Mercurial > repos > galaxyp > openms_cvinspector
diff CVInspector.xml @ 13:3b585b370ab8 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
| author | galaxyp |
|---|---|
| date | Wed, 09 Sep 2020 20:14:44 +0000 |
| parents | 8a11c915c25b |
| children | 53695d887eaa |
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--- a/CVInspector.xml Fri May 17 09:58:29 2019 -0400 +++ b/CVInspector.xml Wed Sep 09 20:14:44 2020 +0000 @@ -1,94 +1,102 @@ <?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="2.3.0"> +<tool id="CVInspector" name="CVInspector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <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="references"/> - <expand macro="stdio"/> <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[CVInspector - --cv_files - #for token in $param_cv_files: - $token - #end for + <expand macro="stdio"/> + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re -#if $rep_param_cv_names: --cv_names - #for token in $rep_param_cv_names: - #if " " in str(token): - "$token.param_cv_names" - #else - $token.param_cv_names - #end if - #end for +## Preprocessing +mkdir cv_files && +${ ' '.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($mapping_file.ext)' && +#end if +#if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir html && #end if -#if $param_mapping_file: - -mapping_file $param_mapping_file + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-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($mapping_file.ext)' +#end if +#if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -html + 'html/output.${gxy2omsext("html")}' +#end if +#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 + | tee '$stdout' #end if -#if $rep_param_ignore_cv: --ignore_cv - #for token in $rep_param_ignore_cv: - #if " " in str(token): - "$token.param_ignore_cv" - #else - $token.param_ignore_cv - #end if - #end for +## Postprocessing +#if "html_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'html/output.${gxy2omsext("html")}' '$html' #end if -#if $param_html: - -html $param_html -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +#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_cv_files" type="data" format="obo" multiple="true" optional="False" size="30" label="List of ontology files in OBO format" help="(-cv_files) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <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"/> + </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> - <repeat name="rep_param_cv_names" min="1" title="param_cv_names"> - <param name="param_cv_names" type="text" size="30" label="List of identifiers (one for each ontology file)" help="(-cv_names) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <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> - </repeat> - <param name="param_mapping_file" type="data" format="xml" optional="True" label="Mapping file in CVMapping (XML) format" help="(-mapping_file) "/> - <repeat name="rep_param_ignore_cv" min="0" max="1" title="param_ignore_cv"> - <param name="param_ignore_cv" type="text" size="30" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help="(-ignore_cv) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - </repeat> - <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> + <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> + <option value="html_FLAG">html (Enables the test mode (needed for internal use only))</option> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> + </param> </inputs> <outputs> - <data name="param_html" format="html"/> + <data name="html" label="${tool.name} on ${on_string}: html" format="html"> + <filter>OPTIONAL_OUTPUTS is not None and "html_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + <data name="stdout" format="txt" label="${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>A tool for visualization and validation of PSI mapping and CV files. + <tests> + <expand macro="autotest_CVInspector"/> + <expand macro="manutest_CVInspector"/> + </tests> + <help><![CDATA[A tool for visualization and validation of PSI mapping and CV files. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_CVInspector.html</help> +For more information, visit http://www.openms.de/documentation/UTILS_CVInspector.html]]></help> + <expand macro="references"/> </tool>