Mercurial > repos > bgruening > text_processing
annotate 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 |
| rev | line source |
|---|---|
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26
f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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changeset
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1 <tool id="tp_cut_tool" name="Advanced Cut" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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2 <description>columns from a table (cut)</description> |
| 4 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <version_command>cut --version | head -n 1</version_command> | |
| 0 | 8 <command> |
| 4 | 9 <![CDATA[ |
| 10 cut | |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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11 $complement |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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12 $cut_type_options.cut_element |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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13 #if $cut_type_options.cut_element != '-f' |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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14 '$cut_type_options.list' |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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15 #else |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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16 '$cut_type_options.colnames_option.list' |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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17 #if str($cut_type_options.delimiter) != '': |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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18 -d"$cut_type_options.delimiter" |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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19 #end if |
| 4 | 20 #end if |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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21 '$input' |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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22 > '$output' |
| 4 | 23 ]]> |
| 0 | 24 </command> |
| 25 <inputs> | |
| 4 | 26 <param name="input" format="txt" type="data" label="File to cut" /> |
| 0 | 27 <param name="complement" type="select" label="Operation"> |
| 28 <option value="">Keep</option> | |
| 29 <option value="--complement">Discard</option> | |
| 30 </param> | |
| 4 | 31 <conditional name="cut_type_options"> |
| 32 <param name="cut_element" type="select" label="Cut by"> | |
| 33 <option value="-f">fields</option> | |
| 34 <option value="-c">characters</option> | |
| 35 </param> | |
| 36 <when value="-f"> | |
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26
f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
parents:
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37 <param name="delimiter" type="select" label="Delimited by"> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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38 <option value="">Tab</option> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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39 <option value=" ">Whitespace</option> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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40 <option value=".">Dot</option> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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41 <option value=",">Comma</option> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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42 <option value="-">Dash</option> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
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43 <option value="_">Underscore</option> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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44 <option value="|">Pipe</option> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
parents:
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45 </param> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
parents:
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changeset
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46 <conditional name="colnames_option"> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
parents:
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47 <param name="header" type="select" label="Is there a header for the data's columns ?"> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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48 <option value="Y">Yes</option> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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49 <option value="N" selected="true">No</option> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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50 </param> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
parents:
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changeset
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51 <when value="Y"> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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52 <param name="list" type="data_column" data_ref="input" use_header_names="true" multiple="true" label="List of Fields" help="(-f)" /> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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53 </when> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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changeset
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54 <when value="N"> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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changeset
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55 <param name="list" type="data_column" data_ref="input" multiple="true" label="List of Fields" help="(-f)" /> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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56 </when> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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changeset
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57 </conditional> |
| 4 | 58 </when> |
| 59 <when value="-c"> | |
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c78b1767db2b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
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changeset
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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 | 61 <sanitizer> |
| 62 <valid initial="string.printable"> | |
| 63 <remove value="'"/> | |
| 64 </valid> | |
| 65 </sanitizer> | |
| 66 </param> | |
| 67 </when> | |
| 68 </conditional> | |
| 0 | 69 </inputs> |
| 1 | 70 <outputs> |
| 71 <!--<data format="tabular" name="output" />--> | |
| 72 <!-- WIP, not sure that will work with the complement option --> | |
| 73 <data format="tabular" name="output"> | |
| 4 | 74 <actions> |
| 75 <conditional name="cut_type_options.cut_element"> | |
| 76 <!-- fields --> | |
| 77 <when value="-f"> | |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
parents:
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78 <conditional name="cut_type_options.delimiter"> |
| 4 | 79 <when value="T"> |
| 80 <conditional name="input"> | |
| 81 <when datatype_isinstance="interval"> | |
| 82 <action type="format" default="tabular"> | |
| 83 <option type="from_param" name="list" column="0" offset="0"> <!-- chromCol is 1--> | |
| 84 <filter type="insert_column" column="0" value="interval"/> | |
| 85 <filter type="insert_column" ref="list" /> <!-- startCol --> | |
| 86 <filter type="insert_column" ref="list" /> <!-- endCol --> | |
| 1 | 87 |
| 4 | 88 <filter type="multiple_splitter" column="1" separator=","/> |
| 89 <filter type="column_strip" column="1"/> <!-- get rid of all external whitespace --> | |
| 90 <filter type="string_function" column="1" name="lower" /> | |
| 91 <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/> | |
| 92 <filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's --> | |
| 93 <filter type="boolean" column="1" cast="int" /> | |
| 1 | 94 |
| 4 | 95 <filter type="multiple_splitter" column="2" separator=","/> |
| 96 <filter type="column_strip" column="2"/> <!-- get rid of all external whitespace --> | |
| 97 <filter type="string_function" column="2" name="lower" /> | |
| 98 <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/> | |
| 99 <filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's --> | |
| 100 <filter type="boolean" column="2" cast="int" /> | |
| 1 | 101 |
| 4 | 102 <filter type="multiple_splitter" column="3" separator=","/> |
| 103 <filter type="column_strip" column="3"/> <!-- get rid of all external whitespace --> | |
| 104 <filter type="string_function" column="3" name="lower" /> | |
| 105 <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/> | |
| 106 <filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's --> | |
| 107 <filter type="boolean" column="3" cast="int" /> | |
| 1 | 108 |
| 4 | 109 <filter type="metadata_value" ref="input" name="chromCol" column="1" /> |
| 110 <filter type="metadata_value" ref="input" name="startCol" column="2" /> | |
| 111 <filter type="metadata_value" ref="input" name="endCol" column="3" /> | |
| 112 </option> | |
| 113 </action> | |
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7725ab6dab67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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114 </when> |
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7725ab6dab67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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115 </conditional> |
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7725ab6dab67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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116 </when> |
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7725ab6dab67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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117 </conditional> |
| 1 | 118 <conditional name="output"> |
| 4 | 119 <when datatype_isinstance="interval"> |
| 120 <action type="metadata" name="chromCol"> | |
| 121 <option type="from_param" name="list" column="0" offset="0"> <!-- chromCol is 0--> | |
| 122 <filter type="multiple_splitter" column="0" separator=","/> | |
| 123 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> | |
| 124 <filter type="string_function" column="0" name="lower" /> | |
| 125 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> | |
| 126 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> | |
| 127 <filter type="insert_column" value="1" iterate="True" column="0"/> | |
| 7 | 128 <filter type="boolean" column="1" cast="int" /> |
| 4 | 129 <filter type="metadata_value" ref="input" name="chromCol" column="1" /> |
| 130 </option> | |
| 131 </action> | |
| 7 | 132 |
| 4 | 133 <action type="metadata" name="startCol"> |
| 134 <option type="from_param" name="list" column="0" offset="0"> <!-- startCol is 0--> | |
| 135 <filter type="multiple_splitter" column="0" separator=","/> | |
| 136 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> | |
| 137 <filter type="string_function" column="0" name="lower" /> | |
| 138 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> | |
| 139 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> | |
| 140 <filter type="insert_column" value="1" iterate="True" column="0"/> | |
| 141 <filter type="boolean" column="1" cast="int" /> | |
| 142 <filter type="metadata_value" ref="input" name="startCol" column="1" /> | |
| 143 </option> | |
| 144 </action> | |
| 7 | 145 |
| 4 | 146 <action type="metadata" name="endCol"> |
| 147 <option type="from_param" name="list" column="0" offset="0"> <!-- endCol is 0--> | |
| 148 <filter type="multiple_splitter" column="0" separator=","/> | |
| 149 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> | |
| 150 <filter type="string_function" column="0" name="lower" /> | |
| 151 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> | |
| 152 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> | |
| 153 <filter type="insert_column" value="1" iterate="True" column="0"/> | |
| 154 <filter type="boolean" column="1" cast="int" /> | |
| 155 <filter type="metadata_value" ref="input" name="endCol" column="1" /> | |
| 156 </option> | |
| 157 </action> | |
| 7 | 158 |
| 4 | 159 <action type="metadata" name="nameCol" default="0"> |
| 160 <option type="from_param" name="list" column="0" offset="0"> <!-- nameCol is 0--> | |
| 161 <filter type="multiple_splitter" column="0" separator=","/> | |
| 162 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> | |
| 163 <filter type="string_function" column="0" name="lower" /> | |
| 164 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> | |
| 165 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> | |
| 166 <filter type="insert_column" value="1" iterate="True" column="0"/> | |
| 167 <filter type="boolean" column="1" cast="int" /> | |
| 168 <filter type="metadata_value" ref="input" name="nameCol" column="1" /> | |
| 169 </option> | |
| 170 </action> | |
| 7 | 171 |
| 4 | 172 <action type="metadata" name="strandCol" default="0"> |
| 173 <option type="from_param" name="list" column="0" offset="0"> <!-- strandCol is 0--> | |
| 174 <filter type="multiple_splitter" column="0" separator=","/> | |
| 175 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace --> | |
| 176 <filter type="string_function" column="0" name="lower" /> | |
| 177 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> | |
| 178 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's --> | |
| 179 <filter type="insert_column" value="1" iterate="True" column="0"/> | |
| 180 <filter type="boolean" column="1" cast="int" /> | |
| 181 <filter type="metadata_value" ref="input" name="strandCol" column="1" /> | |
| 182 </option> | |
| 183 </action> | |
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7725ab6dab67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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changeset
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184 </when> |
| 1 | 185 </conditional> |
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14
7725ab6dab67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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186 </when> |
| 1 | 187 </conditional> |
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7725ab6dab67
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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188 </actions> |
| 1 | 189 </data> |
| 190 </outputs> | |
| 0 | 191 <tests> |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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192 <test expect_num_outputs="1"> |
| 6 | 193 <param name="input" value="cut1.txt"/> |
| 194 <param name="list" value="1,3,4"/> | |
| 195 <param name="delimiter" value=""/> | |
| 196 <output name="output" file="cut_results1.txt"/> | |
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f22a309187a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
bgruening
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197 <assert_command> |
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198 <has_text text="-f '1,3,4'"/> |
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199 </assert_command> |
| 0 | 200 </test> |
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201 |
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202 <test expect_num_outputs="1"> |
| 6 | 203 <param name="input" value="cut1.txt"/> |
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204 <conditional name="cut_type_options"> |
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205 <param name="delimiter" value="" /> |
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206 <conditional name="colnames_option"> |
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207 <param name="header" value="Y"/> |
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208 <!-- in the test we can (apparently) not select by header name --> |
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209 <param name="list" value="2" /> |
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210 </conditional> |
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211 </conditional> |
| 6 | 212 <param name="complement" value="--complement" /> |
| 213 <output name="output" file="cut_results2.txt"/> | |
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214 <assert_command> |
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215 <has_text text="-f '2'"/> |
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216 </assert_command> |
| 6 | 217 </test> |
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218 <test expect_num_outputs="1"> |
| 6 | 219 <param name="input" value="cut1.txt"/> |
| 220 <param name="list" value="-3" /> | |
| 221 <param name="delimiter" value="" /> | |
| 222 <param name="cut_element" value="-c" /> | |
| 223 <output name="output" file="cut_results3.txt"/> | |
| 0 | 224 </test> |
| 225 </tests> | |
| 226 <help> | |
| 4 | 227 <![CDATA[ |
| 0 | 228 **What it does** |
| 229 | |
| 230 This tool runs the **cut** unix command, which extract or delete columns from a file. | |
| 231 | |
| 232 ----- | |
| 233 | |
| 234 Field List Example: | |
| 235 | |
| 236 **1,3,7** - Cut specific fields/characters. | |
| 237 | |
| 238 **3-** - Cut from the third field/character to the end of the line. | |
| 239 | |
| 240 **2-5** - Cut from the second to the fifth field/character. | |
| 241 | |
| 242 **-8** - Cut from the first to the eight field/characters. | |
| 243 | |
| 244 | |
| 245 Input Example:: | |
| 246 | |
| 247 fruit color price weight | |
| 248 apple red 1.4 0.5 | |
| 249 orange orange 1.5 0.3 | |
| 250 banana yellow 0.9 0.3 | |
| 251 | |
| 252 | |
| 253 Output Example ( **Keeping fields 1,3,4** ):: | |
| 254 | |
| 255 fruit price weight | |
| 256 apple 1.4 0.5 | |
| 257 orange 1.5 0.3 | |
| 258 banana 0.9 0.3 | |
| 259 | |
| 260 Output Example ( **Discarding field 2** ):: | |
| 261 | |
| 262 fruit price weight | |
| 263 apple 1.4 0.5 | |
| 264 orange 1.5 0.3 | |
| 265 banana 0.9 0.3 | |
| 266 | |
| 267 Output Example ( **Keeping 3 characters** ):: | |
| 268 | |
| 269 fru | |
| 270 app | |
| 271 ora | |
| 272 ban | |
| 273 | |
| 4 | 274 @REFERENCES@ |
| 275 ]]> | |
| 0 | 276 </help> |
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277 <expand macro="citations" /> |
| 0 | 278 </tool> |