Mercurial > repos > galaxyp > openms_xmlvalidator
diff XMLValidator.xml @ 14:ad2ba3a95a02 draft default tip
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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--- a/XMLValidator.xml Thu Dec 01 19:11:46 2022 +0000 +++ b/XMLValidator.xml Fri Jun 14 21:37:46 2024 +0000 @@ -1,8 +1,7 @@ -<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> -<!--Proposed Tool Section: [Utilities]--> +<!--Proposed Tool Section: [[for Developers]]--> <tool id="XMLValidator" name="XMLValidator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Validates XML files against an XSD schema.</description> + <description>Validates XML files against an XSD schema</description> <macros> <token name="@EXECUTABLE@">XMLValidator</token> <import>macros.xml</import> @@ -15,10 +14,10 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #if $schema: mkdir schema && - ln -s '$schema' 'schema/${re.sub("[^\w\-_]", "_", $schema.element_identifier)}.$gxy2omsext($schema.ext)' && + cp '$schema' 'schema/${re.sub("[^\w\-_]", "_", $schema.element_identifier)}.$gxy2omsext($schema.ext)' && #end if ## Main program call @@ -44,11 +43,11 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <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)"/> - <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)"/> + <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)"/> + <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)"/> <expand macro="adv_opts_macro"> <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -64,17 +63,32 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> - <param name="adv_opts|test" value="true"/> - <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> - <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4"> - <assert_contents><has_text text="Success: the file is valid!"/></assert_contents> - </output> - </test> -</tests> + <tests> + <test expect_num_outputs="1"> + <!-- just chosen an arbitrary input and autgenerated output--> + <param name="adv_opts|test" value="true"/> + <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> + <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4"> + <assert_contents> + <has_text text="Success: the file is valid!"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <!-- just chosen an arbitrary input and autgenerated output--> + <param name="adv_opts|test" value="true"/> + <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> + <param name="schema" ftype="xsd" location="https://raw.githubusercontent.com/HUPO-PSI/mzML/master/schema/schema_1.1/mzML1.1.0.xsd"/> + <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4"> + <assert_contents> + <has_text text="Success: the file is valid!"/> + </assert_contents> + </output> + </test> + </tests> <help><![CDATA[Validates XML files against an XSD schema. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_XMLValidator.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_XMLValidator.html]]></help> <expand macro="references"/> </tool>