annotate linksBed.xml @ 1:82aac94b06c3 draft

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author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
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1 <tool id="bedtools_links" name="LinksBed" version="@WRAPPER_VERSION@.0">
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2 <description></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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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![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 ]]>
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17 </command>
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18 <inputs>
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19 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
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20 <param name="basename" type="text" value="http://genome.ucsc.edu"
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21 label="The 'basename' for the UCSC genome browser" />
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22 <param name="org" type="text" value="human" label="Organism name" help="e.g. mouse, human (-org)" />
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23 <param name="db" type="text" value="hg19" label="The genome build" help="(-db)"/>
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24 </inputs>
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25 <outputs>
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26 <data name="output" format="html" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input" value="linksBed1.bed" ftype="bed" />
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31 <param name="basename" value="http://genome.ucsc.edu" />
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32 <param name="org" value="" />
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33 <param name="db" value="" />
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34 <output name="output" file="linksBed_result1.html" lines_diff="2" ftype="html" />
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35 </test>
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36 <test>
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37 <param name="input" value="linksBed1.bed" ftype="bed" />
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38 <param name="basename" value="http://genome.ucsc.edu" />
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39 <param name="org" value="mouse" />
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40 <param name="db" value="mm9" />
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41 <output name="output" file="linksBed_result2.html" lines_diff="2" ftype="html" />
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42 </test>
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43 </tests>
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44 <help>
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45 <![CDATA[
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46 **What it does**
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47
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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.
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49
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50 @REFERENCES@
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51 ]]>
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52 </help>
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53 <expand macro="citations" />
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54 </tool>