Mercurial > repos > galaxyp > openms_featurefindersuperhirn
diff FeatureFinderSuperHirn.xml @ 11:c42075bb5123 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
---|---|
date | Thu, 03 Sep 2020 16:16:49 +0000 |
parents | f0ae67837629 |
children | f35d5aa5d58a |
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--- a/FeatureFinderSuperHirn.xml Fri May 17 09:26:00 2019 -0400 +++ b/FeatureFinderSuperHirn.xml Thu Sep 03 16:16:49 2020 +0000 @@ -1,177 +1,109 @@ <?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: [Quantitation]--> -<tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="2.3.0"> +<tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Finds mass spectrometric features in mass spectra.</description> <macros> <token name="@EXECUTABLE@">FeatureFinderSuperHirn</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[FeatureFinderSuperHirn + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $param_algorithm_centroiding_active: - -algorithm:centroiding:active -#end if -#if $param_algorithm_centroiding_window_width: - -algorithm:centroiding:window_width $param_algorithm_centroiding_window_width -#end if -#if $param_algorithm_centroiding_absolute_isotope_mass_precision: - -algorithm:centroiding:absolute_isotope_mass_precision $param_algorithm_centroiding_absolute_isotope_mass_precision -#end if -#if $param_algorithm_centroiding_relative_isotope_mass_precision: - -algorithm:centroiding:relative_isotope_mass_precision $param_algorithm_centroiding_relative_isotope_mass_precision -#end if -#if $param_algorithm_centroiding_minimal_peak_height: - -algorithm:centroiding:minimal_peak_height $param_algorithm_centroiding_minimal_peak_height -#end if -#if $param_algorithm_centroiding_min_ms_signal_intensity: - -algorithm:centroiding:min_ms_signal_intensity $param_algorithm_centroiding_min_ms_signal_intensity -#end if +## Preprocessing +mkdir in && +ln -s '$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("featurexml")}' -#if $rep_param_algorithm_ms1_precursor_detection_scan_levels: --algorithm:ms1:precursor_detection_scan_levels - #for token in $rep_param_algorithm_ms1_precursor_detection_scan_levels: - #if " " in str(token): - "$token.param_algorithm_ms1_precursor_detection_scan_levels" - #else - $token.param_algorithm_ms1_precursor_detection_scan_levels - #end if - #end for -#end if -#if $param_algorithm_ms1_max_inter_scan_distance: - -algorithm:ms1:max_inter_scan_distance $param_algorithm_ms1_max_inter_scan_distance -#end if -#if $param_algorithm_ms1_tr_resolution: - -algorithm:ms1:tr_resolution $param_algorithm_ms1_tr_resolution -#end if -#if $param_algorithm_ms1_intensity_threshold: - -algorithm:ms1:intensity_threshold $param_algorithm_ms1_intensity_threshold -#end if -#if $param_algorithm_ms1_max_inter_scan_rt_distance: - -algorithm:ms1:max_inter_scan_rt_distance $param_algorithm_ms1_max_inter_scan_rt_distance -#end if -#if $param_algorithm_ms1_min_nb_cluster_members: - -algorithm:ms1:min_nb_cluster_members $param_algorithm_ms1_min_nb_cluster_members -#end if -#if $param_algorithm_ms1_detectable_isotope_factor: - -algorithm:ms1:detectable_isotope_factor $param_algorithm_ms1_detectable_isotope_factor -#end if -#if $param_algorithm_ms1_intensity_cv: - -algorithm:ms1:intensity_cv $param_algorithm_ms1_intensity_cv -#end if -#if $param_algorithm_ms1_retention_time_tolerance: - -algorithm:ms1:retention_time_tolerance $param_algorithm_ms1_retention_time_tolerance -#end if -#if $param_algorithm_ms1_mz_tolerance: - -algorithm:ms1:mz_tolerance $param_algorithm_ms1_mz_tolerance -#end if -#if $param_algorithm_ms1_feature_merger_active: - -algorithm:ms1_feature_merger:active - #if " " in str($param_algorithm_ms1_feature_merger_active): - "$param_algorithm_ms1_feature_merger_active" - #else - $param_algorithm_ms1_feature_merger_active - #end if -#end if -#if $param_algorithm_ms1_feature_merger_tr_resolution: - -algorithm:ms1_feature_merger:tr_resolution $param_algorithm_ms1_feature_merger_tr_resolution -#end if -#if $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance: - -algorithm:ms1_feature_merger:initial_apex_tr_tolerance $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance -#end if -#if $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance: - -algorithm:ms1_feature_merger:feature_merging_tr_tolerance $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance -#end if -#if $param_algorithm_ms1_feature_merger_intensity_variation_percentage: - -algorithm:ms1_feature_merger:intensity_variation_percentage $param_algorithm_ms1_feature_merger_intensity_variation_percentage -#end if -#if $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering: - -algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering -#end if -#if $param_algorithm_ms1_feature_selection_options_start_elution_window: - -algorithm:ms1_feature_selection_options:start_elution_window $param_algorithm_ms1_feature_selection_options_start_elution_window -#end if -#if $param_algorithm_ms1_feature_selection_options_end_elution_window: - -algorithm:ms1_feature_selection_options:end_elution_window $param_algorithm_ms1_feature_selection_options_end_elution_window -#end if -#if $param_algorithm_ms1_feature_selection_options_mz_range_min: - -algorithm:ms1_feature_selection_options:mz_range_min $param_algorithm_ms1_feature_selection_options_mz_range_min -#end if -#if $param_algorithm_ms1_feature_selection_options_mz_range_max: - -algorithm:ms1_feature_selection_options:mz_range_max $param_algorithm_ms1_feature_selection_options_mz_range_max -#end if -#if $param_algorithm_ms1_feature_selection_options_chrg_range_min: - -algorithm:ms1_feature_selection_options:chrg_range_min $param_algorithm_ms1_feature_selection_options_chrg_range_min -#end if -#if $param_algorithm_ms1_feature_selection_options_chrg_range_max: - -algorithm:ms1_feature_selection_options:chrg_range_max $param_algorithm_ms1_feature_selection_options_chrg_range_max -#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("featurexml")}' '$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 profile data file" help="(-in) "/> - <param name="param_algorithm_centroiding_active" display="radio" type="boolean" truevalue="-algorithm:centroiding:active" falsevalue="" checked="false" optional="True" label="MS1 data centroid data" help="(-active) "/> - <param name="param_algorithm_centroiding_window_width" type="integer" min="1" optional="True" value="5" label="Centroid window width" help="(-window_width) "/> - <param name="param_algorithm_centroiding_absolute_isotope_mass_precision" type="float" min="0.0" optional="True" value="0.01" label="Absolute isotope mass precision (Da)" help="(-absolute_isotope_mass_precision) "/> - <param name="param_algorithm_centroiding_relative_isotope_mass_precision" type="float" min="0.0" optional="True" value="10.0" label="Relative isotope mass precision" help="(-relative_isotope_mass_precision) "/> - <param name="param_algorithm_centroiding_minimal_peak_height" type="float" min="0.0" optional="True" value="0.0" label="Minimal peak height" help="(-minimal_peak_height) "/> - <param name="param_algorithm_centroiding_min_ms_signal_intensity" type="float" min="0.0" optional="True" value="50.0" label="Minimal Centroid MS Signal Intensity" help="(-min_ms_signal_intensity) "/> - <repeat name="rep_param_algorithm_ms1_precursor_detection_scan_levels" min="0" max="1" title="param_algorithm_ms1_precursor_detection_scan_levels"> - <param name="param_algorithm_ms1_precursor_detection_scan_levels" type="text" size="30" value="1" label="Precursor detection scan levels" help="(-precursor_detection_scan_levels) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input profile data file" help=" select mzml data sets(s)"/> + <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> + <section name="centroiding" title="" help="" expanded="false"> + <param name="active" argument="-algorithm:centroiding:active" type="boolean" truevalue="true" falsevalue="false" checked="false" label="MS1 data centroid data" help=""/> + <param name="window_width" argument="-algorithm:centroiding:window_width" type="integer" optional="true" min="1" value="5" label="Centroid window width" help=""/> + <param name="absolute_isotope_mass_precision" argument="-algorithm:centroiding:absolute_isotope_mass_precision" type="float" optional="true" min="0.0" value="0.01" label="Absolute isotope mass precision (Da)" help=""/> + <param name="relative_isotope_mass_precision" argument="-algorithm:centroiding:relative_isotope_mass_precision" type="float" optional="true" min="0.0" value="10.0" label="Relative isotope mass precision" help=""/> + <param name="minimal_peak_height" argument="-algorithm:centroiding:minimal_peak_height" type="float" optional="true" min="0.0" value="0.0" label="Minimal peak height" help=""/> + <param name="min_ms_signal_intensity" argument="-algorithm:centroiding:min_ms_signal_intensity" type="float" optional="true" min="0.0" value="50.0" label="Minimal Centroid MS Signal Intensity" help=""/> + </section> + <section name="ms1" title="" help="" expanded="false"> + <param name="precursor_detection_scan_levels" argument="-algorithm:ms1:precursor_detection_scan_levels" type="text" optional="true" value="1" label="Precursor detection scan levels" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_integer_valsan"/> + </param> + <param name="max_inter_scan_distance" argument="-algorithm:ms1:max_inter_scan_distance" type="integer" optional="true" min="0" value="0" label="MS1 max inter scan distance" help=""/> + <param name="tr_resolution" argument="-algorithm:ms1:tr_resolution" type="float" optional="true" min="0.0" value="0.01" label="MS1 LC retention time resolution" help=""/> + <param name="intensity_threshold" argument="-algorithm:ms1:intensity_threshold" type="float" optional="true" min="0.0" value="1000.0" label="FT peak detect MS1 intensity min threshold" help=""/> + <param name="max_inter_scan_rt_distance" argument="-algorithm:ms1:max_inter_scan_rt_distance" type="float" optional="true" min="0.0" value="0.1" label="MS1 max inter scan distance" help=""/> + <param name="min_nb_cluster_members" argument="-algorithm:ms1:min_nb_cluster_members" type="integer" optional="true" min="0" value="4" label="FT peak detect MS1 min nb peak members" help=""/> + <param name="detectable_isotope_factor" argument="-algorithm:ms1:detectable_isotope_factor" type="float" optional="true" min="0.0" value="0.05" label="Detectable isotope facto" help=""/> + <param name="intensity_cv" argument="-algorithm:ms1:intensity_cv" type="float" optional="true" min="0.0" value="0.9" label="IntensityCV" help=""/> + <param name="retention_time_tolerance" argument="-algorithm:ms1:retention_time_tolerance" type="float" optional="true" min="0.0" value="0.5" label="MS1 retention time tolerance (minutes)" help=""/> + <param name="mz_tolerance" argument="-algorithm:ms1:mz_tolerance" type="float" optional="true" min="0.0" value="0.0" label="MS1 m/z tolerance (ppm)" help=""/> + </section> + <section name="ms1_feature_merger" title="" help="" expanded="false"> + <param name="active" argument="-algorithm:ms1_feature_merger:active" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Activation of MS1 feature merging post processing" help=""/> + <param name="tr_resolution" argument="-algorithm:ms1_feature_merger:tr_resolution" type="float" optional="true" min="0.0" value="0.01" label="MS1 LC retention time resolution" help=""/> + <param name="initial_apex_tr_tolerance" argument="-algorithm:ms1_feature_merger:initial_apex_tr_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Initial Apex Tr tolerance" help=""/> + <param name="feature_merging_tr_tolerance" argument="-algorithm:ms1_feature_merger:feature_merging_tr_tolerance" type="float" optional="true" min="0.0" value="1.0" label="MS1 feature Tr merging tolerance" help=""/> + <param name="intensity_variation_percentage" argument="-algorithm:ms1_feature_merger:intensity_variation_percentage" type="float" optional="true" min="0.0" max="100.0" value="25.0" label="Percentage of intensity variation between LC border peaks" help=""/> + <param name="ppm_tolerance_for_mz_clustering" argument="-algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering" type="float" optional="true" min="0.0" value="10.0" label="PPM value for the m/z clustering of merging candidates" help=""/> + </section> + <section name="ms1_feature_selection_options" title="" help="" expanded="false"> + <param name="start_elution_window" argument="-algorithm:ms1_feature_selection_options:start_elution_window" type="float" optional="true" min="0.0" value="0.0" label="start elution window (minutes)" help=""/> + <param name="end_elution_window" argument="-algorithm:ms1_feature_selection_options:end_elution_window" type="float" optional="true" min="0.0" value="180.0" label="end elution window (minutes)" help=""/> + <param name="mz_range_min" argument="-algorithm:ms1_feature_selection_options:mz_range_min" type="float" optional="true" min="0.0" value="0.0" label="MS1 feature mz range min" help=""/> + <param name="mz_range_max" argument="-algorithm:ms1_feature_selection_options:mz_range_max" type="float" optional="true" min="0.0" value="2000.0" label="MS1 feature mz range max" help=""/> + <param name="chrg_range_min" argument="-algorithm:ms1_feature_selection_options:chrg_range_min" type="integer" optional="true" min="0" value="1" label="MS1 feature CHRG range min" help=""/> + <param name="chrg_range_max" argument="-algorithm:ms1_feature_selection_options:chrg_range_max" type="integer" optional="true" min="0" value="5" label="MS1 feature CHRG range max" help=""/> + </section> + </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> - </repeat> - <param name="param_algorithm_ms1_max_inter_scan_distance" type="integer" min="0" optional="True" value="0" label="MS1 max inter scan distance" help="(-max_inter_scan_distance) "/> - <param name="param_algorithm_ms1_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution) "/> - <param name="param_algorithm_ms1_intensity_threshold" type="float" min="0.0" optional="True" value="1000.0" label="FT peak detect MS1 intensity min threshold" help="(-intensity_threshold) "/> - <param name="param_algorithm_ms1_max_inter_scan_rt_distance" type="float" min="0.0" optional="True" value="0.1" label="MS1 max inter scan distance" help="(-max_inter_scan_rt_distance) "/> - <param name="param_algorithm_ms1_min_nb_cluster_members" type="integer" min="0" optional="True" value="4" label="FT peak detect MS1 min nb peak members" help="(-min_nb_cluster_members) "/> - <param name="param_algorithm_ms1_detectable_isotope_factor" type="float" min="0.0" optional="True" value="0.05" label="Detectable isotope facto" help="(-detectable_isotope_factor) "/> - <param name="param_algorithm_ms1_intensity_cv" type="float" min="0.0" optional="True" value="0.9" label="IntensityCV" help="(-intensity_cv) "/> - <param name="param_algorithm_ms1_retention_time_tolerance" type="float" min="0.0" optional="True" value="0.5" label="MS1 retention time tolerance (minutes)" help="(-retention_time_tolerance) "/> - <param name="param_algorithm_ms1_mz_tolerance" type="float" min="0.0" optional="True" value="0.0" label="MS1 m/z tolerance (ppm)" help="(-mz_tolerance) "/> - <param name="param_algorithm_ms1_feature_merger_active" display="radio" type="select" optional="False" value="true" label="Activation of MS1 feature merging post processing" help="(-active) "> - <option value="true" selected="true">true</option> - <option value="false">false</option> + </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> - <param name="param_algorithm_ms1_feature_merger_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution) "/> - <param name="param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Initial Apex Tr tolerance" help="(-initial_apex_tr_tolerance) "/> - <param name="param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance" type="float" min="0.0" optional="True" value="1.0" label="MS1 feature Tr merging tolerance" help="(-feature_merging_tr_tolerance) "/> - <param name="param_algorithm_ms1_feature_merger_intensity_variation_percentage" type="float" min="0.0" max="100.0" optional="True" value="25.0" label="Percentage of intensity variation between LC border peaks" help="(-intensity_variation_percentage) "/> - <param name="param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering" type="float" min="0.0" optional="True" value="10.0" label="PPM value for the m/z clustering of merging candidates" help="(-ppm_tolerance_for_mz_clustering) "/> - <param name="param_algorithm_ms1_feature_selection_options_start_elution_window" type="float" min="0.0" optional="True" value="0.0" label="start elution window (minutes)" help="(-start_elution_window) "/> - <param name="param_algorithm_ms1_feature_selection_options_end_elution_window" type="float" min="0.0" optional="True" value="180.0" label="end elution window (minutes)" help="(-end_elution_window) "/> - <param name="param_algorithm_ms1_feature_selection_options_mz_range_min" type="float" min="0.0" optional="True" value="0.0" label="MS1 feature mz range min" help="(-mz_range_min) "/> - <param name="param_algorithm_ms1_feature_selection_options_mz_range_max" type="float" min="0.0" optional="True" value="2000.0" label="MS1 feature mz range max" help="(-mz_range_max) "/> - <param name="param_algorithm_ms1_feature_selection_options_chrg_range_min" type="integer" min="0" optional="True" value="1" label="MS1 feature CHRG range min" help="(-chrg_range_min) "/> - <param name="param_algorithm_ms1_feature_selection_options_chrg_range_max" type="integer" min="0" optional="True" value="5" label="MS1 feature CHRG range max" help="(-chrg_range_max) "/> - <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="featurexml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Finds mass spectrometric features in mass spectra. + <tests> + <expand macro="autotest_FeatureFinderSuperHirn"/> + <expand macro="manutest_FeatureFinderSuperHirn"/> + </tests> + <help><![CDATA[Finds mass spectrometric features in mass spectra. - -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderSuperHirn.html</help> +For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_FeatureFinderSuperHirn.html]]></help> + <expand macro="references"/> </tool>