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comparison unsorted_uniq.xml @ 4:56e80527c482 draft

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author bgruening
date Wed, 07 Jan 2015 11:10:52 -0500
parents 7068d1548234
children 8928e6d1e7ba
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3:7068d1548234 4:56e80527c482
1 <tool id="tp_sorted_uniq" name="Unique" version="0.3"> 1 <tool id="tp_sorted_uniq" name="Unique" version="@BASE_VERSION@.0">
2 <description>occurrences of each record</description> 2 <description>occurrences of each record</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="8.21">gnu_coreutils</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <command interpreter='python'> 6 <expand macro="requirements" />
7 unsorted_uniq.py 7 <version_command>sort --version | head -n 1</version_command>
8 $ignore_case 8 <command>
9 $is_numeric 9 <![CDATA[
10 #if $adv_opts.adv_opts_selector=="advanced": 10 sort -u
11 $adv_opts.column_start 11 $ignore_case
12 $adv_opts.column_end 12 $is_numeric
13 #end if 13 -t ' '
14 $outfile 14 #if $adv_opts.adv_opts_selector == "advanced":
15 $infile 15 -k$adv_opts.column_start,$adv_opts.column_end
16 #end if
17 -o "$outfile"
18 "$infile"
19 ]]>
16 </command> 20 </command>
17 <inputs> 21 <inputs>
18 <param name="infile" type="data" format="tabular,txt" label="File to scan for unique values" /> 22 <param name="infile" type="data" format="tabular" label="File to scan for unique values" />
19 <param name="ignore_case" type="boolean" label="ignore differences in case when comparing (-f)" truevalue="-f" falsevalue="false" checked="false"/> 23 <param name="ignore_case" type="boolean" truevalue="-f" falsevalue="" checked="False"
20 <param name="is_numeric" type="boolean" label="column only contains numeric values (-n)" truevalue="-n" falsevalue="false" checked="false" /> 24 label="Ignore differences in case when comparing" help="(-f)"/>
25 <param name="is_numeric" type="boolean" truevalue="-n" falsevalue="" checked="False"
26 label="Column only contains numeric values" help="(-n)" />
21 <conditional name="adv_opts"> 27 <conditional name="adv_opts">
22 <param name="adv_opts_selector" type="select" label="Advanced Options"> 28 <param name="adv_opts_selector" type="select" label="Advanced Options">
23 <option value="basic" selected="True">Hide Advanced Options</option> 29 <option value="basic" selected="True">Hide Advanced Options</option>
24 <option value="advanced">Show Advanced Options</option> 30 <option value="advanced">Show Advanced Options</option>
25 </param> 31 </param>
26 <when value="basic" /> 32 <when value="basic" />
27 <when value="advanced"> 33 <when value="advanced">
28 <param name="column_start" label="Column start" type="data_column" data_ref="infile" help="Unique on specific column range"/> 34 <param name="column_start" type="data_column" data_ref="infile" label="Column start" help="Unique on specific column range"/>
29 <param name="column_end" label="Column end" type="data_column" data_ref="infile" help="Unique on specific column range"/> 35 <param name="column_end" type="data_column" data_ref="infile" label="Column end" help="Unique on specific column range"/>
30 </when> 36 </when>
31 </conditional> 37 </conditional>
32 </inputs> 38 </inputs>
33 <outputs> 39 <outputs>
34 <data format="infile" name="outfile" metadata_source="infile"/> 40 <data format="input" name="outfile" metadata_source="infile"/>
35 </outputs> 41 </outputs>
36 <tests> 42 <tests>
37 <test> 43 <test>
44 <param name="infile" value="1.bed"/>
45 <param name="is_numeric" value="True"/>
46 <param name="ignore_case" value="True"/>
47 <param name="adv_opts_selector" value="advanced"/>
48 <param name="column_start" value="2"/>
49 <param name="column_end" value="3"/>
50 <output name="outfile" file="unique_results1.bed"/>
38 </test> 51 </test>
39 </tests> 52 </tests>
40 <help> 53 <help>
41 54 <![CDATA[
42 .. class:: infomark 55 .. class:: infomark
43 56
44 **Syntax** 57 **Syntax**
45 58
46 This tool returns all unique lines using the 'sort -u' command. It can be used with unsorted files. 59 This tool returns all unique lines using the 'sort -u' command. It can be used with unsorted files.
72 chr1 105 200 gene2 85 chr1 105 200 gene2
73 chr2 10 100 gene4 86 chr2 10 100 gene4
74 chr2 1000 1900 gene5 87 chr2 1000 1900 gene5
75 chr3 15 1656 gene6 88 chr3 15 1656 gene6
76 89
77 90 @REFERENCES@
91 ]]>
78 </help> 92 </help>
79 </tool> 93 </tool>