Mercurial > repos > bgruening > text_processing

comparison unsorted_uniq.xml @ 30:5907d248dee3 draft default tip

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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 00:56:56 +0000
parents 08cdbfffce67
children
comparison
equal deleted inserted replaced
29:4f7cade041cb 30:5907d248dee3
2 <description>occurrences of each record</description> 2 <description>occurrences of each record</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="creator"/>
7 <expand macro="requirements" /> 7 <expand macro="requirements">
8 <requirement type="package" version="4.9">sed</requirement>
9 </expand>
8 <version_command>sort --version | head -n 1</version_command> 10 <version_command>sort --version | head -n 1</version_command>
9 <command> 11 <command>
10 <![CDATA[ 12 <![CDATA[
11 sort -u 13 (
12 $ignore_case 14 export LC_ALL=C;
13 $is_numeric 15 #if int($header) > 0:
14 -t ' ' 16 sed -u '${header}'q &&
15 #if $adv_opts.adv_opts_selector == "advanced":
16 -k$adv_opts.column_start,$adv_opts.column_end
17 #end if 17 #end if
18 -o '$outfile' 18 sort -u
19 '$infile' 19 $ignore_case
20 $is_numeric
21 -t ' '
22 #if $adv_opts.adv_opts_selector == "advanced":
23 -k$adv_opts.column_start,$adv_opts.column_end
24 #end if
25 ) < '$infile' > '$outfile'
20 ]]> 26 ]]>
21 </command> 27 </command>
22 <inputs> 28 <inputs>
23 <param name="infile" type="data" format="tabular" label="File to scan for unique values" /> 29 <param name="infile" type="data" format="tabular" label="File to scan for unique values" />
24 <param name="ignore_case" type="boolean" truevalue="-f" falsevalue="" checked="False" 30 <param name="ignore_case" type="boolean" truevalue="-f" falsevalue=""
25 label="Ignore differences in case when comparing" help="(-f)"/> 31 label="Ignore differences in case when comparing" help="(-f)"/>
26 <param name="is_numeric" type="boolean" truevalue="-n" falsevalue="" checked="False" 32 <param name="is_numeric" type="boolean" truevalue="-n" falsevalue=""
27 label="Column only contains numeric values" help="(-n)" /> 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)." />
34 <param name="header" type="integer" value="0" label="Number of header lines" help="These will be ignored during sort.">
35 <validator type="in_range" message="Negative values are not allowed." min="0"/>
36 </param>
28 <conditional name="adv_opts"> 37 <conditional name="adv_opts">
29 <param name="adv_opts_selector" type="select" label="Advanced Options"> 38 <param name="adv_opts_selector" type="select" label="Advanced Options">
30 <option value="basic" selected="True">Hide Advanced Options</option> 39 <option value="basic" selected="true">Hide Advanced Options</option>
31 <option value="advanced">Show Advanced Options</option> 40 <option value="advanced">Show Advanced Options</option>
32 </param> 41 </param>
33 <when value="basic" /> 42 <when value="basic" />
34 <when value="advanced"> 43 <when value="advanced">
35 <param name="column_start" type="data_column" data_ref="infile" label="Column start" help="Unique on specific column range"/> 44 <param name="column_start" type="data_column" data_ref="infile" label="Column start" help="Unique on specific column range"/>
41 <data name="outfile" format_source="infile" metadata_source="infile"/> 50 <data name="outfile" format_source="infile" metadata_source="infile"/>
42 </outputs> 51 </outputs>
43 <tests> 52 <tests>
44 <test> 53 <test>
45 <param name="infile" value="1.bed"/> 54 <param name="infile" value="1.bed"/>
46 <param name="is_numeric" value="True"/> 55 <param name="is_numeric" value="true"/>
47 <param name="ignore_case" value="True"/> 56 <param name="ignore_case" value="true"/>
48 <conditional name="adv_opts"> 57 <conditional name="adv_opts">
49 <param name="adv_opts_selector" value="advanced"/> 58 <param name="adv_opts_selector" value="advanced"/>
50 <param name="column_start" value="2"/> 59 <param name="column_start" value="2"/>
51 <param name="column_end" value="3"/> 60 <param name="column_end" value="3"/>
52 </conditional> 61 </conditional>
53 <output name="outfile" file="unique_results1.bed"/> 62 <output name="outfile" file="unique_results1.bed"/>
63 </test>
64 <test>
65 <param name="infile" value="1.bed"/>
66 <param name="is_numeric" value="true"/>
67 <param name="ignore_case" value="true"/>
68 <param name="header" value="1"/>
69 <conditional name="adv_opts">
70 <param name="adv_opts_selector" value="advanced"/>
71 <param name="column_start" value="2"/>
72 <param name="column_end" value="3"/>
73 </conditional>
74 <output name="outfile" file="unique_results2.bed"/>
75 </test>
76 <test>
77 <param name="infile" value="1_dup.bed"/>
78 <param name="is_numeric" value="false"/>
79 <param name="ignore_case" value="true"/>
80 <output name="outfile" file="unique_results3.bed"/>
54 </test> 81 </test>
55 </tests> 82 </tests>
56 <help> 83 <help>
57 <![CDATA[ 84 <![CDATA[
58 .. class:: infomark 85 .. class:: infomark