="list" value="1,3,4"/> <param name="delimiter" value=""/> <output name="output" file="cut_results1.txt"/> + <assert_command> + <has_text text="-f '1,3,4'"/> + </assert_command> </test> - <test> + + <test expect_num_outputs="1"> <param name="input" value="cut1.txt"/> - <param name="list" value="2" /> - <param name="delimiter" value="" /> + <conditional name="cut_type_options"> + <param name="delimiter" value="" /> + <conditional name="colnames_option"> + <param name="header" value="Y"/> + <!-- in the test we can (apparently) not select by header name --> + <param name="list" value="2" /> + </conditional> + </conditional> <param name="complement" value="--complement" /> <output name="output" file="cut_results2.txt"/> + <assert_command> + <has_text text="-f '2'"/> + </assert_command> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="cut1.txt"/> <param name="list" value="-3" /> <param name="delimiter" value="" />