Mercurial > repos > galaxyp > openms_openswathdiaprescoring

annotate OpenSwathDIAPreScoring.xml @ 0:b1af731ae341 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:59:14 -0500
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b1af731ae341 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="2.1.0">
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5 <description>Scoring spectra using the DIA scores.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</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>OpenSwathDIAPreScoring
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14
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15 #if $param_tr:
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16 -tr $param_tr
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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 -swath_files
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22 #for token in $param_swath_files:
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23 $token
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24 #end for
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25 #if $param_min_upper_edge_dist:
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26 -min_upper_edge_dist $param_min_upper_edge_dist
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27 #end if
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28 #if $adv_opts.adv_opts_selector=='advanced':
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29 #if $adv_opts.param_force:
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30 -force
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31 #end if
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32 #end if
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33 </command>
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34 <inputs>
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35 <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
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36 <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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37 <sanitizer>
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38 <valid initial="string.printable">
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39 <remove value="'"/>
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40 <remove value="&quot;"/>
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41 </valid>
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42 </sanitizer>
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43 </param>
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44 <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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45 <expand macro="advanced_options">
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46 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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47 </expand>
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48 </inputs>
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49 <outputs>
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50 <data name="param_out" format="tabular"/>
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51 </outputs>
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52 <help>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/doxygen/parameters/output/TOPP_OpenSwathDIAPreScoring.html</help>
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56 </tool>