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comparison linksBed.xml @ 50:df28283b3778 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:54:22 -0400
parents 2f457890d8c8
children 7a06bb42dbb1
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49:5074e81a5ce1 50:df28283b3778
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>