Mercurial > repos > iuc > bedtools
annotate linksBed.xml @ 17:a2d4c30ba2f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
| author | iuc |
|---|---|
| date | Sun, 21 Jun 2015 22:49:46 -0400 |
| parents | 0d3aa592ce27 |
| children | d279800f4ff9 |
| rev | line source |
|---|---|
| 8 | 1 <tool id="bedtools_links" name="LinksBed" version="@WRAPPER_VERSION@.0"> |
|
17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
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2 <description>create a HTML page of links to UCSC locations</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 bedtools links | |
| 11 -base "${basename}" | |
| 12 -org "${org}" | |
| 13 -db "${db}" | |
| 14 -i "${input}" | |
| 15 > "${output}" | |
| 16 ]]> | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/> | |
| 20 <param name="basename" type="text" value="http://genome.ucsc.edu" | |
| 21 label="The 'basename' for the UCSC genome browser" /> | |
| 22 <param name="org" type="text" value="human" label="Organism name" help="e.g. mouse, human (-org)" /> | |
| 23 <param name="db" type="text" value="hg19" label="The genome build" help="(-db)"/> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data name="output" format="html" /> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="input" value="linksBed1.bed" ftype="bed" /> | |
| 31 <param name="basename" value="http://genome.ucsc.edu" /> | |
| 32 <param name="org" value="" /> | |
| 33 <param name="db" value="" /> | |
| 34 <output name="output" file="linksBed_result1.html" lines_diff="2" ftype="html" /> | |
| 35 </test> | |
| 36 <test> | |
| 37 <param name="input" value="linksBed1.bed" ftype="bed" /> | |
| 38 <param name="basename" value="http://genome.ucsc.edu" /> | |
| 39 <param name="org" value="mouse" /> | |
| 40 <param name="db" value="mm9" /> | |
| 41 <output name="output" file="linksBed_result2.html" lines_diff="2" ftype="html" /> | |
| 42 </test> | |
| 43 </tests> | |
| 44 <help> | |
| 45 <![CDATA[ | |
| 46 **What it does** | |
| 47 | |
| 48 Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. This is useful for cases when one wants to manually inspect through a large set of annotations or features. | |
| 49 | |
| 50 @REFERENCES@ | |
| 51 ]]> | |
| 52 </help> | |
| 53 <expand macro="citations" /> | |
| 54 </tool> |