Mercurial > repos > bgruening > text_processing
diff cut.xml @ 4:56e80527c482 draft
Uploaded
| author | bgruening |
|---|---|
| date | Wed, 07 Jan 2015 11:10:52 -0500 |
| parents | 7068d1548234 |
| children | 8928e6d1e7ba |
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--- a/cut.xml Sun Oct 06 08:22:36 2013 -0400 +++ b/cut.xml Wed Jan 07 11:10:52 2015 -0500 @@ -1,162 +1,179 @@ -<tool id="tp_cut_tool" name="Cut" version="0.1.1"> +<tool id="tp_cut_tool" name="Cut" version="@BASE_VERSION@.0"> <description>columns from a table</description> - <requirements> - <requirement type="package" version="8.21">gnu_coreutils</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <version_command>cut --version | head -n 1</version_command> <command> - cut - #if str($delimiter) != '': - -d"${delimiter}" - #end if - ${complement} ${cut_element} '${list}' '${input}' > '${output}' +<![CDATA[ + cut + #if str($delimiter) != '': + -d"${delimiter}" + #end if + ${complement} + ${cut_type_options.cut_element} + '${cut_type_options.list}' + '${input}' + > '${output}' +]]> </command> - <inputs> - <param format="txt" name="input" type="data" label="file to cut" /> + <param name="input" format="txt" type="data" label="File to cut" /> <param name="complement" type="select" label="Operation"> <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> + <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> - - <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> - - <param name="list" type="text" size="20" value="" label="List of Fields/Characters/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> + <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)" /> + </when> + <when value="-c"> + <param name="list" type="text" size="20" value="" label="List of Fields" 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> + <when value="-b"> + <param name="list" type="text" size="20" 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> <!--<data format="tabular" name="output" />--> <!-- WIP, not sure that will work with the complement option --> <data format="tabular" name="output"> - <actions> - <conditional name="cut_element"> - <when value="-f"> - <conditional name="delimiter"> - <when value="T"> - <conditional name="input"> - <when datatype_isinstance="interval"> - <action type="format" default="tabular"> - <option type="from_param" name="list" column="0" offset="0"> <!-- chromCol is 1--> - - <filter type="insert_column" column="0" value="interval"/> - <filter type="insert_column" ref="list" /> <!-- startCol --> - <filter type="insert_column" ref="list" /> <!-- endCol --> - - <filter type="multiple_splitter" column="1" separator=","/> - <filter type="column_strip" column="1"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="1" name="lower" /> - <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's --> - <filter type="boolean" column="1" cast="int" /> + <actions> + <conditional name="cut_type_options.cut_element"> + <!-- fields --> + <when value="-f"> + <conditional name="delimiter"> + <when value="T"> + <conditional name="input"> + <when datatype_isinstance="interval"> + <action type="format" default="tabular"> + <option type="from_param" name="list" column="0" offset="0"> <!-- chromCol is 1--> + <filter type="insert_column" column="0" value="interval"/> + <filter type="insert_column" ref="list" /> <!-- startCol --> + <filter type="insert_column" ref="list" /> <!-- endCol --> - <filter type="multiple_splitter" column="2" separator=","/> - <filter type="column_strip" column="2"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="2" name="lower" /> - <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's --> - <filter type="boolean" column="2" cast="int" /> + <filter type="multiple_splitter" column="1" separator=","/> + <filter type="column_strip" column="1"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="1" name="lower" /> + <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's --> + <filter type="boolean" column="1" cast="int" /> - <filter type="multiple_splitter" column="3" separator=","/> - <filter type="column_strip" column="3"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="3" name="lower" /> - <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's --> - <filter type="boolean" column="3" cast="int" /> + <filter type="multiple_splitter" column="2" separator=","/> + <filter type="column_strip" column="2"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="2" name="lower" /> + <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's --> + <filter type="boolean" column="2" cast="int" /> - <filter type="metadata_value" ref="input" name="chromCol" column="1" /> - <filter type="metadata_value" ref="input" name="startCol" column="2" /> - <filter type="metadata_value" ref="input" name="endCol" column="3" /> + <filter type="multiple_splitter" column="3" separator=","/> + <filter type="column_strip" column="3"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="3" name="lower" /> + <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's --> + <filter type="boolean" column="3" cast="int" /> - </option> - </action> - + <filter type="metadata_value" ref="input" name="chromCol" column="1" /> + <filter type="metadata_value" ref="input" name="startCol" column="2" /> + <filter type="metadata_value" ref="input" name="endCol" column="3" /> + </option> + </action> <conditional name="output"> - <when datatype_isinstance="interval"> - <action type="metadata" name="chromCol"> - <option type="from_param" name="list" column="0" offset="0"> <!-- chromCol is 0--> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="chromCol" column="1" /> - </option> - </action> - - <action type="metadata" name="startCol"> - <option type="from_param" name="list" column="0" offset="0"> <!-- startCol is 0--> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="startCol" column="1" /> - </option> - </action> - - <action type="metadata" name="endCol"> - <option type="from_param" name="list" column="0" offset="0"> <!-- endCol is 0--> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="endCol" column="1" /> - </option> - </action> - - <action type="metadata" name="nameCol" default="0"> - <option type="from_param" name="list" column="0" offset="0"> <!-- nameCol is 0--> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="nameCol" column="1" /> - </option> - </action> - - <action type="metadata" name="strandCol" default="0"> - <option type="from_param" name="list" column="0" offset="0"> <!-- strandCol is 0--> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="strandCol" column="1" /> - </option> - </action> + <when datatype_isinstance="interval"> + <action type="metadata" name="chromCol"> + <option type="from_param" name="list" column="0" offset="0"> <!-- chromCol is 0--> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="chromCol" column="1" /> + </option> + </action> + + <action type="metadata" name="startCol"> + <option type="from_param" name="list" column="0" offset="0"> <!-- startCol is 0--> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="startCol" column="1" /> + </option> + </action> + + <action type="metadata" name="endCol"> + <option type="from_param" name="list" column="0" offset="0"> <!-- endCol is 0--> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="endCol" column="1" /> + </option> + </action> + + <action type="metadata" name="nameCol" default="0"> + <option type="from_param" name="list" column="0" offset="0"> <!-- nameCol is 0--> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="nameCol" column="1" /> + </option> + </action> + + <action type="metadata" name="strandCol" default="0"> + <option type="from_param" name="list" column="0" offset="0"> <!-- strandCol is 0--> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="strandCol" column="1" /> + </option> + </action> </when> </conditional> - </when> </conditional> </when> @@ -180,9 +197,8 @@ <output name="output" file="eq-cut.dat" /> </test> </tests> - <help> - +<![CDATA[ **What it does** This tool runs the **cut** unix command, which extract or delete columns from a file. @@ -229,5 +245,7 @@ ora ban +@REFERENCES@ +]]> </help> </tool>