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comparison mzml_validator.xml @ 0:5961146e0d1a draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator commit d9676cbf7a1f8bd1cf0af742585893459d4861aa
author recetox
date Fri, 20 Jan 2023 12:41:59 +0000
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1 <tool id="mzml_validator" name="mzML Schema Validator" version="0.1.0+galaxy0" profile="21.05">
2 <description>validates mzML files against XML Schema Definition (XSD)</description>
3 <creator>
4 <person
5 givenName="Maksym"
6 familyName="Skoryk"
7 url="https://github.com/maximskorik"
8 identifier="0000-0003-2056-8018" />
9 <organization
10 url="https://www.recetox.muni.cz/"
11 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
12 name="RECETOX MUNI" />
13 </creator>
14
15 <requirements>
16 <requirement type="package" version="4.9.1">lxml</requirement>
17 </requirements>
18 <command detect_errors="exit_code"><![CDATA[
19 python3 '${__tool_directory__}/mzml_validator_wrapper.py'
20 --input_file '$input'
21 --schemas_dir '${__tool_directory__}/schemas'
22 --xsd_versions $xsd_versions
23 --log_file '$log'
24 ]]></command>
25 <inputs>
26 <param name="input" type="data" format="mzml" label="Input mzML file"/>
27 <param name="xsd_versions" type="select" label="Schema version to validate against" multiple="true" display="checkboxes"
28 help="select XML schema definition (XSD) version to validate the file against. If both are selected, a file is valid if matches against any of the versions.">
29 <option value="1.1.1">1.1.1</option>
30 <option value="1.1.0">1.1.0</option>
31 </param>
32 </inputs>
33 <outputs>
34 <data name="log" format="txt" label="mzML Validation on ${on_string}" />
35 </outputs>
36 <tests>
37 <test> <!-- test 1: validate mzML 1.1.1 against both XSDs -->
38 <param name="input" value="small_pwiz_1.1.1_truncated.mzML" />
39 <param name="xsd_versions" value="1.1.0,1.1.1" />
40 <output name="log">
41 <assert_contents>
42 <has_text text="Validated against mzML XML Schema Definition v1.1.1" />
43 </assert_contents>
44 </output>
45 </test>
46 <test expect_failure="true" expect_exit_code="1"> <!-- test 2: try validate mzML 1.1.1 against XSD v1.1.0 -->
47 <param name="input" value="small_pwiz_1.1.1_truncated.mzML" />
48 <param name="xsd_versions" value="1.1.0" />
49 <assert_stderr>
50 <has_text text="Failed to validate against mzML XML Schema Definition v1.1.0" />
51 </assert_stderr>
52 </test>
53 <test expect_failure="true" expect_exit_code="1"> <!-- test 3: validate corrupted mzML -->
54 <param name="input" value="mbr_truncated.mzml" />
55 <param name="xsd_versions" value="1.1.0,1.1.1" />
56 <assert_stderr>
57 <has_text text="Failed to validate against mzML XML Schema Definition v1.1.0" />
58 <has_text text="Failed to validate against mzML XML Schema Definition v1.1.1" />
59 </assert_stderr>
60 </test>
61 </tests>
62 <help><![CDATA[
63 **mzML Schema Validator** validates mzML files against XML Schema Definition (XSD) developed by HUPO Proteomics Standard Initiative
64 (https://www.psidev.info/mzML).
65 ]]></help>
66 </tool>