Mercurial > repos > bgruening > text_processing

annotate unsorted_uniq.xml @ 25:ab83aa685821 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
author bgruening
date Sat, 17 Jan 2026 00:57:38 +0000
parents 3dc70b59608c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
12615d397df7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
bgruening
parents: 6
diff changeset
1 <tool id="tp_sorted_uniq" name="Unique" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
2 <description>occurrences of each record</description>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
3 <macros>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
4 <import>macros.xml</import>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
5 </macros>
19
12615d397df7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
bgruening
parents: 6
diff changeset
6 <expand macro="creator"/>
25
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
7 <expand macro="requirements">
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
8 <requirement type="package" version="4.9">sed</requirement>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
9 </expand>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
10 <version_command>sort --version | head -n 1</version_command>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
11 <command>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
12 <![CDATA[
25
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
13 (
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
14 export LC_ALL=C;
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
15 #if int($header) > 0:
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
16 sed -u '${header}'q &&
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
17 #end if
25
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
18 sort -u
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
19 $ignore_case
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
20 $is_numeric
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
21 -t ' '
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
22 #if $adv_opts.adv_opts_selector == "advanced":
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
23 -k$adv_opts.column_start,$adv_opts.column_end
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
24 #end if
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
25 ) < '$infile' > '$outfile'
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
26 ]]>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
27 </command>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
28 <inputs>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
29 <param name="infile" type="data" format="tabular" label="File to scan for unique values" />
25
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
30 <param name="ignore_case" type="boolean" truevalue="-f" falsevalue=""
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
31 label="Ignore differences in case when comparing" help="(-f)"/>
25
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
32 <param name="is_numeric" type="boolean" truevalue="-n" falsevalue=""
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
33 label="Compare numeric values at start of records" help="This will try to detect numeric values at the start of each record and base comparisons only on these numbers (or the empty string if no starting number is found) (-n)." />
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
34 <param name="header" type="integer" value="0" label="Number of header lines" help="These will be ignored during sort.">
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
35 <validator type="in_range" message="Negative values are not allowed." min="0"/>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
36 </param>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
37 <conditional name="adv_opts">
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
38 <param name="adv_opts_selector" type="select" label="Advanced Options">
25
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
39 <option value="basic" selected="true">Hide Advanced Options</option>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
40 <option value="advanced">Show Advanced Options</option>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
41 </param>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
42 <when value="basic" />
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
43 <when value="advanced">
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
44 <param name="column_start" type="data_column" data_ref="infile" label="Column start" help="Unique on specific column range"/>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
45 <param name="column_end" type="data_column" data_ref="infile" label="Column end" help="Unique on specific column range"/>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
46 </when>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
47 </conditional>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
48 </inputs>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
49 <outputs>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
50 <data name="outfile" format_source="infile" metadata_source="infile"/>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
51 </outputs>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
52 <tests>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
53 <test>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
54 <param name="infile" value="1.bed"/>
25
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
55 <param name="is_numeric" value="true"/>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
56 <param name="ignore_case" value="true"/>
22
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
57 <conditional name="adv_opts">
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
58 <param name="adv_opts_selector" value="advanced"/>
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
59 <param name="column_start" value="2"/>
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
60 <param name="column_end" value="3"/>
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
61 </conditional>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
62 <output name="outfile" file="unique_results1.bed"/>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
63 </test>
25
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
64 <test>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
65 <param name="infile" value="1.bed"/>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
66 <param name="is_numeric" value="true"/>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
67 <param name="ignore_case" value="true"/>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
68 <param name="header" value="1"/>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
69 <conditional name="adv_opts">
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
70 <param name="adv_opts_selector" value="advanced"/>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
71 <param name="column_start" value="2"/>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
72 <param name="column_end" value="3"/>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
73 </conditional>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
74 <output name="outfile" file="unique_results2.bed"/>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
75 </test>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
76 <test>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
77 <param name="infile" value="1_dup.bed"/>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
78 <param name="is_numeric" value="false"/>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
79 <param name="ignore_case" value="true"/>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
80 <output name="outfile" file="unique_results3.bed"/>
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
bgruening
parents: 22
diff changeset
81 </test>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
82 </tests>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
83 <help>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
84 <![CDATA[
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
85 .. class:: infomark
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
86
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
87 **Syntax**
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
88
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
89 This tool returns all unique lines using the 'sort -u' command. It can be used with unsorted files.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
90 If you need additional options, like grouping or counting your unique results, please use the 'Unique lines from sorted file' tool.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
91
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
92 -----
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
93
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
94 .. class:: infomark
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
95
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
96 The input file needs to be tab separated. Please convert your file if necessary.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
97
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
98 -----
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
99
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
100 **Example**
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
101
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
102 - Input file::
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
103
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
104 chr1 10 100 gene1
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
105 chr1 105 200 gene2
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
106 chr1 10 100 gene1
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
107 chr2 10 100 gene4
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
108 chr2 1000 1900 gene5
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
109 chr3 15 1656 gene6
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
110 chr2 10 100 gene4
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
111
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
112 - Unique lines will result in::
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
113
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
114 chr1 10 100 gene1
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
115 chr1 105 200 gene2
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
116 chr2 10 100 gene4
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
117 chr2 1000 1900 gene5
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
118 chr3 15 1656 gene6
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
119
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
120 ]]>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
121 </help>
6
60edf2f8c28f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents: 0
diff changeset
122 <expand macro="citations" />
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
123 </tool>