Mercurial > repos > recetox > mzml_validator

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author recetox
date Thu, 12 Oct 2023 13:30:39 +0000
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1 <tool id="mzml_validator" name="mzML Schema Validator" version="0.1.0+galaxy2" profile="21.05">
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2 <description>validates mzML files against XML Schema Definition (XSD)</description>
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3 <creator>
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4 <person
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5 givenName="Maksym"
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6 familyName="Skoryk"
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7 url="https://github.com/maximskorik"
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8 identifier="0000-0003-2056-8018" />
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9 <organization
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10 url="https://www.recetox.muni.cz/"
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11 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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12 name="RECETOX MUNI" />
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13 </creator>
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15 <requirements>
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16 <requirement type="package" version="4.9.1">lxml</requirement>
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17 </requirements>
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18 <command detect_errors="exit_code"><![CDATA[
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19 python3 '${__tool_directory__}/mzml_validator_wrapper.py'
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20 --input_file '$input'
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21 --schemas_dir '${__tool_directory__}/schemas'
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22 --xsd_versions $xsd_versions
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23 --log_file '$log'
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24 ]]></command>
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25 <inputs>
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26 <param name="input" type="data" format="mzml" label="Input mzML file"/>
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27 <param name="xsd_versions" type="select" label="Schema version to validate against" multiple="true" display="checkboxes"
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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.">
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29 <option value="1.1.1">1.1.1</option>
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30 <option value="1.1.0">1.1.0</option>
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31 </param>
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32 </inputs>
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33 <outputs>
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34 <data name="log" format="txt" label="mzML Validation on ${on_string}" />
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35 </outputs>
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36 <tests>
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37 <test> <!-- test 1: validate mzML 1.1.1 against both XSDs -->
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38 <param name="input" value="small_pwiz_1.1.1_truncated.mzML" />
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39 <param name="xsd_versions" value="1.1.0,1.1.1" />
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40 <output name="log">
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41 <assert_contents>
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42 <has_text text="Validated against mzML XML Schema Definition v1.1.1" />
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43 </assert_contents>
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44 </output>
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45 </test>
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46 <test expect_failure="true" expect_exit_code="1"> <!-- test 2: try validate mzML 1.1.1 against XSD v1.1.0 -->
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47 <param name="input" value="small_pwiz_1.1.1_truncated.mzML" />
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48 <param name="xsd_versions" value="1.1.0" />
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49 <assert_stderr>
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50 <has_text text="Failed to validate against mzML XML Schema Definition v1.1.0" />
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51 </assert_stderr>
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52 </test>
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53 <test expect_failure="true" expect_exit_code="1"> <!-- test 3: validate corrupted mzML -->
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54 <param name="input" value="mbr_truncated.mzml" />
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55 <param name="xsd_versions" value="1.1.0,1.1.1" />
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56 <assert_stderr>
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57 <has_text text="Failed to validate against mzML XML Schema Definition v1.1.0" />
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58 <has_text text="Failed to validate against mzML XML Schema Definition v1.1.1" />
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59 </assert_stderr>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 **mzML Schema Validator** validates mzML files against XML Schema Definition (XSD) developed by HUPO Proteomics Standard Initiative
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64 (https://www.psidev.info/mzML).
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65 ]]></help>
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66
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67 <citations>
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68 <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
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69 </citations>
0
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70 </tool>