Mercurial > repos > galaxyp > openms_metaprosip
diff MetaProSIP.xml @ 13:819ed5aae76f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 18:58:27 +0000 |
| parents | c18e6eb07aa9 |
| children | 5f72a8fa935d |
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--- a/MetaProSIP.xml Fri Nov 06 20:29:40 2020 +0000 +++ b/MetaProSIP.xml Thu Dec 01 18:58:27 2022 +0000 @@ -1,13 +1,11 @@ <?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="MetaProSIP" name="MetaProSIP" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="MetaProSIP" name="MetaProSIP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Performs proteinSIP on peptide features for elemental flux analysis.</description> <macros> <token name="@EXECUTABLE@">MetaProSIP</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -53,56 +51,56 @@ <configfile name="hardcoded_json"><![CDATA[{"r_executable": "R", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in_mzML" argument="-in_mzML" type="data" format="mzml" optional="false" label="Centroided MS1 data" help=" select mzml data sets(s)"/> - <param name="in_fasta" argument="-in_fasta" type="data" format="fasta" optional="false" label="Protein sequence database" help=" select fasta data sets(s)"/> - <param name="in_featureXML" argument="-in_featureXML" type="data" format="featurexml" optional="false" label="Feature data annotated with identifications (IDMapper)" help=" select featurexml data sets(s)"/> - <param name="mz_tolerance_ppm" argument="-mz_tolerance_ppm" type="float" optional="true" value="10.0" label="Tolerance in ppm" help=""/> - <param name="rt_tolerance_s" argument="-rt_tolerance_s" type="float" optional="true" value="30.0" label="Rolerance window around feature rt for XIC extraction" help=""/> - <param name="intensity_threshold" argument="-intensity_threshold" type="float" optional="true" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help=""/> - <param name="correlation_threshold" argument="-correlation_threshold" type="float" optional="true" value="0.7" label="Correlation threshold for reporting a RIA" help=""/> - <param name="xic_threshold" argument="-xic_threshold" type="float" optional="true" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/> - <param name="decomposition_threshold" argument="-decomposition_threshold" type="float" optional="true" value="0.7" label="Minimum R-squared of decomposition that must be achieved for a peptide to be reported" help=""/> - <param name="weight_merge_window" argument="-weight_merge_window" type="float" optional="true" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help=""/> - <param name="plot_extension" argument="-plot_extension" display="radio" type="select" optional="false" label="Extension used for plots (png|svg|pdf)" help=""> + <param argument="-in_mzML" type="data" format="mzml" optional="false" label="Centroided MS1 data" help=" select mzml data sets(s)"/> + <param argument="-in_fasta" type="data" format="fasta" optional="false" label="Protein sequence database" help=" select fasta data sets(s)"/> + <param argument="-in_featureXML" type="data" format="featurexml" optional="false" label="Feature data annotated with identifications (IDMapper)" help=" select featurexml data sets(s)"/> + <param argument="-mz_tolerance_ppm" type="float" optional="true" value="10.0" label="Tolerance in ppm" help=""/> + <param argument="-rt_tolerance_s" type="float" optional="true" value="30.0" label="Rolerance window around feature rt for XIC extraction" help=""/> + <param argument="-intensity_threshold" type="float" optional="true" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help=""/> + <param argument="-correlation_threshold" type="float" optional="true" value="0.7" label="Correlation threshold for reporting a RIA" help=""/> + <param argument="-xic_threshold" type="float" optional="true" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/> + <param argument="-decomposition_threshold" type="float" optional="true" value="0.7" label="Minimum R-squared of decomposition that must be achieved for a peptide to be reported" help=""/> + <param argument="-weight_merge_window" type="float" optional="true" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help=""/> + <param argument="-plot_extension" type="select" optional="true" label="Extension used for plots (png|svg|pdf)" help=""> <option value="png" selected="true">png</option> <option value="svg">svg</option> <option value="pdf">pdf</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="plot_extension"/> </param> - <param name="qc_output_directory" argument="-qc_output_directory" type="text" optional="true" value="" label="Output directory for the quality report" help=""> - <expand macro="list_string_san"/> + <param argument="-qc_output_directory" type="text" optional="true" value="" label="Output directory for the quality report" help=""> + <expand macro="list_string_san" name="qc_output_directory"/> </param> - <param name="labeling_element" argument="-labeling_element" display="radio" type="select" optional="false" label="Which element (single letter code) is labeled" help=""> + <param argument="-labeling_element" type="select" optional="true" label="Which element (single letter code) is labeled" help=""> <option value="C" selected="true">C</option> <option value="N">N</option> <option value="H">H</option> <option value="O">O</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="labeling_element"/> </param> - <param name="use_unassigned_ids" argument="-use_unassigned_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include identifications not assigned to a feature in pattern detection" help=""/> - <param name="use_averagine_ids" argument="-use_averagine_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use averagine peptides as model to perform pattern detection on unidentified peptides" help=""/> - <param name="report_natural_peptides" argument="-report_natural_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether purely natural peptides are reported in the quality report" help=""/> - <param name="filter_monoisotopic" argument="-filter_monoisotopic" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" help=""/> - <param name="cluster" argument="-cluster" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform grouping" help=""/> + <param argument="-use_unassigned_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include identifications not assigned to a feature in pattern detection" help=""/> + <param argument="-use_averagine_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use averagine peptides as model to perform pattern detection on unidentified peptides" help=""/> + <param argument="-report_natural_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether purely natural peptides are reported in the quality report" help=""/> + <param argument="-filter_monoisotopic" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" help=""/> + <param argument="-cluster" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform grouping" help=""/> <expand macro="adv_opts_macro"> - <param name="min_correlation_distance_to_averagine" argument="-min_correlation_distance_to_averagine" type="float" optional="true" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values <= -1"/> - <param name="pattern_15N_TIC_threshold" argument="-pattern_15N_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/> - <param name="pattern_13C_TIC_threshold" argument="-pattern_13C_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/> - <param name="pattern_2H_TIC_threshold" argument="-pattern_2H_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/> - <param name="pattern_18O_TIC_threshold" argument="-pattern_18O_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/> - <param name="heatmap_bins" argument="-heatmap_bins" type="integer" optional="true" value="20" label="Number of RIA bins for heat map generation" help=""/> - <param name="observed_peak_fraction" argument="-observed_peak_fraction" type="float" optional="true" value="0.5" label="Fraction of observed/expected peaks" help=""/> - <param name="min_consecutive_isotopes" argument="-min_consecutive_isotopes" type="integer" optional="true" value="2" label="Minimum number of consecutive isotopic intensities needed" help=""/> - <param name="score_plot_yaxis_min" argument="-score_plot_yaxis_min" type="float" optional="true" value="0.0" label="The minimum value of the score axis" help="Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/> - <param name="collect_method" argument="-collect_method" display="radio" type="select" optional="false" label="How RIAs are collected" help=""> + <param argument="-min_correlation_distance_to_averagine" type="float" optional="true" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values <= -1"/> + <param argument="-pattern_15N_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/> + <param argument="-pattern_13C_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/> + <param argument="-pattern_2H_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/> + <param argument="-pattern_18O_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/> + <param argument="-heatmap_bins" type="integer" optional="true" value="20" label="Number of RIA bins for heat map generation" help=""/> + <param argument="-observed_peak_fraction" type="float" optional="true" value="0.5" label="Fraction of observed/expected peaks" help=""/> + <param argument="-min_consecutive_isotopes" type="integer" optional="true" value="2" label="Minimum number of consecutive isotopic intensities needed" help=""/> + <param argument="-score_plot_yaxis_min" type="float" optional="true" value="0.0" label="The minimum value of the score axis" help="Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/> + <param argument="-collect_method" type="select" optional="true" label="How RIAs are collected" help=""> <option value="correlation_maximum" selected="true">correlation_maximum</option> <option value="decomposition_maximum">decomposition_maximum</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="collect_method"/> </param> - <param name="lowRIA_correlation_threshold" argument="-lowRIA_correlation_threshold" type="float" optional="true" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="Disable and take correlation_threshold value for negative values"/> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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 argument="-lowRIA_correlation_threshold" type="float" optional="true" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="Disable and take correlation_threshold value for negative values"/> + <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> + <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -116,13 +114,54 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_MetaProSIP"/> - <expand macro="manutest_MetaProSIP"/> + <tests><!-- TOPP_MetaProSIP_1 --> + <test expect_num_outputs="3"> + <section name="adv_opts"> + <param name="min_correlation_distance_to_averagine" value="-1.0"/> + <param name="pattern_15N_TIC_threshold" value="0.95"/> + <param name="pattern_13C_TIC_threshold" value="0.95"/> + <param name="pattern_2H_TIC_threshold" value="0.95"/> + <param name="pattern_18O_TIC_threshold" value="0.95"/> + <param name="heatmap_bins" value="20"/> + <param name="observed_peak_fraction" value="0.5"/> + <param name="min_consecutive_isotopes" value="2"/> + <param name="score_plot_yaxis_min" value="0.0"/> + <param name="collect_method" value="correlation_maximum"/> + <param name="lowRIA_correlation_threshold" value="-1.0"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in_mzML" value="MetaProSIP_1_input.mzML"/> + <param name="in_fasta" value="MetaProSIP_1_input.fasta"/> + <output name="out_csv" file="MetaProSIP_1_output_1.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <param name="in_featureXML" value="MetaProSIP_1_input.featureXML"/> + <param name="mz_tolerance_ppm" value="10.0"/> + <param name="rt_tolerance_s" value="30.0"/> + <param name="intensity_threshold" value="10.0"/> + <param name="correlation_threshold" value="0.7"/> + <param name="xic_threshold" value="0.7"/> + <param name="decomposition_threshold" value="0.7"/> + <param name="weight_merge_window" value="5.0"/> + <param name="plot_extension" value="png"/> + <param name="qc_output_directory" value=""/> + <param name="labeling_element" value="C"/> + <param name="use_unassigned_ids" value="false"/> + <param name="use_averagine_ids" value="false"/> + <param name="report_natural_peptides" value="false"/> + <param name="filter_monoisotopic" value="false"/> + <param name="cluster" value="false"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Performs proteinSIP on peptide features for elemental flux analysis. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MetaProSIP.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MetaProSIP.html]]></help> <expand macro="references"/> </tool>