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annotate sorted_uniq.xml @ 24:c41d78ae5fee draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 4dd118c84ed4d6157303e71438c24446ec4b4f31
author bgruening
date Wed, 04 Jun 2025 15:12:29 +0000
parents 3dc70b59608c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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12615d397df7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
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1 <tool id="tp_uniq_tool" name="Unique lines" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>assuming sorted input file</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="4.8">sed</requirement>
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9 </expand>
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10 <version_command>uniq --version | head -n 1</version_command>
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11 <command>
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12 <![CDATA[
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13 uniq
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14 #if $skipfields:
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15 -f $skipfields
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16 #end if
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17 $ignorecase
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18
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19 #if $grouping.grouping_select == 'yes':
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20 --group=$grouping.group
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21 #else:
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22 $grouping.count
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23 $grouping.repeated
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24 $grouping.uniqueonly
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25 #end if
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26
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27 '$infile'
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28
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29 #if $grouping.grouping_select == 'no' and $grouping.count:
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30 ## count will print the count with spaces in front of the line and
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31 ## with a space (not a tab) after the number, we need to cahnge that
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32 | sed -e 's/ *//' -e 's/ /\t/'
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33 #end if
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34 > '$outfile'
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35 ]]>
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36 </command>
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37 <inputs>
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38 <param name="infile" format="tabular" type="data"
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39 label="File to scan for unique values" help="Make sure you have sorted this file" />
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40
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41 <conditional name="grouping">
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42 <param name="grouping_select" type="select" label="Do you want to group each unique group?">
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43 <option value="no">No</option>
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44 <option value="yes">Yes</option>
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45 </param>
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46 <when value="no">
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47 <param name="count" type="boolean" truevalue="-c" falsevalue=""
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48 label="Counting number of occurrences" help="Prefix lines by the number of occurrences. (-c)" />
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49 <param name="repeated" type="boolean" truevalue="-d" falsevalue=""
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50 label="Only print duplicate lines" help="(-d)"/>
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51 <param name="uniqueonly" type="boolean" checked="True" truevalue="-u" falsevalue=""
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52 label="Only print unique lines" help="(-u)" />
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53 </when>
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54 <when value="yes">
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55 <param name="group" type="select"
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56 label="Output all lines, and delimit each unique group" help="(--group)">
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57 <option value="">No grouping at all</option>
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58 <option value="separate">Separate unique groups with a single delimiter</option>
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59 <option value="prepend">Output a delimiter before each group of unique items</option>
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60 <option value="append">Output a delimiter after each group of unique items</option>
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61 <option value="both">Output a delimiter around each group of unique items</option>
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62 </param>
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63 </when>
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64 </conditional>
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65
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66 <param name="ignorecase" type="boolean" truevalue="-i" falsevalue=""
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67 label="Ignore differences in case when comparing" help="(-i)"/>
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68 <param name="skipfields" type="integer" value="0"
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69 label="Avoid comparing the first N fields" help="Use zero to start from the first field. (-f)" />
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70 </inputs>
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71 <outputs>
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72 <data name="outfile" format_source="infile" metadata_source="infile"/>
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="infile" value="sorted_uniq1.tabular" />
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77 <conditional name="grouping">
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78 <param name="grouping_select" value="no"/>
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79 <param name="count" value="True"/>
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80 <param name="uniqueonly" value="True"/>
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81 </conditional>
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82 <param name="ignorecase" value="True"/>
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83 <output name="outfile" file="sorted_uniq_results1.tabular" />
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84 </test>
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85 <test>
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86 <param name="infile" value="sorted_uniq1.tabular" />
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87 <param name="ignorecase" value="True"/>
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88 <conditional name="grouping">
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89 <param name="grouping_select" value="yes"/>
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90 <param name="group" value="separate"/>
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91 </conditional>
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92 <output name="outfile" file="sorted_uniq_results2.tabular" />
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93 </test>
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94 </tests>
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95 <help>
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96 <![CDATA[
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97 This tool takes a sorted file and look for lines that are unique.
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98
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99 .. class:: warningmark
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100
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101 Please make sure your file is sorted, or else this tool will give you an erroneous output.
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102
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103 .. class:: infomark
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104
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105 You can sort your file using either the "Sort" tool in "Filter and Sort", or the "Sort" tool in "Unix Tools".
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106
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107 ]]>
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108 </help>
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109 <expand macro="citations" />
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110 </tool>