Mercurial > repos > galaxyp > openms_cvinspector
diff CVInspector.xml @ 17:f95704542c63 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
---|---|
date | Thu, 01 Dec 2022 18:56:45 +0000 |
parents | 53695d887eaa |
children | c8e5389abfc5 |
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--- a/CVInspector.xml Fri Nov 06 20:27:11 2020 +0000 +++ b/CVInspector.xml Thu Dec 01 18:56:45 2022 +0000 @@ -1,13 +1,11 @@ <?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="CVInspector" name="CVInspector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="CVInspector" name="CVInspector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>A tool for visualization and validation of PSI mapping and CV files.</description> <macros> <token name="@EXECUTABLE@">CVInspector</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -16,12 +14,15 @@ #import re ## Preprocessing -mkdir cv_files && -${ ' '.join(["ln -s '%s' 'cv_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _]) } -#if $mapping_file: - mkdir mapping_file && - ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && +mkdir cv_files_cond.cv_files && +#if $cv_files_cond.cv_files_select == "no" +mkdir ${' '.join(["'cv_files_cond.cv_files/%s'" % (i) for i, f in enumerate($cv_files_cond.cv_files) if f])} && +${' '.join(["ln -s '%s' 'cv_files_cond.cv_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_files_cond.cv_files) if f])} +#else +ln -s '$cv_files_cond.cv_files' 'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' && #end if +mkdir mapping_file && +ln -s '$mapping_file' 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' && #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir html && #end if @@ -33,11 +34,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && @EXECUTABLE@ -ini @EXECUTABLE@.ctd -cv_files -${' '.join(["'cv_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $cv_files if _])} -#if $mapping_file: - -mapping_file - 'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' +#if $cv_files_cond.cv_files_select == "no" +${' '.join(["'cv_files_cond.cv_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($cv_files_cond.cv_files) if f])} +#else +'cv_files_cond.cv_files/${re.sub("[^\w\-_]", "_", $cv_files_cond.cv_files.element_identifier)}.$gxy2omsext($cv_files_cond.cv_files.ext)' #end if +-mapping_file +'mapping_file/${re.sub("[^\w\-_]", "_", $mapping_file.element_identifier)}.$gxy2omsext($mapping_file.ext)' #if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -html 'html/output.${gxy2omsext("html")}' @@ -58,20 +61,31 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="cv_files" argument="-cv_files" type="data" format="obo" multiple="true" optional="false" label="List of ontology files in OBO format" help=" select obo data sets(s)"/> - <param name="cv_names" argument="-cv_names" type="text" optional="false" value="" label="List of identifiers (one for each ontology file)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_string_val"/> - <expand macro="list_string_san"/> + <conditional name="cv_files_cond"> + <param name="cv_files_select" type="select" label="Run tool in batch mode for -cv_files"> + <option value="no">No: process all datasets jointly</option> + <option value="yes">Yes: process each dataset in an independent job</option> + </param> + <when value="no"> + <param argument="-cv_files" type="data" format="obo" multiple="true" optional="false" label="List of ontology files in OBO format" help=" select obo data sets(s)"/> + </when> + <when value="yes"> + <param argument="-cv_files" type="data" format="obo" multiple="false" optional="false" label="List of ontology files in OBO format" help=" select obo data sets(s)"/> + </when> + </conditional> + <param argument="-cv_names" type="text" optional="false" value="" label="List of identifiers (one for each ontology file)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val" name="cv_names"/> + <expand macro="list_string_san" name="cv_names"/> </param> - <param name="mapping_file" argument="-mapping_file" type="data" format="xml" optional="true" label="Mapping file in CVMapping (XML) format" help=" select xml data sets(s)"/> - <param name="ignore_cv" argument="-ignore_cv" type="text" optional="true" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_string_val"/> - <expand macro="list_string_san"/> + <param argument="-mapping_file" type="data" format="xml" optional="false" label="Mapping file in CVMapping (XML) format" help=" select xml data sets(s)"/> + <param argument="-ignore_cv" type="text" optional="true" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val" name="ignore_cv"/> + <expand macro="list_string_san" name="ignore_cv"/> </param> <expand macro="adv_opts_macro"> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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 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=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -90,13 +104,19 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_CVInspector"/> - <expand macro="manutest_CVInspector"/> - </tests> + <tests><!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml --> + <test expect_num_outputs="1"> + <param name="adv_opts|test" value="true"/> + <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/> + <param name="cv_names" value="XLMOD"/> + <param name="mapping_file" value="MAPPING/ms-mapping.xml"/> + <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/> + <output name="html" ftype="html" value="CVInspector.html"/> + </test> +</tests> <help><![CDATA[A tool for visualization and validation of PSI mapping and CV files. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_CVInspector.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_CVInspector.html]]></help> <expand macro="references"/> </tool>