Mercurial > repos > galaxyp > openms_semanticvalidator
diff SemanticValidator.xml @ 14:a421b4ddf47c 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 21:30:38 +0000 |
| parents | ff9d0d1c2c1c |
| children |
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--- a/SemanticValidator.xml Thu Dec 01 18:57:56 2022 +0000 +++ b/SemanticValidator.xml Fri Jun 14 21:30:38 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="SemanticValidator" name="SemanticValidator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>SemanticValidator for semantically validating certain XML files.</description> + <description>SemanticValidator for semantically validating certain XML files</description> <macros> <token name="@EXECUTABLE@">SemanticValidator</token> <import>macros.xml</import> @@ -15,16 +14,16 @@ ## 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($in.ext)' && mkdir mapping_file && -ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && +cp '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && #if $cv_cond.cv: mkdir cv_cond.cv && #if $cv_cond.cv_select == "no" mkdir ${' '.join(["'cv_cond.cv/%s'" % (i) for i, f in enumerate($cv_cond.cv) if f])} && - ${' '.join(["ln -s '%s' 'cv_cond.cv/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_cond.cv) if f])} + ${' '.join(["cp '%s' 'cv_cond.cv/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_cond.cv) if f])} #else - ln -s '$cv_cond.cv' 'cv_cond.cv/${re.sub("[^\w\-_]", "_", $cv_cond.cv.element_identifier)}.$gxy2omsext($cv_cond.cv.ext)' && + cp '$cv_cond.cv' 'cv_cond.cv/${re.sub("[^\w\-_]", "_", $cv_cond.cv.element_identifier)}.$gxy2omsext($cv_cond.cv.ext)' && #end if #end if @@ -57,8 +56,8 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="mzdata,mzid,mzml,traml,xml" optional="false" label="Input file (any xml file)" help=" select mzdata,mzid,mzml,traml,xml data sets(s)"/> - <param argument="-mapping_file" type="data" format="xml" optional="false" label="Mapping file which is used to semantically validate the given XML file against this mapping file (see 'share/OpenMS/MAPPING' for templates)" help=" select xml data sets(s)"/> + <param argument="-in" type="data" format="mzdata,mzid,mzml,traml,xml" label="Input file (any xml file)" help=" select mzdata,mzid,mzml,traml,xml data sets(s)"/> + <param argument="-mapping_file" type="data" format="xml" label="Mapping file which is used to semantically validate the given XML file against this mapping file (see 'share/OpenMS/MAPPING' for templates)" help=" select xml data sets(s)"/> <conditional name="cv_cond"> <param name="cv_select" type="select" label="Run tool in batch mode for -cv"> <option value="no">No: process all datasets jointly</option> @@ -68,12 +67,12 @@ <param argument="-cv" type="data" format="obo" multiple="true" optional="true" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help=" select obo data sets(s)"/> </when> <when value="yes"> - <param argument="-cv" type="data" format="obo" multiple="false" optional="true" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help=" select obo data sets(s)"/> + <param argument="-cv" type="data" format="obo" optional="true" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help=" select obo data sets(s)"/> </when> </conditional> <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> @@ -89,18 +88,22 @@ <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 (same as XMLValidator) and autgenerated output--> - <param name="adv_opts|test" value="true"/> - <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> - <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/> - <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4"> - <assert_contents><has_text text="Congratulations, the file is valid!"/></assert_contents> - </output> - </test> -</tests> + <tests> + <test expect_num_outputs="1"> + <!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output--> + <param name="adv_opts|test" value="true"/> + <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> + <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/> + <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4"> + <assert_contents> + <has_text text="Congratulations, the file is valid!"/> + </assert_contents> + </output> + </test> + </tests> <help><![CDATA[SemanticValidator for semantically validating certain XML files. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SemanticValidator.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SemanticValidator.html]]></help> <expand macro="references"/> </tool>