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annotate linksBed.xml @ 41:7ab85ac5f64b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
author iuc
date Thu, 04 Nov 2021 11:36:55 +0000
parents 3e38c9b3214f
children
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3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
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1 <tool id="bedtools_links" name="bedtools LinksBed" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>create a HTML page of links to UCSC locations</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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7ab85ac5f64b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
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6 <expand macro="bio_tools" />
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <command><![CDATA[
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10 bedtools links
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11 -base '${basename}'
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12 -org '${org}'
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13 -db '${db}'
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14 -i '${input}'
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15 > '${output}'
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16 ]]></command>
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17 <inputs>
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18 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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19 <param name="basename" argument="-base" type="text" value="http://genome.ucsc.edu"
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20 label="The 'basename' for the UCSC genome browser" />
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21 <param argument="-org" type="text" value="human" label="Organism name" help="E.g. mouse, human" />
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22 <param argument="-db" type="text" value="hg19" label="The genome build" />
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23 </inputs>
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24 <outputs>
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25 <data name="output" format="html" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="input" value="linksBed1.bed" ftype="bed" />
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30 <param name="basename" value="http://genome.ucsc.edu" />
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31 <param name="org" value="" />
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32 <param name="db" value="" />
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33 <output name="output" file="linksBed_result1.html" lines_diff="2" ftype="html" />
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34 </test>
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35 <test>
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36 <param name="input" value="linksBed1.bed" ftype="bed" />
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37 <param name="basename" value="http://genome.ucsc.edu" />
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38 <param name="org" value="mouse" />
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39 <param name="db" value="mm9" />
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40 <output name="output" file="linksBed_result2.html" lines_diff="2" ftype="html" />
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44 **What it does**
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45
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46 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.
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47
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48 @REFERENCES@
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49 ]]></help>
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50 <expand macro="citations" />
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51 </tool>