text_processing: cut.xml annotate

annotate cut.xml @ 29:4f7cade041cb draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 4dd118c84ed4d6157303e71438c24446ec4b4f31

author	bgruening
date	Wed, 04 Jun 2025 15:11:51 +0000
parents	08cdbfffce67
children

rev	line source
27 08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	1 <tool id="tp_cut_tool" name="Advanced Cut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
10 c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 7 diff changeset	2 <description>columns from a table (cut)</description>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	3 <macros>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	4 <import>macros.xml</import>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	5 </macros>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	6 <expand macro="requirements" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	7 <version_command>cut --version \| head -n 1</version_command>
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	8 <command>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	9 <![CDATA[
56e80527c482 Uploaded bgruening parents: 3 diff changeset	10 cut
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	11 $complement
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	12 $cut_type_options.cut_element
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	13 #if $cut_type_options.cut_element != '-f'
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	14 '$cut_type_options.list'
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	15 #else
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	16 '$cut_type_options.colnames_option.list'
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	17 #if str($cut_type_options.delimiter) != '':
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	18 -d"$cut_type_options.delimiter"
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	19 #end if
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	20 #end if
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	21 '$input'
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	22 > '$output'
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	23 ]]>
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	24 </command>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	25 <inputs>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	26 <param name="input" format="txt" type="data" label="File to cut" />
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	27 <param name="complement" type="select" label="Operation">
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	28 <option value="">Keep</option>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	29 <option value="--complement">Discard</option>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	30 </param>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	31 <conditional name="cut_type_options">
56e80527c482 Uploaded bgruening parents: 3 diff changeset	32 <param name="cut_element" type="select" label="Cut by">
56e80527c482 Uploaded bgruening parents: 3 diff changeset	33 <option value="-f">fields</option>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	34 <option value="-c">characters</option>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	35 </param>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	36 <when value="-f">
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	37 <param name="delimiter" type="select" label="Delimited by">
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	38 <option value="">Tab</option>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	39 <option value=" ">Whitespace</option>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	40 <option value=".">Dot</option>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	41 <option value=",">Comma</option>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	42 <option value="-">Dash</option>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	43 <option value="_">Underscore</option>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	44 <option value="\|">Pipe</option>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	45 </param>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	46 <conditional name="colnames_option">
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	47 <param name="header" type="select" label="Is there a header for the data's columns ?">
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	48 <option value="Y">Yes</option>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	49 <option value="N" selected="true">No</option>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	50 </param>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	51 <when value="Y">
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	52 <param name="list" type="data_column" data_ref="input" use_header_names="true" multiple="true" label="List of Fields" help="(-f)" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	53 </when>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	54 <when value="N">
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	55 <param name="list" type="data_column" data_ref="input" multiple="true" label="List of Fields" help="(-f)" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	56 </when>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	57 </conditional>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	58 </when>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	59 <when value="-c">
10 c78b1767db2b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty bgruening parents: 7 diff changeset	60 <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">
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	61 <sanitizer>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	62 <valid initial="string.printable">
56e80527c482 Uploaded bgruening parents: 3 diff changeset	63 <remove value="'"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	64 </valid>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	65 </sanitizer>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	66 </param>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	67 </when>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	68 </conditional>
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	69 </inputs>
1 a4ad586d1403 Uploaded bgruening parents: 0 diff changeset	70 <outputs>
a4ad586d1403 Uploaded bgruening parents: 0 diff changeset	71 <!--<data format="tabular" name="output" />-->
a4ad586d1403 Uploaded bgruening parents: 0 diff changeset	72 <!-- WIP, not sure that will work with the complement option -->
a4ad586d1403 Uploaded bgruening parents: 0 diff changeset	73 <data format="tabular" name="output">
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	74 <actions>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	75 <conditional name="cut_type_options.cut_element">
56e80527c482 Uploaded bgruening parents: 3 diff changeset	76 <!-- fields -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	77 <when value="-f">
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	78 <conditional name="cut_type_options.delimiter">
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	79 <when value="T">
56e80527c482 Uploaded bgruening parents: 3 diff changeset	80 <conditional name="input">
56e80527c482 Uploaded bgruening parents: 3 diff changeset	81 <when datatype_isinstance="interval">
56e80527c482 Uploaded bgruening parents: 3 diff changeset	82 <action type="format" default="tabular">
56e80527c482 Uploaded bgruening parents: 3 diff changeset	83 <option type="from_param" name="list" column="0" offset="0"> <!-- chromCol is 1-->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	84 <filter type="insert_column" column="0" value="interval"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	85 <filter type="insert_column" ref="list" /> <!-- startCol -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	86 <filter type="insert_column" ref="list" /> <!-- endCol -->
1 a4ad586d1403 Uploaded bgruening parents: 0 diff changeset	87
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	88 <filter type="multiple_splitter" column="1" separator=","/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	89 <filter type="column_strip" column="1"/> <!-- get rid of all external whitespace -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	90 <filter type="string_function" column="1" name="lower" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	91 <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	92 <filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	93 <filter type="boolean" column="1" cast="int" />
1 a4ad586d1403 Uploaded bgruening parents: 0 diff changeset	94
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	95 <filter type="multiple_splitter" column="2" separator=","/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	96 <filter type="column_strip" column="2"/> <!-- get rid of all external whitespace -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	97 <filter type="string_function" column="2" name="lower" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	98 <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	99 <filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	100 <filter type="boolean" column="2" cast="int" />
1 a4ad586d1403 Uploaded bgruening parents: 0 diff changeset	101
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	102 <filter type="multiple_splitter" column="3" separator=","/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	103 <filter type="column_strip" column="3"/> <!-- get rid of all external whitespace -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	104 <filter type="string_function" column="3" name="lower" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	105 <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	106 <filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	107 <filter type="boolean" column="3" cast="int" />
1 a4ad586d1403 Uploaded bgruening parents: 0 diff changeset	108
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	109 <filter type="metadata_value" ref="input" name="chromCol" column="1" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	110 <filter type="metadata_value" ref="input" name="startCol" column="2" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	111 <filter type="metadata_value" ref="input" name="endCol" column="3" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	112 </option>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	113 </action>
14 7725ab6dab67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: 10 diff changeset	114 </when>
7725ab6dab67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: 10 diff changeset	115 </conditional>
7725ab6dab67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: 10 diff changeset	116 </when>
7725ab6dab67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: 10 diff changeset	117 </conditional>
1 a4ad586d1403 Uploaded bgruening parents: 0 diff changeset	118 <conditional name="output">
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	119 <when datatype_isinstance="interval">
56e80527c482 Uploaded bgruening parents: 3 diff changeset	120 <action type="metadata" name="chromCol">
56e80527c482 Uploaded bgruening parents: 3 diff changeset	121 <option type="from_param" name="list" column="0" offset="0"> <!-- chromCol is 0-->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	122 <filter type="multiple_splitter" column="0" separator=","/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	123 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	124 <filter type="string_function" column="0" name="lower" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	125 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	126 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	127 <filter type="insert_column" value="1" iterate="True" column="0"/>
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	128 <filter type="boolean" column="1" cast="int" />
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	129 <filter type="metadata_value" ref="input" name="chromCol" column="1" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	130 </option>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	131 </action>
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	132
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	133 <action type="metadata" name="startCol">
56e80527c482 Uploaded bgruening parents: 3 diff changeset	134 <option type="from_param" name="list" column="0" offset="0"> <!-- startCol is 0-->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	135 <filter type="multiple_splitter" column="0" separator=","/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	136 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	137 <filter type="string_function" column="0" name="lower" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	138 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	139 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	140 <filter type="insert_column" value="1" iterate="True" column="0"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	141 <filter type="boolean" column="1" cast="int" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	142 <filter type="metadata_value" ref="input" name="startCol" column="1" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	143 </option>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	144 </action>
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	145
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	146 <action type="metadata" name="endCol">
56e80527c482 Uploaded bgruening parents: 3 diff changeset	147 <option type="from_param" name="list" column="0" offset="0"> <!-- endCol is 0-->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	148 <filter type="multiple_splitter" column="0" separator=","/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	149 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	150 <filter type="string_function" column="0" name="lower" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	151 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	152 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	153 <filter type="insert_column" value="1" iterate="True" column="0"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	154 <filter type="boolean" column="1" cast="int" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	155 <filter type="metadata_value" ref="input" name="endCol" column="1" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	156 </option>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	157 </action>
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	158
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	159 <action type="metadata" name="nameCol" default="0">
56e80527c482 Uploaded bgruening parents: 3 diff changeset	160 <option type="from_param" name="list" column="0" offset="0"> <!-- nameCol is 0-->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	161 <filter type="multiple_splitter" column="0" separator=","/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	162 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	163 <filter type="string_function" column="0" name="lower" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	164 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	165 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	166 <filter type="insert_column" value="1" iterate="True" column="0"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	167 <filter type="boolean" column="1" cast="int" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	168 <filter type="metadata_value" ref="input" name="nameCol" column="1" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	169 </option>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	170 </action>
7 d64eace4f9f3 Uploaded bgruening parents: 6 diff changeset	171
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	172 <action type="metadata" name="strandCol" default="0">
56e80527c482 Uploaded bgruening parents: 3 diff changeset	173 <option type="from_param" name="list" column="0" offset="0"> <!-- strandCol is 0-->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	174 <filter type="multiple_splitter" column="0" separator=","/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	175 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	176 <filter type="string_function" column="0" name="lower" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	177 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	178 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
56e80527c482 Uploaded bgruening parents: 3 diff changeset	179 <filter type="insert_column" value="1" iterate="True" column="0"/>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	180 <filter type="boolean" column="1" cast="int" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	181 <filter type="metadata_value" ref="input" name="strandCol" column="1" />
56e80527c482 Uploaded bgruening parents: 3 diff changeset	182 </option>
56e80527c482 Uploaded bgruening parents: 3 diff changeset	183 </action>
14 7725ab6dab67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: 10 diff changeset	184 </when>
1 a4ad586d1403 Uploaded bgruening parents: 0 diff changeset	185 </conditional>
14 7725ab6dab67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: 10 diff changeset	186 </when>
1 a4ad586d1403 Uploaded bgruening parents: 0 diff changeset	187 </conditional>
14 7725ab6dab67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: 10 diff changeset	188 </actions>
1 a4ad586d1403 Uploaded bgruening parents: 0 diff changeset	189 </data>
a4ad586d1403 Uploaded bgruening parents: 0 diff changeset	190 </outputs>
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	191 <tests>
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	192 <test expect_num_outputs="1">
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	193 <param name="input" value="cut1.txt"/>
27 08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	194 <conditional name="cut_type_options">
08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	195 <param name="cut_element" value="-f"/>
08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	196 <param name="delimiter" value="" />
08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	197 <conditional name="colnames_option">
08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	198 <param name="header" value="Y"/>
08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	199 <param name="list" value="1,3,4"/>
08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	200 </conditional>
08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	201 </conditional>
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	202 <output name="output" file="cut_results1.txt"/>
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	203 <assert_command>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	204 <has_text text="-f '1,3,4'"/>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	205 </assert_command>
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	206 </test>
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	207 <test expect_num_outputs="1">
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	208 <param name="input" value="cut1.txt"/>
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	209 <conditional name="cut_type_options">
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	210 <param name="delimiter" value="" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	211 <conditional name="colnames_option">
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	212 <param name="header" value="Y"/>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	213 <!-- in the test we can (apparently) not select by header name -->
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	214 <param name="list" value="2" />
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	215 </conditional>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	216 </conditional>
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	217 <param name="complement" value="--complement" />
8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	218 <output name="output" file="cut_results2.txt"/>
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	219 <assert_command>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	220 <has_text text="-f '2'"/>
f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	221 </assert_command>
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	222 </test>
26 f22a309187a3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7 bgruening parents: 23 diff changeset	223 <test expect_num_outputs="1">
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	224 <param name="input" value="cut1.txt"/>
27 08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	225 <conditional name="cut_type_options">
08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	226 <param name="cut_element" value="-c" />
08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	227 <param name="list" value="-3" />
08cdbfffce67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b bgruening parents: 26 diff changeset	228 </conditional>
6 8928e6d1e7ba Uploaded bgruening parents: 4 diff changeset	229 <output name="output" file="cut_results3.txt"/>
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	230 </test>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	231 </tests>
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	232 <help>
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	233 <![CDATA[
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	234 What it does
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	235
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	236 This tool runs the cut unix command, which extract or delete columns from a file.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	237
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	238 -----
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	239
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	240 Field List Example:
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	241
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	242 1,3,7 - Cut specific fields/characters.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	243
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	244 3- - Cut from the third field/character to the end of the line.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	245
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	246 2-5 - Cut from the second to the fifth field/character.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	247
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	248 -8 - Cut from the first to the eight field/characters.
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	249
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	250
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	251 Input Example::
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	252
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	253 fruit color price weight
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	254 apple red 1.4 0.5
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	255 orange orange 1.5 0.3
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	256 banana yellow 0.9 0.3
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	257
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	258
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	259 Output Example ( Keeping fields 1,3,4 )::
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	260
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	261 fruit price weight
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	262 apple 1.4 0.5
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	263 orange 1.5 0.3
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	264 banana 0.9 0.3
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	265
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	266 Output Example ( Discarding field 2 )::
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	267
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	268 fruit price weight
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	269 apple 1.4 0.5
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	270 orange 1.5 0.3
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	271 banana 0.9 0.3
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	272
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	273 Output Example ( Keeping 3 characters )::
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	274
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	275 fru
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	276 app
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	277 ora
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	278 ban
ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	279
4 56e80527c482 Uploaded bgruening parents: 3 diff changeset	280 @REFERENCES@
56e80527c482 Uploaded bgruening parents: 3 diff changeset	281 ]]>
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	282 </help>
14 7725ab6dab67 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n' bgruening parents: 10 diff changeset	283 <expand macro="citations" />
0 ec66f9d90ef0 initial uploaded bgruening parents: diff changeset	284 </tool>

Mercurial > repos > bgruening > text_processing

annotate cut.xml @ 29:4f7cade041cb draft default tip