Mercurial > repos > galaxyp > openms_rnpxlxicfilter
diff RNPxlXICFilter.xml @ 8:8a2e37503e3e 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 19:48:37 -0400 |
parents | 397b489a4f8d |
children | c2827f0ca312 |
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--- a/RNPxlXICFilter.xml Fri May 17 10:22:24 2019 -0400 +++ b/RNPxlXICFilter.xml Thu Aug 27 19:48:37 2020 -0400 @@ -1,56 +1,78 @@ <?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="RNPxlXICFilter" name="RNPxlXICFilter" version="2.3.0"> +<tool id="RNPxlXICFilter" name="RNPxlXICFilter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Remove MS2 spectra from treatment based on the fold change between control and treatment.</description> <macros> <token name="@EXECUTABLE@">RNPxlXICFilter</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[RNPxlXICFilter + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re + +## Preprocessing +mkdir control && +ln -s '$control' 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)' && +mkdir treatment && +ln -s '$treatment' 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)' && +mkdir out && + +## Main program call -#if $param_control: - -control $param_control -#end if -#if $param_treatment: - -treatment $param_treatment -#end if -#if $param_fold_change: - -fold_change $param_fold_change -#end if -#if $param_rt_tol: - -rt_tol $param_rt_tol -#end if -#if $param_mz_tol: - -mz_tol $param_mz_tol -#end if -#if $param_out: - -out $param_out -#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 +-control +'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)' +-treatment +'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)' +-out +'out/output.${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_control" type="data" format="mzml" optional="False" label="input mzML file" help="(-control) "/> - <param name="param_treatment" type="data" format="mzml" optional="False" label="input mzML file" help="(-treatment) "/> - <param name="param_fold_change" type="float" value="2.0" label="fold change between XICs" help="(-fold_change) "/> - <param name="param_rt_tol" type="float" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help="(-rt_tol) "/> - <param name="param_mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help="(-mz_tol) "/> - <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) "/> + <param name="control" argument="-control" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/> + <param name="treatment" argument="-treatment" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/> + <param name="fold_change" argument="-fold_change" type="float" optional="true" value="2.0" label="fold change between XICs" help=""/> + <param name="rt_tol" argument="-rt_tol" type="float" optional="true" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/> + <param name="mz_tol" argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/> + <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>Remove MS2 spectra from treatment based on the fold change between control and treatment. + <tests> + <expand macro="autotest_RNPxlXICFilter"/> + <expand macro="manutest_RNPxlXICFilter"/> + </tests> + <help><![CDATA[Remove MS2 spectra from treatment based on the fold change between control and treatment. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_RNPxlXICFilter.html</help> +For more information, visit http://www.openms.de/documentation/UTILS_RNPxlXICFilter.html]]></help> + <expand macro="references"/> </tool>