Mercurial > repos > galaxyp > openms_qcmerger
diff QCMerger.xml @ 9:aeb80a19bda0 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, 27 Aug 2020 19:42:35 -0400 |
parents | 8c627b0c8276 |
children | 786873b9c3e3 |
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--- a/QCMerger.xml Fri May 17 09:55:08 2019 -0400 +++ b/QCMerger.xml Thu Aug 27 19:42:35 2020 -0400 @@ -1,59 +1,73 @@ <?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="QCMerger" name="QCMerger" version="2.3.0"> +<tool id="QCMerger" name="QCMerger" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Merges two qcml files together.</description> <macros> <token name="@EXECUTABLE@">QCMerger</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[QCMerger + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re +## Preprocessing +mkdir in && +${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } +mkdir out && + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd -in - #for token in $param_in: - $token - #end for -#if $param_out: - -out $param_out -#end if -#if $param_setname: - -setname "$param_setname" -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} +-out +'out/output.${gxy2omsext("qcml")}' + +## Postprocessing +&& mv 'out/output.${gxy2omsext("qcml")}' '$out' +#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="qcml" multiple="true" optional="False" size="30" label="List of qcml files to be merged" help="(-in) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="in" argument="-in" type="data" format="qcml" multiple="true" optional="false" label="List of qcml files to be merged" help=" select qcml data sets(s)"/> + <param name="setname" argument="-setname" type="text" optional="true" value="" label="Use only when all given qcml files belong to one set, which will be held under the given name" help=""> + <expand macro="list_string_san"/> </param> - <param name="param_setname" type="text" size="30" label="Use only when all given qcml files belong to one set, which will be held under the given name" help="(-setname) "> - <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> + </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_out" format="qcml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Merges two qcml files together. + <tests> + <expand macro="autotest_QCMerger"/> + <expand macro="manutest_QCMerger"/> + </tests> + <help><![CDATA[Merges two qcml files together. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_QCMerger.html</help> +For more information, visit http://www.openms.de/documentation/UTILS_QCMerger.html]]></help> + <expand macro="references"/> </tool>