annotate SemanticValidator.xml @ 3:64a7eedf3ef1 draft

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date Sat, 28 Oct 2017 05:31:20 -0400
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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: [Utilities]-->
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4 <tool id="SemanticValidator" name="SemanticValidator" version="2.2.0.1">
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5 <description>SemanticValidator for semantically validating certain XML files.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SemanticValidator</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>SemanticValidator
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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_mapping_file:
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19 -mapping_file $param_mapping_file
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20 #end if
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21 -cv
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22 #for token in $param_cv:
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23 $token
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24 #end for
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25 #if $adv_opts.adv_opts_selector=='advanced':
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26 #if $adv_opts.param_force:
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27 -force
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28 #end if
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29 #end if
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30 &gt; $param_stdout
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31 </command>
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32 <inputs>
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33 <param name="param_in" type="data" format="analysisXML,mzml,traml,mzid,mzData,xml" optional="False" label="Input file (any xml file)" help="(-in) "/>
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34 <param name="param_mapping_file" type="data" format="xml" optional="False" label="Mapping file which is used to semantically validate the given XML file against this mapping file (see 'share/OpenMS/MAPPING' for templates)" help="(-mapping_file) "/>
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35 <param name="param_cv" type="data" format="obo" multiple="true" optional="True" size="30" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help="(-cv) ">
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36 <sanitizer>
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37 <valid initial="string.printable">
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38 <remove value="'"/>
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39 <remove value="&quot;"/>
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40 </valid>
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41 </sanitizer>
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42 </param>
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43 <expand macro="advanced_options">
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44 <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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45 </expand>
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46 </inputs>
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47 <outputs>
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48 <data name="param_stdout" format="txt" label="Output from stdout"/>
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49 </outputs>
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50 <help>SemanticValidator for semantically validating certain XML files.
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51
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52
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53 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SemanticValidator.html</help>
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54 </tool>