Mercurial > repos > galaxyp > openms_semanticvalidator
diff SemanticValidator.xml @ 9:702ed84d9f4c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
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date | Thu, 03 Sep 2020 16:18:18 +0000 |
parents | 6f22beeb9f32 |
children | b60c5420dac6 |
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--- a/SemanticValidator.xml Fri May 17 09:21:26 2019 -0400 +++ b/SemanticValidator.xml Thu Sep 03 16:18:18 2020 +0000 @@ -1,54 +1,83 @@ <?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]--> -<tool id="SemanticValidator" name="SemanticValidator" version="2.3.0"> +<tool id="SemanticValidator" name="SemanticValidator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>SemanticValidator for semantically validating certain XML files.</description> <macros> <token name="@EXECUTABLE@">SemanticValidator</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> + <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[SemanticValidator + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re -#if $param_in: - -in $param_in -#end if -#if $param_mapping_file: - -mapping_file $param_mapping_file +## Preprocessing +mkdir in && +ln -s '$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)' && +#if $cv: + mkdir cv && + ${ ' '.join(["ln -s '%s' 'cv/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _]) } #end if --cv - #for token in $param_cv: - $token - #end for -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +-mapping_file +'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' +#if $cv: + -cv + ${' '.join(["'cv/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv if _])} #end if -#end if -> $param_stdout -]]></command> +| tee '$stdout' + +## Postprocessing +#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS + && mv '@EXECUTABLE@.ctd' '$ctd_out' +#end if]]></command> + <configfiles> + <inputs name="args_json" data_style="paths"/> + <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> + </configfiles> <inputs> - <param name="param_in" type="data" format="analysisXML,mzml,traml,mzid,mzData,xml" optional="False" label="Input file (any xml file)" help="(-in) "/> - <param name="param_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="(-mapping_file) "/> - <param name="param_cv" type="data" format="obo" multiple="true" optional="True" size="30" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help="(-cv) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="in" 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 name="mapping_file" 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 name="cv" 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)"/> + <expand macro="adv_opts_macro"> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> + <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san"/> + </param> + </expand> + <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> - <expand macro="advanced_options"> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> - </expand> </inputs> <outputs> - <data name="param_stdout" format="txt" label="Output from stdout"/> + <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> + <filter>OPTIONAL_OUTPUTS is None</filter> + </data> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>SemanticValidator for semantically validating certain XML files. + <tests> + <expand macro="autotest_SemanticValidator"/> + <expand macro="manutest_SemanticValidator"/> + </tests> + <help><![CDATA[SemanticValidator for semantically validating certain XML files. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SemanticValidator.html</help> +For more information, visit http://www.openms.de/documentation/UTILS_SemanticValidator.html]]></help> + <expand macro="references"/> </tool>