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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="2.0.0">
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3 <description>Scoring spectra using the DIA scores.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</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>OpenSwathDIAPreScoring
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11
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12 #if $param_tr:
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13 -tr $param_tr
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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 -swath_files
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19 #for token in $param_swath_files:
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20 $token
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21 #end for
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22 #if $param_min_upper_edge_dist:
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23 -min_upper_edge_dist $param_min_upper_edge_dist
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24 #end if
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25 -threads \${GALAXY_SLOTS:-24}
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26 #if $adv_opts.adv_opts_selector=='advanced':
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27 #if $adv_opts.param_force:
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28 -force
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29 #end if
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30 #end if
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31 </command>
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32 <inputs>
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33 <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
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34 <param name="param_swath_files" type="data" format="mzml" multiple="true" optional="True" size="30" label="Swath files that were used to extract the transitions" help="(-swath_files) If present, SWATH specific scoring will be applied">
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35 <sanitizer>
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36 <valid initial="string.printable">
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37 <remove value="'"/>
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38 <remove value="""/>
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39 </valid>
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40 </sanitizer>
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41 </param>
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42 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help="(-min_upper_edge_dist) "/>
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43 <expand macro="advanced_options">
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44 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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45 </expand>
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46 </inputs>
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47 <outputs>
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48 <data name="param_out" format="tabular"/>
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49 </outputs>
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50 <help>**What it does**
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51
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52 Scoring spectra using the DIA scores.
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53
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54
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55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDIAPreScoring.html</help>
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56 <expand macro="references"/>
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57 </tool>
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