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1 <tool id="create_genome_tracks" name="Create genome tracks" version="1.0.0">
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2 <description>from IDEAS statistics</description>
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3 <requirements>
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4 <requirement type="package" version="2.4.27">bedops</requirement>
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5 <requirement type="package" version="1.4.4">r-optparse</requirement>
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6 <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript '$__tool_directory__/create_genome_tracks.R'
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10 -b $parameter_file.metadata.dbkey
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11 -c '$chromInfo'
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1
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12 -f test
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13 -p '$parameter_file'
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14 -s '$state_file'
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15 -t 'http://bx.psu.edu/~yuzhang/tmp/'
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16 -u '$output_track_db'
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17 -v '$output_build'
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18 -w '$output_hub']]></command>
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19 <inputs>
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20 <param name="state_file" type="data" format="txt" label="IDEAS epigenetic states and position classes dataset">
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21 <validator type="empty_field"/>
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22 <validator type="unspecified_build"/>
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23 </param>
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24 <param name="parameter_file" type="data" format="tabular" label="IDEAS epigenetic state frequency, mean and variance parameters dataset">
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25 <validator type="empty_field"/>
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26 <validator type="unspecified_build"/>
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27 </param>
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28 </inputs>
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29 <outputs>
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30 <data name="output_track_db" format="bigbed" label="${tool.name} (track db) on ${on_string}"/>
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31 <data name="output_build" format="txt" label="${tool.name} (genome build) on ${on_string}"/>
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32 <data name="output_hub" format="txt" label="${tool.name} (hub) on ${on_string}"/>
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33 </outputs>
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34 <tests>
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35 <test>
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36 </test>
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37 </tests>
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38 <help>
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39 **What it does**
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40
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41 -----
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42
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43 **Required options**
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44
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45 </help>
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46 <citations>
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47 <citation type="doi">10.1093/nar/gkw278</citation>
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48 </citations>
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49 </tool>
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