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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Targeted Experiments]-->
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4 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="2.0.0">
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5 <description>Compute confidence scores for OpenSwath results</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>OpenSwathConfidenceScoring
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_lib:
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19 -lib $param_lib
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_trafo:
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25 -trafo $param_trafo
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26 #end if
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27 #if $param_decoys:
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28 -decoys $param_decoys
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29 #end if
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30 #if $param_transitions:
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31 -transitions $param_transitions
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32 #end if
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33 -threads \${GALAXY_SLOTS:-24}
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34 #if $adv_opts.adv_opts_selector=='advanced':
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35 #if $adv_opts.param_force:
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36 -force
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37 #end if
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38 #if $adv_opts.param_GLM_intercept:
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39 -GLM:intercept $adv_opts.param_GLM_intercept
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40 #end if
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41 #if $adv_opts.param_GLM_delta_rt:
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42 -GLM:delta_rt $adv_opts.param_GLM_delta_rt
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43 #end if
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44 #if $adv_opts.param_GLM_dist_int:
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45 -GLM:dist_int $adv_opts.param_GLM_dist_int
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46 #end if
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47 #end if
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48 </command>
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49 <inputs>
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50 <param format="xml" help="(-in) " label="Input file (OpenSwath results)" name="param_in" optional="False" type="data"/>
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51 <param format="traml" help="(-lib) " label="Assay library" name="param_lib" optional="False" type="data"/>
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52 <param format="trafoxml" help="(-trafo) " label="Retention time transformation" name="param_trafo" optional="True" type="data"/>
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53 <param help="(-decoys) " label="Number of decoy assays to select from the library for every true assay (0 for &quot;all&quot;)" min="0" name="param_decoys" optional="True" type="integer" value="1000"/>
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54 <param help="(-transitions) " label="Number of transitions per feature to consider (highest intensities first; 0 for &quot;all&quot;)" min="0" name="param_transitions" optional="True" type="integer" value="6"/>
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55 <expand macro="advanced_options">
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56 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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57 <param help="(-intercept) " label="Intercept term" name="param_GLM_intercept" type="float" value="3.87333466"/>
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58 <param help="(-delta_rt) " label="Coefficient of retention time difference" name="param_GLM_delta_rt" type="float" value="-0.02898629"/>
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59 <param help="(-dist_int) " label="Coefficient of intensity distance" name="param_GLM_dist_int" type="float" value="-7.75880768"/>
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60 </expand>
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61 </inputs>
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62 <outputs>
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63 <data format="xml" name="param_out"/>
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64 </outputs>
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65 <help>Compute confidence scores for OpenSwath results
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67
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68 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathConfidenceScoring.html</help>
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69 </tool>