Mercurial > repos > galaxyp > openms_spectrafilternormalizer
diff SpectraFilterNormalizer.xml @ 9:8904d228594a draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
---|---|
date | Thu, 03 Sep 2020 16:24:06 +0000 |
parents | d82bd07d8190 |
children | d736764156d9 |
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--- a/SpectraFilterNormalizer.xml Fri May 17 10:04:45 2019 -0400 +++ b/SpectraFilterNormalizer.xml Thu Sep 03 16:24:06 2020 +0000 @@ -1,52 +1,77 @@ <?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: [Identification]--> -<tool id="SpectraFilterNormalizer" name="SpectraFilterNormalizer" version="2.3.0"> +<tool id="SpectraFilterNormalizer" name="SpectraFilterNormalizer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Normalizes intensity of peak spectra.</description> <macros> <token name="@EXECUTABLE@">SpectraFilterNormalizer</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[SpectraFilterNormalizer + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re + +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +mkdir out && + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +-out +'out/output.${gxy2omsext("mzml")}' -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $param_algorithm_method: - -algorithm:method - #if " " in str($param_algorithm_method): - "$param_algorithm_method" - #else - $param_algorithm_method - #end if -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +## Postprocessing +&& mv 'out/output.${gxy2omsext("mzml")}' '$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="mzml" optional="False" label="input file" help="(-in) "/> - <param name="param_algorithm_method" display="radio" type="select" optional="False" value="to_one" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="(-method) intensity of one ('to_one') per spectrum"> - <option value="to_one" selected="true">to_one</option> - <option value="to_TIC">to_TIC</option> + <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> + <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false"> + <param name="method" argument="-algorithm:method" display="radio" type="select" optional="false" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="intensity of one ('to_one') per spectrum"> + <option value="to_one" selected="true">to_one</option> + <option value="to_TIC">to_TIC</option> + <expand macro="list_string_san"/> + </param> + </section> + <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="mzml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Normalizes intensity of peak spectra. + <tests> + <expand macro="autotest_SpectraFilterNormalizer"/> + <expand macro="manutest_SpectraFilterNormalizer"/> + </tests> + <help><![CDATA[Normalizes intensity of peak spectra. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_SpectraFilterNormalizer.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_SpectraFilterNormalizer.html]]></help> + <expand macro="references"/> </tool>