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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="CVInspector" name="CVInspector" version="2.0.0">
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3 <description>A tool for visualization and validation of PSI mapping and CV files.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">CVInspector</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>CVInspector
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11
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12 -cv_files
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13 #for token in $param_cv_files:
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14 $token
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15 #end for
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16
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17 #if $rep_param_cv_names:
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18 -cv_names
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19 #for token in $rep_param_cv_names:
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20 #if " " in str(token):
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21 "$token.param_cv_names"
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22 #else
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23 $token.param_cv_names
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24 #end if
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25 #end for
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26 #end if
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27 #if $param_mapping_file:
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28 -mapping_file $param_mapping_file
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29 #end if
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30
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31 #if $rep_param_ignore_cv:
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32 -ignore_cv
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33 #for token in $rep_param_ignore_cv:
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34 #if " " in str(token):
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35 "$token.param_ignore_cv"
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36 #else
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37 $token.param_ignore_cv
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38 #end if
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39 #end for
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40 #end if
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41 #if $param_html:
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42 -html $param_html
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43 #end if
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44 -threads \${GALAXY_SLOTS:-24}
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45 #if $adv_opts.adv_opts_selector=='advanced':
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46 #if $adv_opts.param_force:
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47 -force
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48 #end if
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49 #end if
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50 </command>
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51 <inputs>
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52 <param name="param_cv_files" type="data" format="obo" multiple="true" optional="False" size="30" label="List of ontology files in OBO format" help="(-cv_files) ">
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53 <sanitizer>
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54 <valid initial="string.printable">
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55 <remove value="'"/>
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56 <remove value="""/>
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57 </valid>
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58 </sanitizer>
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59 </param>
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60 <repeat name="rep_param_cv_names" min="1" title="param_cv_names">
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61 <param name="param_cv_names" type="text" size="30" label="List of identifiers (one for each ontology file)" help="(-cv_names) ">
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62 <sanitizer>
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63 <valid initial="string.printable">
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64 <remove value="'"/>
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65 <remove value="""/>
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66 </valid>
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67 </sanitizer>
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68 </param>
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69 </repeat>
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70 <param name="param_mapping_file" type="data" format="xml" optional="True" label="Mapping file in CVMapping (XML) format" help="(-mapping_file) "/>
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71 <repeat name="rep_param_ignore_cv" min="0" max="1" title="param_ignore_cv">
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72 <param name="param_ignore_cv" type="text" size="30" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help="(-ignore_cv) ">
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73 <sanitizer>
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74 <valid initial="string.printable">
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75 <remove value="'"/>
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76 <remove value="""/>
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77 </valid>
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78 </sanitizer>
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79 </param>
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80 </repeat>
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81 <expand macro="advanced_options">
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82 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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83 </expand>
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84 </inputs>
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85 <outputs>
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86 <data name="param_html" format="html"/>
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87 </outputs>
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88 <help>**What it does**
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89
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90 A tool for visualization and validation of PSI mapping and CV files.
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91
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92
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93 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_CVInspector.html</help>
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94 <expand macro="references"/>
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95 </tool>
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