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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
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0:2064ae2602b1 1:d4fb020c19ca
1 <tool id="bg_uniq" name="Unique" version="0.3"> 1 <tool id="bg_uniq" name="unique" version="0.4">
2 <description>occurrences of each record</description> 2 <description>occurrences of each record</description>
3 <command interpreter='python'> 3 <requirements>
4 uniq.py 4 <requirement type="package" version="2.7.12">python</requirement>
5 $ignore_case 5 </requirements>
6 <command>
7 <![CDATA[
8 python '$__tool_directory__/uniq.py'
9 $ignore_case
6 $is_numeric 10 $is_numeric
7 #if $adv_opts.adv_opts_selector=="advanced": 11 #if $adv_opts.adv_opts_selector=="advanced":
8 $adv_opts.column_start 12 $adv_opts.column_start
9 $adv_opts.column_end 13 $adv_opts.column_end
10 #end if 14 #end if
11 $outfile 15 '$outfile'
12 $input 16 '$input'
17 ]]>
13 </command> 18 </command>
14 <inputs> 19 <inputs>
15 <param name="input" type="data" format="tabular,text" label="from query" /> 20 <param name="input" type="data" format="tabular,text" label="from query" />
16 <param name="ignore_case" type="boolean" label="ignore differences in case when comparing" truevalue="-f" falsevalue="false" checked="false" help="ignore differences in case when comparing"/> 21 <param name="ignore_case" type="boolean" label="Ignore differences in case when comparing" truevalue="-f" falsevalue="false" checked="false" />
17 <param name="is_numeric" type="boolean" label="column only contains numeric values" truevalue="-n" falsevalue="false" checked="false" help="did the calumn have numeric values"/> 22 <param name="is_numeric" type="boolean" label="Column only contains numeric values" truevalue="-n" falsevalue="false" checked="false" />
18 <conditional name="adv_opts"> 23 <conditional name="adv_opts">
19 <param name="adv_opts_selector" type="select" label="Advanced Options"> 24 <param name="adv_opts_selector" type="select" label="Advanced Options">
20 <option value="basic" selected="True">Hide Advanced Options</option> 25 <option value="basic" selected="True">Hide Advanced Options</option>
21 <option value="advanced">Show Advanced Options</option> 26 <option value="advanced">Show Advanced Options</option>
22 </param> 27 </param>
30 <outputs> 35 <outputs>
31 <data format="input" name="outfile" /> 36 <data format="input" name="outfile" />
32 </outputs> 37 </outputs>
33 <tests> 38 <tests>
34 <test> 39 <test>
40 <param name="input" value="1.bed"/>
41 <param name="is_numeric" value="True"/>
42 <param name="ignore_case" value="True"/>
43 <param name="adv_opts_selector" value="advanced"/>
44 <param name="column_start" value="2"/>
45 <param name="column_end" value="3"/>
46 <output name="outfile" file="uniq_results1.bed"/>
47 </test>
48 <test>
49 <param name="input" value="1.bed"/>
50 <param name="is_numeric" value="False"/>
51 <param name="ignore_case" value="True"/>
52 <param name="adv_opts_selector" value="advanced"/>
53 <param name="column_start" value="1"/>
54 <param name="column_end" value="1"/>
55 <output name="outfile" file="uniq_results2.bed"/>
35 </test> 56 </test>
36 </tests> 57 </tests>
37 <help> 58 <help>
38 59 <![CDATA[
39 .. class:: infomark
40 60
41 **Syntax** 61
62 **What it does**
42 63
43 This tool returns all unique lines using the 'sort -u' command. 64 This tool returns all unique lines using the 'sort -u' command.
44 65
45 ----- 66 **Input**
46
47 .. class:: infomark
48 67
49 The input file needs to be tab separated. Please convert your file if necessary. 68 The input file needs to be tab separated. Please convert your file if necessary.
50 69
51 ----- 70 **Output**
52 71
53 **Example** 72 This tool returns all unique lines:
73
74 Example:
54 75
55 - Input file:: 76 - Input file::
56 77
57 chr1 10 100 gene1 78 chr1 10 100 gene1
58 chr1 105 200 gene2 79 chr1 105 200 gene2
59 chr1 10 100 gene1 80 chr1 10 100 gene1
60 chr2 10 100 gene4 81 chr2 10 100 gene4
61 chr2 1000 1900 gene5 82 chr2 1000 1900 gene5
69 chr2 10 100 gene4 90 chr2 10 100 gene4
70 chr2 1000 1900 gene5 91 chr2 1000 1900 gene5
71 chr3 15 1656 gene6 92 chr3 15 1656 gene6
72 93
73 94
74 </help> 95 ]]>
96 </help>
97 <citations>
98 <citation type="bibtex">
99 @ARTICLE{bgruening_galaxytools,
100 Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
101 keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
102 title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
103 url = {https://github.com/bgruening/galaxytools}
104 }
105 </citation>
106 </citations>
75 </tool> 107 </tool>