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1 <?xml version="1.0"?>
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2 <tool id="roi_filter" name="ROI Filter">
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3 <description>Filter ROI files</description>
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4
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5 <command interpreter="bash">
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6 roi_filter.sh $numeric -c $column -o $operator -v $value <$input >$output
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7 </command>
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8
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9 <!--
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10 Input Files and Parameters
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11 -->
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12 <inputs>
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13 <param name="input" format="roi" type="data" label="ROI file to filter." />
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14
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15 <param name="column" type="integer" label="column (starts with 1)" value="5" />
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16
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17 <param name="operator" type="select" label="operator">
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18 <option value="gt" selected="true">></option>
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19 <option value="lt"><</option>
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20 <option value="geq">>=</option>
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21 <option value="leq"><=</option>
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22 <option value="eq">==</option>
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23 <option value="neq">!=</option>
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24 </param>
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25
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26 <param name="value" type="text" label="value" value="100" />
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27
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28 <param name="numeric" type="boolean" label="compare as number" checked="true" truevalue="-n" falsevalue="" />
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29 </inputs>
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30
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31 <!--
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32 Output Files
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33 -->
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34 <outputs>
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35 <data name="output" format="roi" label="${input.name}_sorted_${by}" />
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36 </outputs>
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37
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38 <!--
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39 Recognize errors by return code and not output to stderr.
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40 -->
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41 <stdio>
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42 <exit_code range="1:" level="fatal" />
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43 <exit_code range=":-1" level="fatal" />
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44 </stdio>
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45
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46 <!--
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47 Tool Help
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48 -->
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49 <help>No help yet.</help>
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50 </tool>
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