Mercurial > repos > devteam > cut_columns

annotate cutWrapper.xml @ 3:cec635fab700 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
author devteam
date Fri, 05 Aug 2016 16:38:13 -0400
parents 842fab69c940
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
1 <tool id="Cut1" name="Cut" version="1.0.2">
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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2 <description>columns from a table</description>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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3 <command>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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4 perl $__tool_directory__/cutWrapper.pl
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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5 "${input}"
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
6 "${columnList}"
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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7 "${delimiter}"
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
8 "${out_file1}"
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
9 </command>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
10 <inputs>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
11 <param name="columnList" type="text" value="c1,c2" label="Cut columns"/>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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12 <param name="delimiter" type="select" label="Delimited by">
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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13 <option value="T">Tab</option>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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14 <option value="Sp">Whitespace</option>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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15 <option value="Dt">Dot</option>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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16 <option value="C">Comma</option>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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17 <option value="D">Dash</option>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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18 <option value="U">Underscore</option>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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19 <option value="P">Pipe</option>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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20 </param>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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21 <param format="txt" name="input" type="data" label="From"/>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
22 </inputs>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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23 <outputs>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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24 <data format="tabular" name="out_file1" >
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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25 <actions>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
26 <conditional name="delimiter">
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
27 <when value="T">
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
28 <conditional name="input">
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
29 <when datatype_isinstance="interval">
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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30 <action type="format" default="tabular">
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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31 <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 1-->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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32
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
33 <filter type="insert_column" column="0" value="interval"/>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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34
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
35 <filter type="insert_column" ref="columnList" /> <!-- startCol -->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
36
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
37 <filter type="insert_column" ref="columnList" /> <!-- endCol -->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
38
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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39 <filter type="multiple_splitter" column="1" separator=","/>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
40 <filter type="column_strip" column="1"/> <!-- get rid of all external whitespace -->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
41 <filter type="string_function" column="1" name="lower" />
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
42 <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
43 <filter type="column_strip" column="1" strip="c"/> <!-- get rid of c's -->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
44 <filter type="boolean" column="1" cast="int" />
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
45
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
46 <filter type="multiple_splitter" column="2" separator=","/>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
47 <filter type="column_strip" column="2"/> <!-- get rid of all external whitespace -->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
48 <filter type="string_function" column="2" name="lower" />
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
49 <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
50 <filter type="column_strip" column="2" strip="c"/> <!-- get rid of c's -->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
51 <filter type="boolean" column="2" cast="int" />
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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52
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
53 <filter type="multiple_splitter" column="3" separator=","/>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
54 <filter type="column_strip" column="3"/> <!-- get rid of all external whitespace -->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
55 <filter type="string_function" column="3" name="lower" />
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
56 <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
57 <filter type="column_strip" column="3" strip="c"/> <!-- get rid of c's -->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
58 <filter type="boolean" column="3" cast="int" />
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
59
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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60 <filter type="metadata_value" ref="input" name="chromCol" column="1" />
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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61 <filter type="metadata_value" ref="input" name="startCol" column="2" />
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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62 <filter type="metadata_value" ref="input" name="endCol" column="3" />
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
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parents: 2
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63
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
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parents: 2
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64 </option>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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65 </action>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
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parents: 2
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66
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
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parents: 2
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67 <conditional name="out_file1">
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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68 <when datatype_isinstance="interval">
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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69 <action type="metadata" name="chromCol">
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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70 <option type="from_param" name="columnList" column="0" offset="0"> <!-- chromCol is 0-->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
71 <filter type="multiple_splitter" column="0" separator=","/>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
72 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
73 <filter type="string_function" column="0" name="lower" />
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
74 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
75 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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76 <filter type="insert_column" value="1" iterate="True" column="0"/>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
77 <filter type="boolean" column="1" cast="int" />
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
78 <filter type="metadata_value" ref="input" name="chromCol" column="1" />
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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79 </option>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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80 </action>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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81
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
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parents: 2
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82 <action type="metadata" name="startCol">
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
83 <option type="from_param" name="columnList" column="0" offset="0"> <!-- startCol is 0-->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
84 <filter type="multiple_splitter" column="0" separator=","/>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
85 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
86 <filter type="string_function" column="0" name="lower" />
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
87 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
diff changeset
88 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
devteam
parents: 2
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89 <filter type="insert_column" value="1" iterate="True" column="0"/>
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90 <filter type="boolean" column="1" cast="int" />
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91 <filter type="metadata_value" ref="input" name="startCol" column="1" />
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92 </option>
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93 </action>
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94
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95 <action type="metadata" name="endCol">
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96 <option type="from_param" name="columnList" column="0" offset="0"> <!-- endCol is 0-->
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97 <filter type="multiple_splitter" column="0" separator=","/>
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98 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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99 <filter type="string_function" column="0" name="lower" />
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100 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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101 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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102 <filter type="insert_column" value="1" iterate="True" column="0"/>
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103 <filter type="boolean" column="1" cast="int" />
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104 <filter type="metadata_value" ref="input" name="endCol" column="1" />
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105 </option>
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106 </action>
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107
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108 <action type="metadata" name="nameCol" default="0">
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109 <option type="from_param" name="columnList" column="0" offset="0"> <!-- nameCol is 0-->
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110 <filter type="multiple_splitter" column="0" separator=","/>
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111 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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112 <filter type="string_function" column="0" name="lower" />
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113 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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114 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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115 <filter type="insert_column" value="1" iterate="True" column="0"/>
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116 <filter type="boolean" column="1" cast="int" />
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117 <filter type="metadata_value" ref="input" name="nameCol" column="1" />
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118 </option>
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119 </action>
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120
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121 <action type="metadata" name="strandCol" default="0">
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122 <option type="from_param" name="columnList" column="0" offset="0"> <!-- strandCol is 0-->
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
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123 <filter type="multiple_splitter" column="0" separator=","/>
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124 <filter type="column_strip" column="0"/> <!-- get rid of all external whitespace -->
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125 <filter type="string_function" column="0" name="lower" />
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126 <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/>
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127 <filter type="column_strip" column="0" strip="c"/> <!-- get rid of c's -->
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128 <filter type="insert_column" value="1" iterate="True" column="0"/>
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129 <filter type="boolean" column="1" cast="int" />
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130 <filter type="metadata_value" ref="input" name="strandCol" column="1" />
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131 </option>
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132 </action>
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133 </when>
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134 </conditional>
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135
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136 </when>
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137 </conditional>
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138 </when>
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139 </conditional>
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140 </actions>
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141 </data>
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142 </outputs>
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143 <tests>
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144 <test>
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145 <param name="columnList" value="c1,c4,c2,c3"/>
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146 <param name="delimiter" value="T"/>
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147 <param name="input" value="1.bed"/>
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148 <output name="out_file1" file="eq-cut.dat"/>
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149 </test>
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150 <test>
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151 <param name="columnList" value="c1,c4,c2-c3" />
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152 <param name="delimiter" value="T" />
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153 <param name="input" value="1.bed" />
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154 <output name="out_file1" file="eq-cut.dat" />
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155 </test>
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156 </tests>
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157 <help>
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158
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159 .. class:: warningmark
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160
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161 **WARNING: This tool breaks column assignments.** To re-establish column assignments run the tools and click on the pencil icon in the latest history item.
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162
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163 .. class:: infomark
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164
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165 The output of this tool is always in tabular format (e.g., if your original delimiters are commas, they will be replaced with tabs). For example:
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166
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167 Cutting columns 1 and 3 from::
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168
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169 apple,is,good
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170 windows,is,bad
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171 linux,is,best
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172
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173 will give::
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174
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
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175 apple good
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
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176 windows bad
cec635fab700 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns commit e3d5231ad1ca93ad49117e9804266f371d863e82
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177 linux best
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178
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179 -----
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180
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181 **What it does**
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182
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183 This tool selects (cuts out) specified columns from the dataset.
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184
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185 - Columns are specified as **c1**, **c2**, and so on. Column count begins with **1**
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186 - Columns can be specified in any order (e.g., **c2,c1,c6**)
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187 - If you specify more columns than actually present - empty spaces will be filled with dots
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188
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189 -----
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190
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191 **Example**
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192
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193 Input dataset (six columns: c1, c2, c3, c4, c5, and c6)::
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194
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195 chr1 10 1000 gene1 0 +
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196 chr2 100 1500 gene2 0 +
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197
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198 **cut** on columns "**c1,c4,c6**" will return::
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199
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200 chr1 gene1 +
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201 chr2 gene2 +
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202
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203 **cut** on columns "**c6,c5,c4,c1**" will return::
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204
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205 + 0 gene1 chr1
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206 + 0 gene2 chr2
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207
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208 **cut** on columns "**c1-c3**" will return::
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209
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210 chr1 10 1000
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211 chr2 100 1500
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212
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213
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214 **cut** on columns "**c8,c7,c4**" will return::
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215
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216 . . gene1
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217 . . gene2
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218 </help>
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219 </tool>