Mercurial > repos > galaxyp > openms_baselinefilter
diff BaselineFilter.xml @ 13:2c6de76669fe draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
---|---|
date | Thu, 27 Aug 2020 19:36:32 -0400 |
parents | f5946590b034 |
children | 1936361a3dbb |
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--- a/BaselineFilter.xml Fri May 17 09:38:48 2019 -0400 +++ b/BaselineFilter.xml Thu Aug 27 19:36:32 2020 -0400 @@ -1,56 +1,54 @@ <?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: [Signal processing and preprocessing]--> -<tool id="BaselineFilter" name="BaselineFilter" version="2.3.0"> +<tool id="BaselineFilter" name="BaselineFilter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Removes the baseline from profile spectra using a top-hat filter.</description> <macros> <token name="@EXECUTABLE@">BaselineFilter</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[BaselineFilter + <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 -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $param_struc_elem_length: - -struc_elem_length $param_struc_elem_length -#end if -#if $param_struc_elem_unit: - -struc_elem_unit - #if " " in str($param_struc_elem_unit): - "$param_struc_elem_unit" - #else - $param_struc_elem_unit - #end if -#end if -#if $param_method: - -method - #if " " in str($param_method): - "$param_method" - #else - $param_method - #end if -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__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")}' + +## 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 raw data file" help="(-in) "/> - <param name="param_struc_elem_length" type="float" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help="(-struc_elem_length) "/> - <param name="param_struc_elem_unit" display="radio" type="select" optional="False" value="Thomson" label="Unit of 'struc_elem_length' paramete" help="(-struc_elem_unit) "> + <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/> + <param name="struc_elem_length" argument="-struc_elem_length" type="float" optional="true" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/> + <param name="struc_elem_unit" argument="-struc_elem_unit" display="radio" type="select" optional="false" label="Unit of 'struc_elem_length' paramete" help=""> <option value="Thomson" selected="true">Thomson</option> <option value="DataPoints">DataPoints</option> + <expand macro="list_string_san"/> </param> - <param name="param_method" type="select" optional="False" value="tophat" label="The name of the morphological filter to be applied" help="(-method) If you are unsure, use the default"> + <param name="method" argument="-method" type="select" optional="false" label="The name of the morphological filter to be applied" help="If you are unsure, use the default"> <option value="identity">identity</option> <option value="erosion">erosion</option> <option value="dilation">dilation</option> @@ -61,16 +59,31 @@ <option value="bothat">bothat</option> <option value="erosion_simple">erosion_simple</option> <option value="dilation_simple">dilation_simple</option> + <expand macro="list_string_san"/> </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 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> </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>Removes the baseline from profile spectra using a top-hat filter. + <tests> + <expand macro="autotest_BaselineFilter"/> + <expand macro="manutest_BaselineFilter"/> + </tests> + <help><![CDATA[Removes the baseline from profile spectra using a top-hat filter. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_BaselineFilter.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_BaselineFilter.html]]></help> + <expand macro="references"/> </tool>