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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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5
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4 <requirement type="package" version="2.4.27">bedops</requirement>
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5 <requirement type="package" version="1.10.4">r-data.table</requirement>
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6 <requirement type="package" version="1.4.4">r-optparse</requirement>
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7 <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 Rscript '$__tool_directory__/create_genome_tracks.R'
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11 -b $parameter_file.metadata.dbkey
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12 -c '$chromInfo'
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13 -f test
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14 -p '$parameter_file'
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15 -s '$state_file'
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16 -t 'http://bx.psu.edu/~yuzhang/tmp/'
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17 -u '$output_track_db'
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18 -v '$output_build'
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19 -w '$output_hub']]></command>
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20 <inputs>
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21 <param name="state_file" type="data" format="txt" label="IDEAS epigenetic states and position classes dataset">
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22 <validator type="empty_field"/>
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23 <validator type="unspecified_build"/>
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24 </param>
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25 <param name="parameter_file" type="data" format="tabular" label="IDEAS epigenetic state frequency, mean and variance parameters dataset">
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26 <validator type="empty_field"/>
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27 <validator type="unspecified_build"/>
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data name="output_track_db" format="bigbed" label="${tool.name} (track db) on ${on_string}"/>
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32 <data name="output_build" format="txt" label="${tool.name} (genome build) on ${on_string}"/>
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33 <data name="output_hub" format="txt" label="${tool.name} (hub) on ${on_string}"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37 </test>
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38 </tests>
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39 <help>
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40 **What it does**
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41
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42 -----
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43
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44 **Required options**
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45
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46 </help>
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47 <citations>
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48 <citation type="doi">10.1093/nar/gkw278</citation>
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49 </citations>
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50 </tool>
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