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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation commit f3cda75b01f512edd8723f157db104fca819ce0c
author bgruening
date Tue, 13 Dec 2016 03:02:52 -0500
parents 2064ae2602b1
children
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d4fb020c19ca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation commit f3cda75b01f512edd8723f157db104fca819ce0c
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1 <tool id="bg_uniq" name="unique" version="0.4">
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2 <description>occurrences of each record</description>
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3 <requirements>
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4 <requirement type="package" version="2.7.12">python</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8 python '$__tool_directory__/uniq.py'
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9 $ignore_case
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10 $is_numeric
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11 #if $adv_opts.adv_opts_selector=="advanced":
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12 $adv_opts.column_start
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13 $adv_opts.column_end
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14 #end if
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15 '$outfile'
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16 '$input'
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="input" type="data" format="tabular,text" label="from query" />
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21 <param name="ignore_case" type="boolean" label="Ignore differences in case when comparing" truevalue="-f" falsevalue="false" checked="false" />
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22 <param name="is_numeric" type="boolean" label="Column only contains numeric values" truevalue="-n" falsevalue="false" checked="false" />
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23 <conditional name="adv_opts">
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24 <param name="adv_opts_selector" type="select" label="Advanced Options">
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25 <option value="basic" selected="True">Hide Advanced Options</option>
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26 <option value="advanced">Show Advanced Options</option>
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27 </param>
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28 <when value="basic" />
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29 <when value="advanced">
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30 <param name="column_start" label="Column start" type="data_column" data_ref="input" help="Unique on specific column range"/>
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31 <param name="column_end" label="Column end" type="data_column" data_ref="input" help="Unique on specific column range"/>
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32 </when>
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33 </conditional>
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34 </inputs>
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35 <outputs>
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36 <data format="input" name="outfile" />
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37 </outputs>
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38 <tests>
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39 <test>
1
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40 <param name="input" value="1.bed"/>
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41 <param name="is_numeric" value="True"/>
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42 <param name="ignore_case" value="True"/>
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43 <param name="adv_opts_selector" value="advanced"/>
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44 <param name="column_start" value="2"/>
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45 <param name="column_end" value="3"/>
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46 <output name="outfile" file="uniq_results1.bed"/>
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47 </test>
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48 <test>
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49 <param name="input" value="1.bed"/>
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50 <param name="is_numeric" value="False"/>
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51 <param name="ignore_case" value="True"/>
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52 <param name="adv_opts_selector" value="advanced"/>
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53 <param name="column_start" value="1"/>
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54 <param name="column_end" value="1"/>
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55 <output name="outfile" file="uniq_results2.bed"/>
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56 </test>
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57 </tests>
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58 <help>
1
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59 <![CDATA[
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60
1
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61
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62 **What it does**
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63
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64 This tool returns all unique lines using the 'sort -u' command.
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65
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66 **Input**
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67
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68 The input file needs to be tab separated. Please convert your file if necessary.
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69
1
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70 **Output**
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71
1
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72 This tool returns all unique lines:
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73
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74 Example:
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75
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76 - Input file::
1
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77
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78 chr1 10 100 gene1
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79 chr1 105 200 gene2
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80 chr1 10 100 gene1
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81 chr2 10 100 gene4
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82 chr2 1000 1900 gene5
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83 chr3 15 1656 gene6
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84 chr2 10 100 gene4
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85
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86 - Unique lines will result in::
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87
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88 chr1 10 100 gene1
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89 chr1 105 200 gene2
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90 chr2 10 100 gene4
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91 chr2 1000 1900 gene5
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92 chr3 15 1656 gene6
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93
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94
1
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95 ]]>
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96 </help>
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97 <citations>
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98 <citation type="bibtex">
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99 @ARTICLE{bgruening_galaxytools,
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100 Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
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101 keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
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102 title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
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103 url = {https://github.com/bgruening/galaxytools}
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104 }
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105 </citation>
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106 </citations>
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107 </tool>