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comparison sorted_uniq.xml @ 26:f22a309187a3 draft

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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 1e974b82380d
children 08cdbfffce67
comparison
equal deleted inserted replaced
25:cd83b5644eab 26:f22a309187a3
1 <tool id="tp_uniq_tool" name="Unique lines" version="@BASE_VERSION@.1"> 1 <tool id="tp_uniq_tool" name="Unique lines" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>assuming sorted input file</description> 2 <description>assuming sorted input file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="creator"/>
6 <expand macro="requirements"> 7 <expand macro="requirements">
7 <requirement type="package" version="4.4">sed</requirement> 8 <requirement type="package" version="4.8">sed</requirement>
8 </expand> 9 </expand>
9 <version_command>uniq --version | head -n 1</version_command> 10 <version_command>uniq --version | head -n 1</version_command>
10 <command> 11 <command>
11 <![CDATA[ 12 <![CDATA[
12 uniq 13 uniq
21 $grouping.count 22 $grouping.count
22 $grouping.repeated 23 $grouping.repeated
23 $grouping.uniqueonly 24 $grouping.uniqueonly
24 #end if 25 #end if
25 26
26 "$infile" 27 '$infile'
27 28
28 #if $grouping.grouping_select == 'no' and $grouping.count: 29 #if $grouping.grouping_select == 'no' and $grouping.count:
29 ## count will print the count with spaces in front of the line and 30 ## count will print the count with spaces in front of the line and
30 ## with a space (not a tab) after the number, we need to cahnge that 31 ## with a space (not a tab) after the number, we need to cahnge that
31 | sed -e 's/ *//' -e 's/ /\t/' 32 | sed -e 's/ *//' -e 's/ /\t/'
32 #end if 33 #end if
33 > "$outfile" 34 > '$outfile'
34 ]]> 35 ]]>
35 </command> 36 </command>
36 <inputs> 37 <inputs>
37 <param name="infile" format="tabular" type="data" 38 <param name="infile" format="tabular" type="data"
38 label="File to scan for unique values" help="Make sure you have sorted this file" /> 39 label="File to scan for unique values" help="Make sure you have sorted this file" />
97 98
98 .. class:: infomark 99 .. class:: infomark
99 100
100 You can sort your file using either the "Sort" tool in "Filter and Sort", or the "Sort" tool in "Unix Tools". 101 You can sort your file using either the "Sort" tool in "Filter and Sort", or the "Sort" tool in "Unix Tools".
101 102
102 @REFERENCES@
103 ]]> 103 ]]>
104 </help> 104 </help>
105 <expand macro="citations" /> 105 <expand macro="citations" />
106 </tool> 106 </tool>