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comparison XMLValidator.xml @ 14:ad2ba3a95a02 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:37:46 +0000
parents f036e8cf1a55
children
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13:f036e8cf1a55 14:ad2ba3a95a02
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 CTDConverter.--> 1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 2 <!--Proposed Tool Section: [[for Developers]]-->
4 <tool id="XMLValidator" name="XMLValidator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="XMLValidator" name="XMLValidator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Validates XML files against an XSD schema.</description> 4 <description>Validates XML files against an XSD schema</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">XMLValidator</token> 6 <token name="@EXECUTABLE@">XMLValidator</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 #if $schema: 18 #if $schema:
20 mkdir schema && 19 mkdir schema &&
21 ln -s '$schema' 'schema/${re.sub("[^\w\-_]", "_", $schema.element_identifier)}.$gxy2omsext($schema.ext)' && 20 cp '$schema' 'schema/${re.sub("[^\w\-_]", "_", $schema.element_identifier)}.$gxy2omsext($schema.ext)' &&
22 #end if 21 #end if
23 22
24 ## Main program call 23 ## Main program call
25 24
26 set -o pipefail && 25 set -o pipefail &&
42 <configfiles> 41 <configfiles>
43 <inputs name="args_json" data_style="paths"/> 42 <inputs name="args_json" data_style="paths"/>
44 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
45 </configfiles> 44 </configfiles>
46 <inputs> 45 <inputs>
47 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzdata,mzid,mzml,mzxml,pepxml,traml,xml" optional="false" label="file to validate" help=" select consensusxml,featurexml,idxml,mzdata,mzid,mzml,mzxml,pepxml,traml,xml data sets(s)"/> 46 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzdata,mzid,mzml,mzxml,pepxml,traml,xml" label="file to validate" help=" select consensusxml,featurexml,idxml,mzdata,mzid,mzml,mzxml,pepxml,traml,xml data sets(s)"/>
48 <param argument="-schema" type="data" format="xml" optional="true" label="schema to validate against" help="If no schema is given, the file is validated against the latest schema of the file type select xml data sets(s)"/> 47 <param argument="-schema" type="data" format="xsd" optional="true" label="schema to validate against" help="If no schema is given, the file is validated against the latest schema of the file type select xsd data sets(s)"/>
49 <expand macro="adv_opts_macro"> 48 <expand macro="adv_opts_macro">
50 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 49 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
51 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 50 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
52 <expand macro="list_string_san" name="test"/> 51 <expand macro="list_string_san" name="test"/>
53 </param> 52 </param>
54 </expand> 53 </expand>
55 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 54 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
56 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 55 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
62 </data> 61 </data>
63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 62 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
64 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 63 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
65 </data> 64 </data>
66 </outputs> 65 </outputs>
67 <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> 66 <tests>
68 <param name="adv_opts|test" value="true"/> 67 <test expect_num_outputs="1">
69 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> 68 <!-- just chosen an arbitrary input and autgenerated output-->
70 <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4"> 69 <param name="adv_opts|test" value="true"/>
71 <assert_contents><has_text text="Success: the file is valid!"/></assert_contents> 70 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
72 </output> 71 <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
73 </test> 72 <assert_contents>
74 </tests> 73 <has_text text="Success: the file is valid!"/>
74 </assert_contents>
75 </output>
76 </test>
77 <test expect_num_outputs="1">
78 <!-- just chosen an arbitrary input and autgenerated output-->
79 <param name="adv_opts|test" value="true"/>
80 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
81 <param name="schema" ftype="xsd" location="https://raw.githubusercontent.com/HUPO-PSI/mzML/master/schema/schema_1.1/mzML1.1.0.xsd"/>
82 <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
83 <assert_contents>
84 <has_text text="Success: the file is valid!"/>
85 </assert_contents>
86 </output>
87 </test>
88 </tests>
75 <help><![CDATA[Validates XML files against an XSD schema. 89 <help><![CDATA[Validates XML files against an XSD schema.
76 90
77 91
78 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_XMLValidator.html]]></help> 92 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_XMLValidator.html]]></help>
79 <expand macro="references"/> 93 <expand macro="references"/>
80 </tool> 94 </tool>