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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="OpenSwathConfidenceScoring" name="OpenSwathConfidenceScoring" version="2.0.0">
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3 <description>Compute confidence scores for OpenSwath results</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">OpenSwathConfidenceScoring</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>OpenSwathConfidenceScoring
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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_lib:
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16 -lib $param_lib
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_trafo:
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22 -trafo $param_trafo
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23 #end if
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24 #if $param_decoys:
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25 -decoys $param_decoys
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26 #end if
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27 #if $param_transitions:
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28 -transitions $param_transitions
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29 #end if
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30 -threads \${GALAXY_SLOTS:-24}
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31 #if $adv_opts.adv_opts_selector=='advanced':
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32 #if $adv_opts.param_force:
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33 -force
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34 #end if
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35 #if $adv_opts.param_GLM_intercept:
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36 -GLM:intercept $adv_opts.param_GLM_intercept
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37 #end if
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38 #if $adv_opts.param_GLM_delta_rt:
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39 -GLM:delta_rt $adv_opts.param_GLM_delta_rt
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40 #end if
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41 #if $adv_opts.param_GLM_dist_int:
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42 -GLM:dist_int $adv_opts.param_GLM_dist_int
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43 #end if
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44 #end if
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45 </command>
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46 <inputs>
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47 <param name="param_in" type="data" format="featurexml" optional="False" label="Input file (OpenSwath results)" help="(-in) "/>
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48 <param name="param_lib" type="data" format="traml" optional="False" label="Assay library" help="(-lib) "/>
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49 <param name="param_trafo" type="data" format="trafoxml" optional="True" label="Retention time transformation" help="(-trafo) "/>
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50 <param name="param_decoys" type="integer" min="0" optional="True" value="1000" label="Number of decoy assays to select from the library for every true assay (0 for "all")" help="(-decoys) "/>
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51 <param name="param_transitions" type="integer" min="0" optional="True" value="6" label="Number of transitions per feature to consider (highest intensities first; 0 for "all")" help="(-transitions) "/>
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52 <expand macro="advanced_options">
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53 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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54 <param name="param_GLM_intercept" type="float" value="3.87333466" label="Intercept term" help="(-intercept) "/>
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55 <param name="param_GLM_delta_rt" type="float" value="-0.02898629" label="Coefficient of retention time difference" help="(-delta_rt) "/>
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56 <param name="param_GLM_dist_int" type="float" value="-7.75880768" label="Coefficient of intensity distance" help="(-dist_int) "/>
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57 </expand>
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58 </inputs>
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59 <outputs>
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60 <data name="param_out" format="featurexml"/>
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61 </outputs>
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62 <help>**What it does**
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63
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64 Compute confidence scores for OpenSwath results
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65
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66
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67 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathConfidenceScoring.html</help>
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68 <expand macro="references"/>
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69 </tool>
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