Mercurial > repos > galaxyp > openms_xmlvalidator

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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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b19fb08ca900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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2 <!--Proposed Tool Section: [[for Developers]]-->
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3 <tool id="XMLValidator" name="XMLValidator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Validates XML files against an XSD schema</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">XMLValidator</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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15 ## Preprocessing
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16 mkdir in &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 #if $schema:
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19 mkdir schema &&
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20 cp '$schema' 'schema/${re.sub("[^\w\-_]", "_", $schema.element_identifier)}.$gxy2omsext($schema.ext)' &&
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21 #end if
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23 ## Main program call
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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31 #if $schema:
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32 -schema
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33 'schema/${re.sub("[^\w\-_]", "_", $schema.element_identifier)}.$gxy2omsext($schema.ext)'
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34 #end if
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35 | tee '$stdout'
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37 ## Postprocessing
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38 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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39 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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40 #end if]]></command>
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41 <configfiles>
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42 <inputs name="args_json" data_style="paths"/>
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43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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44 </configfiles>
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45 <inputs>
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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)"/>
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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)"/>
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48 <expand macro="adv_opts_macro">
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49 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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50 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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51 <expand macro="list_string_san" name="test"/>
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52 </param>
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53 </expand>
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54 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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55 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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56 </param>
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57 </inputs>
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58 <outputs>
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59 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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60 <filter>OPTIONAL_OUTPUTS is None</filter>
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61 </data>
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62 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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63 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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64 </data>
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65 </outputs>
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66 <tests>
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67 <test expect_num_outputs="1">
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68 <!-- just chosen an arbitrary input and autgenerated output-->
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69 <param name="adv_opts|test" value="true"/>
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70 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
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71 <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
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72 <assert_contents>
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73 <has_text text="Success: the file is valid!"/>
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74 </assert_contents>
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75 </output>
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76 </test>
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77 <test expect_num_outputs="1">
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78 <!-- just chosen an arbitrary input and autgenerated output-->
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79 <param name="adv_opts|test" value="true"/>
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80 <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
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81 <param name="schema" ftype="xsd" location="https://raw.githubusercontent.com/HUPO-PSI/mzML/master/schema/schema_1.1/mzML1.1.0.xsd"/>
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82 <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
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83 <assert_contents>
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84 <has_text text="Success: the file is valid!"/>
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85 </assert_contents>
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86 </output>
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87 </test>
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88 </tests>
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89 <help><![CDATA[Validates XML files against an XSD schema.
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90
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91
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92 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_XMLValidator.html]]></help>
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93 <expand macro="references"/>
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94 </tool>