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comparison sortBed.xml @ 26:c0fbce5dc84a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author iuc
date Mon, 17 Oct 2016 10:13:20 -0400
parents a2d4c30ba2f9
children d279800f4ff9
comparison
equal deleted inserted replaced
25:6c6963cf9136 26:c0fbce5dc84a
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 sortBed 10 sortBed
11 -i $input 11 -i '$input'
12 $option 12 $option
13 > $output 13 > '$output'
14 ]]> 14 ]]>
15 </command> 15 </command>
16 <inputs> 16 <inputs>
17 <param format="bed" name="input" type="data" label="Sort the following BED file"/> 17 <param format="bed,gff,gff3,vcf" name="input" type="data" label="Sort the following BED file"/>
18 <param name="option" type="select" label="Sort by"> 18 <param name="option" type="select" label="Sort by">
19 <!-- sort -k 1,1 -k2,2 -n a.bed --> 19 <!-- sort -k 1,1 -k2,2 -n a.bed -->
20 <option value="">chromosome, then by start position (asc)</option> 20 <option value="">chromosome, then by start position (asc)</option>
21 <option value="-sizeA">feature size in ascending order.</option> 21 <option value="-sizeA">feature size in ascending order.</option>
22 <option value="-sizeD">feature size in descending order.</option> 22 <option value="-sizeD">feature size in descending order.</option>
25 <option value="-chrThenScoreA">chromosome, then by score (asc).</option> 25 <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
26 <option value="-chrThenScoreD">chromosome, then by score (desc).</option> 26 <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
27 </param> 27 </param>
28 </inputs> 28 </inputs>
29 <outputs> 29 <outputs>
30 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/> 30 <data format_source="input" name="output" metadata_source="input" label="SortBed on ${input.name}"/>
31 </outputs> 31 </outputs>
32 <tests> 32 <tests>
33 <test> 33 <test>
34 <param name="input" value="sortBed1.bed" ftype="bed" /> 34 <param name="input" value="sortBed1.bed" ftype="bed" />
35 <param name="option" value="" /> 35 <param name="option" value="" />