Mercurial > repos > bgruening > text_processing

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