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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="ConsensusMapNormalizer" name="ConsensusMapNormalizer" version="2.0.0">
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3 <description>Normalizes maps of one consensusXML file</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">ConsensusMapNormalizer</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>ConsensusMapNormalizer
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11
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12 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_out:
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16 -out $param_out
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17 #end if
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18 #if $param_algorithm_type:
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19 -algorithm_type
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20 #if " " in str($param_algorithm_type):
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21 "$param_algorithm_type"
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22 #else
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23 $param_algorithm_type
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24 #end if
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25 #end if
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26 #if $param_ratio_threshold:
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27 -ratio_threshold $param_ratio_threshold
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28 #end if
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29 -threads \${GALAXY_SLOTS:-24}
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30 #if $adv_opts.adv_opts_selector=='advanced':
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31 #if $adv_opts.param_force:
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32 -force
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33 #end if
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34 #end if
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35 </command>
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36 <inputs>
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37 <param name="param_in" type="data" format="consensusxml" optional="False" label="input file" help="(-in) "/>
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38 <param name="param_algorithm_type" type="select" optional="True" value="robust_regression" label="The normalization algorithm that is applied" help="(-algorithm_type) ">
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39 <option value="robust_regression">robust_regression</option>
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40 <option value="median">median</option>
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41 <option value="quantile">quantile</option>
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42 </param>
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43 <param name="param_ratio_threshold" type="float" min="0.001" max="1.0" optional="True" value="0.67" label="Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold < intensity ratio < 1/ratio_threshold) and outliers" help="(-ratio_threshold) "/>
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44 <expand macro="advanced_options">
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45 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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46 </expand>
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47 </inputs>
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48 <outputs>
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49 <data name="param_out" format="consensusxml"/>
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50 </outputs>
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51 <help>**What it does**
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52
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53 Normalizes maps of one consensusXML file
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54
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55
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56 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusMapNormalizer.html</help>
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57 <expand macro="references"/>
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58 </tool>
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