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1 <?xml version="."?>
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2 <tool id="bmsb" name="BMSB" version="1.0.0">
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3 <description></description>
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4 <requirements>
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3
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5 <requirement type="package" version="1.3.0">r-optparse</requirement>
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6 <requirement type="package" version="1.20.0">r-getopt</requirement>
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7 <requirement type="package" version="0.9.19">r-jsonlite</requirement>
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8 </requirements>
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9 <command>
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10 <![CDATA[
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11 #import json
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12 Rscript $__tool_directory__/bmsb.R
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13 -o "$output"
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3
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14 #if str($output_r_logging_cond.output_r_logging) == "yes":
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15 -s "true"
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16 -m "$output_r_log"
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17 #end if
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18 #if str($output_r_logging_cond.output_r_logging) == "yes":
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19 -e "true"
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20 -x "$output_ex_report"
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21 #end if
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22 ]]>
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23 </command>
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24 <inputs>
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3
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25 <conditional name="output_r_logging_cond">
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26 <param name="output_r_logging" type="select" label="Output R logging?" help="Generate an additional dataset consisting of R messages.">
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27 <option value="yes" selected="True">Yes</option>
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28 <option value="no">No</option>
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29 </param>
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30 <when value="no"/>
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31 <when value="yes"/>
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32 </conditional>
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33 </inputs>
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34 <outputs>
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3
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35 <data name="output_r_log" format="txt" label="${tool.name} on ${on_string}: R log">
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36 <filter>output_r_logging_cond['output_r_logging'] == "yes"</filter>
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37 </data>
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38 <data name="output_ex_report" format="json" label="${tool.name} on ${on_string}: Experiment report">
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39 <filter>output_experiment_report_cond['output_experiment_report'] == "yes"</filter>
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40 </data>
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41 <data name="output" format="RData"/>
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42 </outputs>
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43 <help>
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44 **What it does**
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45
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46 BMSB prototype tool.
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47 </help>
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48 <citations>
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49 <citation></citation>
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50 </citations>
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51 </tool>
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