Mercurial > repos > galaxyp > openms_precursorionselector
diff PrecursorIonSelector.xml @ 13:1cae2aac2260 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:21:13 +0000 |
| parents | fa7a58de2977 |
| children |
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--- a/PrecursorIonSelector.xml Fri Nov 06 20:38:59 2020 +0000 +++ b/PrecursorIonSelector.xml Thu Dec 01 19:21:13 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: [Targeted Experiments]--> -<tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>PrecursorIonSelector</description> <macros> <token name="@EXECUTABLE@">PrecursorIonSelector</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -106,29 +104,29 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true, "algorithm": {"Preprocessing": {"tmp_dir": "\$TMP_DIR"}}}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="featurexml" optional="false" label="Input feature map file (featureXML)" help=" select featurexml data sets(s)"/> - <param name="ids" argument="-ids" type="data" format="idxml" optional="false" label="file containing results of identification" help=" select idxml data sets(s)"/> - <param name="num_precursors" argument="-num_precursors" type="integer" optional="true" value="1" label="number of precursors to be selected" help=""/> - <param name="raw_data" argument="-raw_data" type="data" format="mzml" optional="true" label="Input profile data" help=" select mzml data sets(s)"/> - <param name="load_preprocessing" argument="-load_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is loaded from file, not calculated" help=""/> - <param name="store_preprocessing" argument="-store_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is stored" help=""/> - <param name="simulation" argument="-simulation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Simulate the whole LC-MS/MS run" help=""/> - <param name="db_path" argument="-db_path" type="data" format="fasta" optional="true" label="db file" help=" select fasta data sets(s)"/> - <param name="rt_model" argument="-rt_model" type="data" format="txt" optional="true" label="SVM Model for RTPredict" help=" select txt data sets(s)"/> - <param name="dt_model" argument="-dt_model" type="data" format="txt" optional="true" label="SVM Model for PTPredict" help=" select txt data sets(s)"/> - <param name="fixed_modifications" argument="-fixed_modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_string_val"/> - <expand macro="list_string_san"/> + <param argument="-in" type="data" format="featurexml" optional="false" label="Input feature map file (featureXML)" help=" select featurexml data sets(s)"/> + <param argument="-ids" type="data" format="idxml" optional="false" label="file containing results of identification" help=" select idxml data sets(s)"/> + <param argument="-num_precursors" type="integer" optional="true" value="1" label="number of precursors to be selected" help=""/> + <param argument="-raw_data" type="data" format="mzml" optional="true" label="Input profile data" help=" select mzml data sets(s)"/> + <param argument="-load_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is loaded from file, not calculated" help=""/> + <param argument="-store_preprocessing" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The preprocessed db is stored" help=""/> + <param argument="-simulation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Simulate the whole LC-MS/MS run" help=""/> + <param argument="-db_path" type="data" format="fasta" optional="true" label="db file" help=" select fasta data sets(s)"/> + <param argument="-rt_model" type="data" format="txt" optional="true" label="SVM Model for RTPredict" help=" select txt data sets(s)"/> + <param argument="-dt_model" type="data" format="txt" optional="true" label="SVM Model for PTPredict" help=" select txt data sets(s)"/> + <param argument="-fixed_modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val" name="fixed_modifications"/> + <expand macro="list_string_san" name="fixed_modifications"/> </param> <section name="algorithm" title="Settings for the compound list creation and rescoring" help="" expanded="false"> - <param name="type" argument="-algorithm:type" type="select" optional="false" label="Strategy for precursor ion selection" help=""> + <param name="type" argument="-algorithm:type" type="select" optional="true" label="Strategy for precursor ion selection" help=""> <option value="ILP_IPS">ILP_IPS</option> <option value="IPS" selected="true">IPS</option> <option value="SPS">SPS</option> <option value="Upshift">Upshift</option> <option value="Downshift">Downshift</option> <option value="DEX">DEX</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="type"/> </param> <param name="max_iteration" argument="-algorithm:max_iteration" type="integer" optional="true" min="1" value="100" label="Maximal number of iterations" help=""/> <param name="rt_bin_capacity" argument="-algorithm:rt_bin_capacity" type="integer" optional="true" min="1" value="10" label="Maximal number of precursors per rt bin" help=""/> @@ -161,28 +159,26 @@ </section> <section name="Preprocessing" title="" help="" expanded="false"> <param name="precursor_mass_tolerance" argument="-algorithm:Preprocessing:precursor_mass_tolerance" type="float" optional="true" min="0.0" value="10.0" label="Precursor mass tolerance which is used to query the peptide database for peptides" help=""/> - <param name="precursor_mass_tolerance_unit" argument="-algorithm:Preprocessing:precursor_mass_tolerance_unit" display="radio" type="select" optional="false" label="Precursor mass tolerance unit" help=""> + <param name="precursor_mass_tolerance_unit" argument="-algorithm:Preprocessing:precursor_mass_tolerance_unit" type="select" optional="true" label="Precursor mass tolerance unit" help=""> <option value="ppm" selected="true">ppm</option> <option value="Da">Da</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="precursor_mass_tolerance_unit"/> </param> <param name="preprocessed_db_path" argument="-algorithm:Preprocessing:preprocessed_db_path" type="text" optional="true" value="" label="Path where the preprocessed database should be stored" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="preprocessed_db_path"/> </param> <param name="preprocessed_db_pred_rt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_rt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="preprocessed_db_pred_rt_path"/> </param> <param name="preprocessed_db_pred_dt_path" argument="-algorithm:Preprocessing:preprocessed_db_pred_dt_path" type="text" optional="true" value="" label="Path where the predicted rts of the preprocessed database should be stored" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="preprocessed_db_pred_dt_path"/> </param> - <param name="max_peptides_per_run" argument="-algorithm:Preprocessing:max_peptides_per_run" type="integer" optional="true" min="1" value="100000" label="Number of peptides for that the pt and rt are parallely predicted" help=""/> + <param name="max_peptides_per_run" argument="-algorithm:Preprocessing:max_peptides_per_run" type="integer" optional="true" min="1" value="100000" label="Number of peptides for that the pt and rt are parallelly predicted" help=""/> <param name="missed_cleavages" argument="-algorithm:Preprocessing:missed_cleavages" type="integer" optional="true" min="0" value="1" label="Number of allowed missed cleavages" help=""/> <param name="taxonomy" argument="-algorithm:Preprocessing:taxonomy" type="text" optional="true" value="" label="Taxonomy" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="taxonomy"/> </param> - <param name="store_peptide_sequences" argument="-algorithm:Preprocessing:store_peptide_sequences" type="text" optional="true" value="false" label="Flag if peptide sequences should be stored" help=""> - <expand macro="list_string_san"/> - </param> + <param name="store_peptide_sequences" argument="-algorithm:Preprocessing:store_peptide_sequences" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag if peptide sequences should be stored" help=""/> <section name="rt_settings" title="" help="" expanded="false"> <param name="min_rt" argument="-algorithm:Preprocessing:rt_settings:min_rt" type="float" optional="true" min="1.0" value="960.0" label="Minimal RT in the experiment (in seconds)" help=""/> <param name="max_rt" argument="-algorithm:Preprocessing:rt_settings:max_rt" type="float" optional="true" value="3840.0" label="Maximal RT in the experiment (in seconds)" help=""/> @@ -193,14 +189,14 @@ </section> </section> <expand macro="adv_opts_macro"> - <param name="solver" argument="-solver" display="radio" type="select" optional="false" label="LP solver type" help=""> + <param argument="-solver" type="select" optional="true" label="LP solver type" help=""> <option value="GLPK" selected="true">GLPK</option> <option value="COINOR">COINOR</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="solver"/> </param> - <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="-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"> @@ -227,13 +223,156 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_PrecursorIonSelector"/> - <expand macro="manutest_PrecursorIonSelector"/> + <tests><!-- TOPP_PrecursorIonSelector_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="solver" value="GLPK"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="PrecursorIonSelector_features.featureXML"/> + <param name="ids" value="PrecursorIonSelector_ids.idXML"/> + <param name="num_precursors" value="1"/> + <param name="load_preprocessing" value="false"/> + <param name="store_preprocessing" value="false"/> + <param name="simulation" value="true"/> + <output name="sim_results" file="PrecursorIonSelector_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/> + <param name="db_path" value="PrecursorIonSelector_db.fasta"/> + <param name="fixed_modifications" value=""/> + <section name="algorithm"> + <param name="type" value="IPS"/> + <param name="max_iteration" value="10"/> + <param name="rt_bin_capacity" value="10"/> + <param name="step_size" value="1"/> + <param name="peptide_min_prob" value="0.2"/> + <param name="sequential_spectrum_order" value="false"/> + <section name="MIPFormulation"> + <section name="thresholds"> + <param name="min_protein_probability" value="0.2"/> + <param name="min_protein_id_probability" value="0.95"/> + <param name="min_pt_weight" value="0.5"/> + <param name="min_mz" value="500.0"/> + <param name="max_mz" value="5000.0"/> + <param name="min_pred_pep_prob" value="0.5"/> + <param name="min_rt_weight" value="0.5"/> + <param name="use_peptide_rule" value="true"/> + <param name="min_peptide_ids" value="2"/> + <param name="min_peptide_probability" value="0.95"/> + </section> + <section name="combined_ilp"> + <param name="k1" value="0.2"/> + <param name="k2" value="0.2"/> + <param name="k3" value="0.4"/> + <param name="scale_matching_probs" value="true"/> + </section> + <section name="feature_based"> + <param name="no_intensity_normalization" value="false"/> + <param name="max_number_precursors_per_feature" value="1"/> + </section> + </section> + <section name="Preprocessing"> + <param name="precursor_mass_tolerance" value="0.9"/> + <param name="precursor_mass_tolerance_unit" value="Da"/> + <param name="preprocessed_db_path" value=""/> + <param name="preprocessed_db_pred_rt_path" value=""/> + <param name="preprocessed_db_pred_dt_path" value=""/> + <param name="max_peptides_per_run" value="100000"/> + <param name="missed_cleavages" value="1"/> + <param name="taxonomy" value=""/> + <param name="store_peptide_sequences" value="false"/> + <section name="rt_settings"> + <param name="min_rt" value="960.0"/> + <param name="max_rt" value="3840.0"/> + <param name="rt_step_size" value="30.0"/> + <param name="gauss_mean" value="-1.0"/> + <param name="gauss_sigma" value="3.0"/> + </section> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,sim_results_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_PrecursorIonSelector_2 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="solver" value="GLPK"/> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="PrecursorIonSelector_features.featureXML"/> + <output name="out" file="PrecursorIonSelector_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <param name="ids" value="PrecursorIonSelector_ids.idXML"/> + <param name="num_precursors" value="1"/> + <param name="load_preprocessing" value="false"/> + <param name="store_preprocessing" value="false"/> + <param name="simulation" value="false"/> + <param name="db_path" value="PrecursorIonSelector_db.fasta"/> + <param name="fixed_modifications" value=""/> + <section name="algorithm"> + <param name="type" value="IPS"/> + <param name="max_iteration" value="10"/> + <param name="rt_bin_capacity" value="10"/> + <param name="step_size" value="1"/> + <param name="peptide_min_prob" value="0.2"/> + <param name="sequential_spectrum_order" value="false"/> + <section name="MIPFormulation"> + <section name="thresholds"> + <param name="min_protein_probability" value="0.2"/> + <param name="min_protein_id_probability" value="0.95"/> + <param name="min_pt_weight" value="0.5"/> + <param name="min_mz" value="500.0"/> + <param name="max_mz" value="5000.0"/> + <param name="min_pred_pep_prob" value="0.5"/> + <param name="min_rt_weight" value="0.5"/> + <param name="use_peptide_rule" value="true"/> + <param name="min_peptide_ids" value="2"/> + <param name="min_peptide_probability" value="0.95"/> + </section> + <section name="combined_ilp"> + <param name="k1" value="0.2"/> + <param name="k2" value="0.2"/> + <param name="k3" value="0.4"/> + <param name="scale_matching_probs" value="true"/> + </section> + <section name="feature_based"> + <param name="no_intensity_normalization" value="false"/> + <param name="max_number_precursors_per_feature" value="1"/> + </section> + </section> + <section name="Preprocessing"> + <param name="precursor_mass_tolerance" value="0.9"/> + <param name="precursor_mass_tolerance_unit" value="Da"/> + <param name="preprocessed_db_path" value=""/> + <param name="preprocessed_db_pred_rt_path" value=""/> + <param name="preprocessed_db_pred_dt_path" value=""/> + <param name="max_peptides_per_run" value="100000"/> + <param name="missed_cleavages" value="1"/> + <param name="taxonomy" value=""/> + <param name="store_peptide_sequences" value="false"/> + <section name="rt_settings"> + <param name="min_rt" value="960.0"/> + <param name="max_rt" value="3840.0"/> + <param name="rt_step_size" value="30.0"/> + <param name="gauss_mean" value="-1.0"/> + <param name="gauss_sigma" value="3.0"/> + </section> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[PrecursorIonSelector -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PrecursorIonSelector.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PrecursorIonSelector.html]]></help> <expand macro="references"/> </tool>