Mercurial > repos > galaxyp > openms_spectrafilterparentpeakmower
diff SpectraFilterParentPeakMower.xml @ 9:e60558a87656 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
---|---|
date | Thu, 03 Sep 2020 16:16:33 +0000 |
parents | d484676f03cd |
children | 75492ef0bff5 |
line wrap: on
line diff
--- a/SpectraFilterParentPeakMower.xml Fri May 17 09:24:23 2019 -0400 +++ b/SpectraFilterParentPeakMower.xml Thu Sep 03 16:16:33 2020 +0000 @@ -1,72 +1,80 @@ <?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="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="2.3.0"> +<tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Applies thresholdfilter to peak spectra.</description> <macros> <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</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[SpectraFilterParentPeakMower + <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_window_size: - -algorithm:window_size $param_algorithm_window_size -#end if -#if $param_algorithm_default_charge: - -algorithm:default_charge $param_algorithm_default_charge -#end if -#if $param_algorithm_consider_NH3_loss: - -algorithm:consider_NH3_loss $param_algorithm_consider_NH3_loss -#end if -#if $param_algorithm_consider_H2O_loss: - -algorithm:consider_H2O_loss $param_algorithm_consider_H2O_loss -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if - #if $adv_opts.param_algorithm_clean_all_charge_states: - -algorithm:clean_all_charge_states $adv_opts.param_algorithm_clean_all_charge_states -#end if - #if $adv_opts.param_algorithm_reduce_by_factor: - -algorithm:reduce_by_factor $adv_opts.param_algorithm_reduce_by_factor -#end if - #if $adv_opts.param_algorithm_factor: - -algorithm:factor $adv_opts.param_algorithm_factor -#end if - #if $adv_opts.param_algorithm_set_to_zero: - -algorithm:set_to_zero $adv_opts.param_algorithm_set_to_zero -#end if -#end if -]]></command> +## Postprocessing +&& mv 'out/output.${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_window_size" type="float" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size" help="(-window_size) "/> - <param name="param_algorithm_default_charge" type="integer" value="2" label="If the precursor has no charge set, the default charge is assumed" help="(-default_charge) "/> - <param name="param_algorithm_consider_NH3_loss" type="integer" value="1" label="Whether NH3 loss peaks from the precursor should be removed" help="(-consider_NH3_loss) "/> - <param name="param_algorithm_consider_H2O_loss" type="integer" value="1" label="Whether H2O loss peaks from the precursor should be removed" help="(-consider_H2O_loss) "/> - <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="param_algorithm_clean_all_charge_states" type="integer" value="1" label="Set to 1 if precursor ions of all possible charge states should be removed" help="(-clean_all_charge_states) "/> - <param name="param_algorithm_reduce_by_factor" type="integer" value="0" label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" help="(-reduce_by_factor) "/> - <param name="param_algorithm_factor" type="float" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" help="(-factor) "/> - <param name="param_algorithm_set_to_zero" type="integer" value="1" label="Reduce the intensities of the precursor and related ions to zero" help="(-set_to_zero) "/> + <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="window_size" argument="-algorithm:window_size" type="float" optional="true" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size" help=""/> + <param name="default_charge" argument="-algorithm:default_charge" type="integer" optional="true" value="2" label="If the precursor has no charge set, the default charge is assumed" help=""/> + <param name="clean_all_charge_states" argument="-algorithm:clean_all_charge_states" type="integer" optional="true" value="1" label="Set to 1 if precursor ions of all possible charge states should be removed" help=""/> + <param name="consider_NH3_loss" argument="-algorithm:consider_NH3_loss" type="integer" optional="true" value="1" label="Whether NH3 loss peaks from the precursor should be removed" help=""/> + <param name="consider_H2O_loss" argument="-algorithm:consider_H2O_loss" type="integer" optional="true" value="1" label="Whether H2O loss peaks from the precursor should be removed" help=""/> + <param name="reduce_by_factor" argument="-algorithm:reduce_by_factor" type="integer" optional="true" value="0" label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" help=""/> + <param name="factor" argument="-algorithm:factor" type="float" optional="true" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" help=""/> + <param name="set_to_zero" argument="-algorithm:set_to_zero" type="integer" optional="true" value="1" label="Reduce the intensities of the precursor and related ions to zero" help=""/> + </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> </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>Applies thresholdfilter to peak spectra. + <tests> + <expand macro="autotest_SpectraFilterParentPeakMower"/> + <expand macro="manutest_SpectraFilterParentPeakMower"/> + </tests> + <help><![CDATA[Applies thresholdfilter to peak spectra. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_SpectraFilterParentPeakMower.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_SpectraFilterParentPeakMower.html]]></help> + <expand macro="references"/> </tool>