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author yating-l
date Mon, 10 Jul 2017 12:47:53 -0400
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1 <?xml version="1.0"?>
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2 <tool id="twobit_to_cytoband" name="twoBitToCytoband" version="1.0">
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3 <description>Creates a cytoband file from a twoBit file</description>
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4
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5 <macros>
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6 <import>ucsc_macros.xml</import>
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7 </macros>
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8
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9 <expand macro="requirements_twobit" />
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10
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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13 twoBitInfo "${twobit_input}" stdout |
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14 sort -k 1,1 -k 2,2n |
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15 awk 'BEGIN { OFS="\t" } { print $1, 0, $2, $1, "gneg" }' > "${bed_output}"
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16 ]]>
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17 </command>
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18
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19 <expand macro="environment_LC_COLLATE" />
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20
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21 <inputs>
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22 <param name="twobit_input" type="data" format="twobit" label="twoBit input file" />
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23 </inputs>
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24 <outputs>
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25 <data name="bed_output" format="bed" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <!-- Test create Cytoband bed file from a twoBit file -->
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30 <param name="twobit_input" value="contigs.2bit" ftype="twobit" />
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31 <output name="bed_output" file="contigs_cytoband.bed" />
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32 </test>
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33 </tests>
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34 <help>
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35 <![CDATA[
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36 **What it does**
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37
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38 This tool creates a `Cytoband file <http://genomewiki.ucsc.edu/index.php/Assembly_Hubs#Cytoband_Track>`_
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39 from a twoBit file to enable quicker navigation of individual scaffolds
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40 in the UCSC Genome Browser.
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41
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42 ]]></help>
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43
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44 <expand macro="citations" />
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45 </tool>