Mercurial > repos > galaxyp > openms_metaprosip
diff MetaProSIP.xml @ 14:5f72a8fa935d draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp |
|---|---|
| date | Fri, 14 Jun 2024 21:38:48 +0000 |
| parents | 819ed5aae76f |
| children |
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--- a/MetaProSIP.xml Thu Dec 01 18:58:27 2022 +0000 +++ b/MetaProSIP.xml Fri Jun 14 21:38:48 2024 +0000 @@ -1,8 +1,7 @@ -<?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]--> +<!--Proposed Tool Section: [Quantitation]--> <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> + <description>Performs proteinSIP on peptide features for elemental flux analysis</description> <macros> <token name="@EXECUTABLE@">MetaProSIP</token> <import>macros.xml</import> @@ -15,13 +14,13 @@ ## Preprocessing mkdir in_mzML && -ln -s '$in_mzML' 'in_mzML/${re.sub("[^\w\-_]", "_", $in_mzML.element_identifier)}.$gxy2omsext($in_mzML.ext)' && +cp '$in_mzML' 'in_mzML/${re.sub("[^\w\-_]", "_", $in_mzML.element_identifier)}.$gxy2omsext($in_mzML.ext)' && mkdir in_fasta && -ln -s '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' && +cp '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' && mkdir out_csv && mkdir out_peptide_centric_csv && mkdir in_featureXML && -ln -s '$in_featureXML' 'in_featureXML/${re.sub("[^\w\-_]", "_", $in_featureXML.element_identifier)}.$gxy2omsext($in_featureXML.ext)' && +cp '$in_featureXML' 'in_featureXML/${re.sub("[^\w\-_]", "_", $in_featureXML.element_identifier)}.$gxy2omsext($in_featureXML.ext)' && ## Main program call @@ -51,17 +50,17 @@ <configfile name="hardcoded_json"><![CDATA[{"r_executable": "R", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <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=""> + <param argument="-in_mzML" type="data" format="mzml" label="Centroided MS1 data" help=" select mzml data sets(s)"/> + <param argument="-in_fasta" type="data" format="fasta" label="Protein sequence database" help=" select fasta data sets(s)"/> + <param argument="-in_featureXML" type="data" format="featurexml" label="Feature data annotated with identifications (IDMapper)" help=" select featurexml data sets(s)"/> + <param argument="-mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help=""/> + <param argument="-rt_tolerance_s" type="float" value="30.0" label="Tolerance window around feature rt for XIC extraction" help=""/> + <param argument="-intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help=""/> + <param argument="-correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help=""/> + <param argument="-xic_threshold" type="float" 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" 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" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help=""/> + <param argument="-plot_extension" type="select" 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> @@ -70,7 +69,7 @@ <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 argument="-labeling_element" type="select" optional="true" label="Which element (single letter code) is labeled" help=""> + <param argument="-labeling_element" type="select" 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> @@ -83,23 +82,23 @@ <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 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=""> + <param argument="-min_correlation_distance_to_averagine" type="float" 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" 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" 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" 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" 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" value="20" label="Number of RIA bins for heat map generation" help=""/> + <param argument="-observed_peak_fraction" type="float" value="0.5" label="Fraction of observed/expected peaks" help=""/> + <param argument="-min_consecutive_isotopes" type="integer" value="2" label="Minimum number of consecutive isotopic intensities needed" help=""/> + <param argument="-score_plot_yaxis_min" type="float" 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" 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" name="collect_method"/> </param> - <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="-lowRIA_correlation_threshold" type="float" 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=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -114,7 +113,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_MetaProSIP_1 --> + <tests> + <!-- TOPP_MetaProSIP_1 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="min_correlation_distance_to_averagine" value="-1.0"/> @@ -133,8 +133,8 @@ </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"/> + <output name="out_csv" value="MetaProSIP_1_output_1.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="out_peptide_centric_csv" value="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"/> @@ -157,11 +157,14 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> </tests> <help><![CDATA[Performs proteinSIP on peptide features for elemental flux analysis. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MetaProSIP.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MetaProSIP.html]]></help> <expand macro="references"/> </tool>