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comparison SemanticValidator.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
comparison
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="SemanticValidator" name="SemanticValidator" 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>SemanticValidator for semantically validating certain XML files.</description> 3 <!--Proposed Tool Section: [Utilities]-->
4 <macros> 4 <tool id="SemanticValidator" name="SemanticValidator" version="2.0.0">
5 <token name="@EXECUTABLE@">SemanticValidator</token> 5 <description>SemanticValidator for semantically validating certain XML files.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">SemanticValidator</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>SemanticValidator 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>SemanticValidator
11 14
12 -in ${param_in} 15 #if $param_in:
13 -mapping_file ${param_mapping_file} 16 -in $param_in
14 -cv ${param_cv} 17 #end if
15 -threads \${GALAXY_SLOTS:-24} 18 #if $param_mapping_file:
19 -mapping_file $param_mapping_file
20 #end if
21 -cv
22 #for token in $param_cv:
23 $token
24 #end for
25 -threads \${GALAXY_SLOTS:-24}
26 #if $adv_opts.adv_opts_selector=='advanced':
27 #if $adv_opts.param_force:
28 -force
29 #end if
30 #end if
31 &gt; $param_stdout
16 </command> 32 </command>
17 <inputs> 33 <inputs>
18 <param name="param_in" type="data" format="mzML" optional="False" label="Input file (any xml file)" help="(-in)"/> 34 <param format="xml,txt,traml,mzml" help="(-in) " label="Input file (any xml file)" name="param_in" optional="False" type="data"/>
19 <param name="param_mapping_file" type="data" format="" 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)"/> 35 <param format="" help="(-mapping_file) " label="Mapping file which is used to semantically validate the given XML file against this mapping file (see 'share/OpenMS/MAPPING' for templates)" name="param_mapping_file" optional="False" type="data"/>
20 <param name="param_cv" type="data" format="" optional="True" size="20" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help="(-cv)"/> 36 <param format="" help="(-cv) " label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" multiple="true" name="param_cv" optional="True" size="30" type="data">
21 </inputs> 37 <sanitizer>
22 <outputs/> 38 <valid initial="string.printable">
23 <help>**What it does** 39 <remove value="'"/>
24 40 <remove value="&quot;"/>
25 SemanticValidator for semantically validating certain XML files. 41 </valid>
42 </sanitizer>
43 </param>
44 <expand macro="advanced_options">
45 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
46 </expand>
47 </inputs>
48 <outputs>
49 <data format="text" label="Output from stdout" name="param_stdout"/>
50 </outputs>
51 <help>SemanticValidator for semantically validating certain XML files.
26 52
27 53
28 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SemanticValidator.html 54 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SemanticValidator.html</help>
29 55 </tool>
30 @REFERENCES@
31 </help>
32 </tool>