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comparison 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
children
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equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="CVInspector" name="CVInspector" version="1.12.0"> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <description>A tool for visualization and validation of PSI mapping and CV files.</description> 3 <!--Proposed Tool Section: [Utilities]-->
4 <macros> 4 <tool id="CVInspector" name="CVInspector" version="2.0.0">
5 <token name="@EXECUTABLE@">CVInspector</token> 5 <description>A tool for visualization and validation of PSI mapping and CV files.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">CVInspector</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>CVInspector 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>CVInspector
11 14
12 -cv_files ${param_cv_files} 15 -cv_files
13 -cv_names ${param_cv_names} 16 #for token in $param_cv_files:
14 -mapping_file ${param_mapping_file} 17 $token
15 -ignore_cv ${param_ignore_cv} 18 #end for
16 -html ${param_html} 19
17 -threads \${GALAXY_SLOTS:-24} 20 #if $rep_param_cv_names:
21 -cv_names
22 #for token in $rep_param_cv_names:
23 #if &quot; &quot; in str(token):
24 &quot;$token.param_cv_names&quot;
25 #else
26 $token.param_cv_names
27 #end if
28 #end for
29 #end if
30 #if $param_mapping_file:
31 -mapping_file $param_mapping_file
32 #end if
33
34 #if $rep_param_ignore_cv:
35 -ignore_cv
36 #for token in $rep_param_ignore_cv:
37 #if &quot; &quot; in str(token):
38 &quot;$token.param_ignore_cv&quot;
39 #else
40 $token.param_ignore_cv
41 #end if
42 #end for
43 #end if
44 #if $param_html:
45 -html $param_html
46 #end if
47 -threads \${GALAXY_SLOTS:-24}
48 #if $adv_opts.adv_opts_selector=='advanced':
49 #if $adv_opts.param_force:
50 -force
51 #end if
52 #end if
18 </command> 53 </command>
19 <inputs> 54 <inputs>
20 <param name="param_cv_files" type="data" format="" optional="False" size="20" label="List of ontology files in OBO format." help="(-cv_files)"/> 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">
21 <param name="param_cv_names" type="text" size="20" label="List of identifiers (one for each ontology file)." help="(-cv_names)"/> 56 <sanitizer>
22 <param name="param_mapping_file" type="data" format="xml" optional="True" label="Mapping file in CVMapping (XML) format." help="(-mapping_file)"/> 57 <valid initial="string.printable">
23 <param name="param_ignore_cv" type="text" size="20" value="UO PATO BTO" label="A list of CV identifiers which should be ignored." help="(-ignore_cv)"/> 58 <remove value="'"/>
24 </inputs> 59 <remove value="&quot;"/>
25 <outputs> 60 </valid>
26 <data name="param_html" label="Writes an HTML version of the mapping file with annotated CV terms" format="html"/> 61 </sanitizer>
27 </outputs> 62 </param>
28 <help>**What it does** 63 <repeat min="1" name="rep_param_cv_names" title="param_cv_names">
29 64 <param help="(-cv_names) " label="List of identifiers (one for each ontology file)" name="param_cv_names" size="30" type="text">
30 A tool for visualization and validation of PSI mapping and CV files. 65 <sanitizer>
66 <valid initial="string.printable">
67 <remove value="'"/>
68 <remove value="&quot;"/>
69 </valid>
70 </sanitizer>
71 </param>
72 </repeat>
73 <param format="xml" help="(-mapping_file) " label="Mapping file in CVMapping (XML) format" name="param_mapping_file" optional="True" type="data"/>
74 <repeat max="1" min="0" name="rep_param_ignore_cv" title="param_ignore_cv">
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">
76 <sanitizer>
77 <valid initial="string.printable">
78 <remove value="'"/>
79 <remove value="&quot;"/>
80 </valid>
81 </sanitizer>
82 </param>
83 </repeat>
84 <expand macro="advanced_options">
85 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
86 </expand>
87 </inputs>
88 <outputs>
89 <data format="html" name="param_html"/>
90 </outputs>
91 <help>A tool for visualization and validation of PSI mapping and CV files.
31 92
32 93
33 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_CVInspector.html 94 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_CVInspector.html</help>
34 95 </tool>
35 @REFERENCES@
36 </help>
37 </tool>