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comparison sortBed.xml @ 54:b06c53665eb6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
author iuc
date Tue, 23 Mar 2021 20:21:30 +0000
parents df28283b3778
children 7a06bb42dbb1
comparison
equal deleted inserted replaced
53:73e3ca75370a 54:b06c53665eb6
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command><![CDATA[ 8 <command><![CDATA[
9 sortBed 9 sortBed
10 -i '$input' 10 -i '$input'
11 $option 11 $option
12 @GENOME_FILE_MAPBED@
12 > '$output' 13 > '$output'
13 ]]></command> 14 ]]></command>
14 <inputs> 15 <inputs>
15 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file" /> 16 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file" />
16 <param name="option" type="select" label="Sort by"> 17 <param name="option" type="select" label="Sort by">
21 <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option> 22 <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option>
22 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option> 23 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option>
23 <option value="-chrThenScoreA">chromosome, then by score (asc).</option> 24 <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
24 <option value="-chrThenScoreD">chromosome, then by score (desc).</option> 25 <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
25 </param> 26 </param>
27 <expand macro="input_optional_genome_file" />
26 </inputs> 28 </inputs>
27 <outputs> 29 <outputs>
28 <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/> 30 <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/>
29 </outputs> 31 </outputs>
30 <tests> 32 <tests>
31 <test> 33 <test>
32 <param name="input" value="sortBed1.bed" ftype="bed" /> 34 <param name="input" value="sortBed1.bed" ftype="bed" />
33 <param name="option" value="" /> 35 <param name="option" value="" />
34 <output name="output" file="sortBed_result1.bed" ftype="bed" /> 36 <output name="output" file="sortBed_result1.bed" ftype="bed" />
37 </test>
38 <test>
39 <param name="input" value="sortBed2.bed" ftype="bed" />
40 <param name="option" value="" />
41 <output name="output" file="sortBed_result2.bed" ftype="bed" />
42 </test>
43 <test>
44 <param name="input" value="sortBed2.bed" ftype="bed" />
45 <param name="option" value="" />
46 <param name="genome_choose" value="-g" />
47 <param name="genome_file_opts_selector" value="hist" />
48 <param name="genome" value="mm9.len" ftype="bed" />
49 <output name="output" file="sortBed_result3.bed" ftype="bed" />
35 </test> 50 </test>
36 </tests> 51 </tests>
37 <help><![CDATA[ 52 <help><![CDATA[
38 **What it does** 53 **What it does**
39 54