Mercurial > repos > galaxyp > openms_cvinspector

comparison CVInspector.xml @ 0:b9ef41d6c0f9 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 12:36:22 -0500
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children ba78f311be89
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-1:000000000000 0:b9ef41d6c0f9
1 <?xml version='1.0' encoding='UTF-8'?>
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 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="CVInspector" name="CVInspector" version="2.1.0">
5 <description>A tool for visualization and validation of PSI mapping and CV files.</description>
6 <macros>
7 <token name="@EXECUTABLE@">CVInspector</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>CVInspector
14
15 -cv_files
16 #for token in $param_cv_files:
17 $token
18 #end for
19
20 #if $rep_param_cv_names:
21 -cv_names
22 #for token in $rep_param_cv_names:
23 #if " " in str(token):
24 "$token.param_cv_names"
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 $rep_param_ignore_cv:
37 #if " " in str(token):
38 "$token.param_ignore_cv"
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 #if $adv_opts.adv_opts_selector=='advanced':
48 #if $adv_opts.param_force:
49 -force
50 #end if
51 #end if
52 </command>
53 <inputs>
54 <param name="param_cv_files" type="data" format="" multiple="true" optional="False" size="30" label="List of ontology files in OBO format" help="(-cv_files) ">
55 <sanitizer>
56 <valid initial="string.printable">
57 <remove value="'"/>
58 <remove value="&quot;"/>
59 </valid>
60 </sanitizer>
61 </param>
62 <repeat name="rep_param_cv_names" min="1" max="1" title="param_cv_names">
63 <param name="param_cv_names" type="text" size="30" label="List of identifiers (one for each ontology file)" help="(-cv_names) ">
64 <sanitizer>
65 <valid initial="string.printable">
66 <remove value="'"/>
67 <remove value="&quot;"/>
68 </valid>
69 </sanitizer>
70 </param>
71 </repeat>
72 <param name="param_mapping_file" type="data" format="xml" optional="True" label="Mapping file in CVMapping (XML) format" help="(-mapping_file) "/>
73 <repeat name="rep_param_ignore_cv" min="0" max="1" title="param_ignore_cv">
74 <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) ">
75 <sanitizer>
76 <valid initial="string.printable">
77 <remove value="'"/>
78 <remove value="&quot;"/>
79 </valid>
80 </sanitizer>
81 </param>
82 </repeat>
83 <expand macro="advanced_options">
84 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
85 </expand>
86 </inputs>
87 <outputs>
88 <data name="param_html" format="html"/>
89 </outputs>
90 <help>A tool for visualization and validation of PSI mapping and CV files.
91
92
93 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_CVInspector.html</help>
94 </tool>