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annotate CVInspector.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
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4
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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="CVInspector" name="CVInspector" version="2.0.0">
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5 <description>A tool for visualization and validation of PSI mapping and CV files.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">CVInspector</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>CVInspector
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14
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15 -cv_files
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16 #for token in $param_cv_files:
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17 $token
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18 #end for
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19
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20 #if $rep_param_cv_names:
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21 -cv_names
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22 #for token in $rep_param_cv_names:
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23 #if &quot; &quot; in str(token):
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24 &quot;$token.param_cv_names&quot;
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25 #else
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26 $token.param_cv_names
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27 #end if
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28 #end for
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29 #end if
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30 #if $param_mapping_file:
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31 -mapping_file $param_mapping_file
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32 #end if
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33
4
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34 #if $rep_param_ignore_cv:
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35 -ignore_cv
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36 #for token in $rep_param_ignore_cv:
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37 #if &quot; &quot; in str(token):
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38 &quot;$token.param_ignore_cv&quot;
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39 #else
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40 $token.param_ignore_cv
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41 #end if
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42 #end for
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43 #end if
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44 #if $param_html:
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45 -html $param_html
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46 #end if
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47 -threads \${GALAXY_SLOTS:-24}
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48 #if $adv_opts.adv_opts_selector=='advanced':
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49 #if $adv_opts.param_force:
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50 -force
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51 #end if
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52 #end if
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53 </command>
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54 <inputs>
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55 <param format="" help="(-cv_files) " label="List of ontology files in OBO format" multiple="true" name="param_cv_files" optional="False" size="30" type="data">
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56 <sanitizer>
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57 <valid initial="string.printable">
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58 <remove value="'"/>
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59 <remove value="&quot;"/>
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60 </valid>
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61 </sanitizer>
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62 </param>
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63 <repeat min="1" name="rep_param_cv_names" title="param_cv_names">
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64 <param help="(-cv_names) " label="List of identifiers (one for each ontology file)" name="param_cv_names" size="30" type="text">
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65 <sanitizer>
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66 <valid initial="string.printable">
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67 <remove value="'"/>
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68 <remove value="&quot;"/>
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69 </valid>
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70 </sanitizer>
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71 </param>
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72 </repeat>
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73 <param format="xml" help="(-mapping_file) " label="Mapping file in CVMapping (XML) format" name="param_mapping_file" optional="True" type="data"/>
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74 <repeat max="1" min="0" name="rep_param_ignore_cv" title="param_ignore_cv">
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75 <param help="(-ignore_cv) " label="A list of CV identifiers which should be ignored" name="param_ignore_cv" size="30" type="text" value="UO PATO BTO">
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76 <sanitizer>
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77 <valid initial="string.printable">
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78 <remove value="'"/>
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79 <remove value="&quot;"/>
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80 </valid>
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81 </sanitizer>
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82 </param>
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83 </repeat>
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84 <expand macro="advanced_options">
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85 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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86 </expand>
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87 </inputs>
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88 <outputs>
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89 <data format="html" name="param_html"/>
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90 </outputs>
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91 <help>A tool for visualization and validation of PSI mapping and CV files.
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92
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93
4
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94 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_CVInspector.html</help>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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95 </tool>