Mercurial > repos > iuc > bedtools
comparison linksBed.xml @ 34:dde39ba9c031 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author | iuc |
---|---|
date | Mon, 29 Apr 2019 05:55:48 -0400 |
parents | 4f7a5ccd2ae9 |
children | 3e38c9b3214f |
comparison
equal
deleted
inserted
replaced
33:87ee588b3d45 | 34:dde39ba9c031 |
---|---|
1 <tool id="bedtools_links" name="bedtools LinksBed" version="@WRAPPER_VERSION@"> | 1 <tool id="bedtools_links" name="bedtools LinksBed" version="@TOOL_VERSION@"> |
2 <description>create a HTML page of links to UCSC locations</description> | 2 <description>create a HTML page of links to UCSC locations</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <expand macro="stdio" /> | 7 <expand macro="stdio" /> |
8 <command> | 8 <command><![CDATA[ |
9 <![CDATA[ | 9 bedtools links |
10 bedtools links | 10 -base '${basename}' |
11 -base "${basename}" | 11 -org '${org}' |
12 -org "${org}" | 12 -db '${db}' |
13 -db "${db}" | 13 -i '${input}' |
14 -i "${input}" | 14 > '${output}' |
15 > "${output}" | 15 ]]></command> |
16 ]]> | |
17 </command> | |
18 <inputs> | 16 <inputs> |
19 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> | 17 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
20 <param name="basename" type="text" value="http://genome.ucsc.edu" | 18 <param name="basename" argument="-base" type="text" value="http://genome.ucsc.edu" |
21 label="The 'basename' for the UCSC genome browser" /> | 19 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)" /> | 20 <param argument="-org" type="text" value="human" label="Organism name" help="E.g. mouse, human" /> |
23 <param name="db" type="text" value="hg19" label="The genome build" help="(-db)"/> | 21 <param argument="-db" type="text" value="hg19" label="The genome build" /> |
24 </inputs> | 22 </inputs> |
25 <outputs> | 23 <outputs> |
26 <data name="output" format="html" /> | 24 <data name="output" format="html" /> |
27 </outputs> | 25 </outputs> |
28 <tests> | 26 <tests> |
39 <param name="org" value="mouse" /> | 37 <param name="org" value="mouse" /> |
40 <param name="db" value="mm9" /> | 38 <param name="db" value="mm9" /> |
41 <output name="output" file="linksBed_result2.html" lines_diff="2" ftype="html" /> | 39 <output name="output" file="linksBed_result2.html" lines_diff="2" ftype="html" /> |
42 </test> | 40 </test> |
43 </tests> | 41 </tests> |
44 <help> | 42 <help><![CDATA[ |
45 <![CDATA[ | |
46 **What it does** | 43 **What it does** |
47 | 44 |
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. | 45 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 | 46 |
50 @REFERENCES@ | 47 @REFERENCES@ |
51 ]]> | 48 ]]></help> |
52 </help> | |
53 <expand macro="citations" /> | 49 <expand macro="citations" /> |
54 </tool> | 50 </tool> |