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| <!--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 and OpenSWATH]--> | ||
| <tool id="AssayGeneratorMetaboSirius" name="AssayGeneratorMetaboSirius" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> | ||
| <description>Assay library generation from a SIRIUS project directory (Metabolomics)</description> | ||
| <macros> | ||
| <token name="@EXECUTABLE@">AssayGeneratorMetaboSirius</token> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"/> | ||
| <expand macro="stdio"/> | ||
| <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | ||
| @EXT_FOO@ | ||
| #import re | ||
| ## Preprocessing | ||
| mkdir in && | ||
| cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && | ||
| mkdir in_compoundinfo && | ||
| cp '$in_compoundinfo' 'in_compoundinfo/${re.sub("[^\w\-_]", "_", $in_compoundinfo.element_identifier)}.$gxy2omsext($in_compoundinfo.ext)' && | ||
| mkdir out && | ||
| ## Main program call | ||
| set -o pipefail && | ||
| @EXECUTABLE@ -write_ctd ./ && | ||
| python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | ||
| @EXECUTABLE@ -ini @EXECUTABLE@.ctd | ||
| -in | ||
| 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' | ||
| -in_compoundinfo | ||
| 'in_compoundinfo/${re.sub("[^\w\-_]", "_", $in_compoundinfo.element_identifier)}.$gxy2omsext($in_compoundinfo.ext)' | ||
| -out | ||
| 'out/output.${out_type}' | ||
| ## Postprocessing | ||
| && mv 'out/output.${out_type}' '$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 argument="-in" type="data" format="txt" label="SIRIUS project directory" help=" select txt data sets(s)"/> | ||
| <param argument="-in_compoundinfo" type="data" format="tabular" label="Compound info table (.tsv file)" help=" select tabular data sets(s)"/> | ||
| <param name="out_type" type="select" label="File type of output out (Assay library output file)"> | ||
| <option value="tsv">tabular (tsv)</option> | ||
| <option value="traML">traml</option> | ||
| <option value="pqp">pqp</option> | ||
| </param> | ||
| <param argument="-ambiguity_resolution_mz_tolerance" type="float" value="10.0" label="Mz tolerance for the resolution of identification ambiguity over multiple files" help=""/> | ||
| <param argument="-ambiguity_resolution_rt_tolerance" type="float" value="10.0" label="RT tolerance in seconds for the resolution of identification ambiguity over multiple files" help=""/> | ||
| <param argument="-total_occurrence_filter" type="float" min="0.0" max="1.0" value="0.1" label="Filter compound based on total occurrence in analysed samples" help=""/> | ||
| <param argument="-fragment_annotation_score_threshold" type="float" min="0.0" max="1.0" value="0.8" label="Filters annotations based on the explained intensity of the peaks in a spectrum" help=""/> | ||
| <param argument="-method" type="select" label="Spectrum with the highest precursor intensity or a consensus spectrum is used for assay library construction (if no fragment annotation is used)" help=""> | ||
| <option value="highest_intensity" selected="true">highest_intensity</option> | ||
| <option value="consensus_spectrum">consensus_spectrum</option> | ||
| <expand macro="list_string_san" name="method"/> | ||
| </param> | ||
| <param argument="-use_exact_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use exact mass for precursor and fragment annotations" help=""/> | ||
| <param argument="-exclude_ms2_precursor" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Excludes precursor in ms2 from transition list" help=""/> | ||
| <param argument="-use_known_unknowns" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use features without identification information" help=""/> | ||
| <param argument="-min_transitions" type="integer" value="3" label="Minimal number of transitions" help=""/> | ||
| <param argument="-max_transitions" type="integer" value="6" label="Maximal number of transitions" help=""/> | ||
| <param argument="-transition_threshold" type="float" value="5.0" label="Further transitions need at least x% of the maximum intensity (default 5%)" help=""/> | ||
| <param argument="-decoy_generation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decoys will be generated using the fragmentation tree re-rooting approach" help="This option does only work in combination with the fragment annotation via Sirius"/> | ||
| <param argument="-decoy_generation_method" type="select" label="Uses different methods for decoy generation" help="Basis for the method is the fragmentation-tree re-rooting approach ('original'). This approach can be extended by using 'resolve_overlap', which will resolve overlapping target/decoy fragments by adding -CH2 mass to the overlapping decoy fragments. 'generate_missing_decoys' will add a -CH2 mass shift to the target fragments and use them as decoys if fragmentation-tree re-rooting failed. 'Both' combines the extended methods (resolve_overlap, generate_missing_decoys)"> | ||
| <option value="original" selected="true">original</option> | ||
| <option value="resolve_overlap">resolve_overlap</option> | ||
| <option value="generate_missing_decoys">generate_missing_decoys</option> | ||
| <option value="both">both</option> | ||
| <expand macro="list_string_san" name="decoy_generation_method"/> | ||
| </param> | ||
| <param argument="-decoy_resolution_mz_tolerance" type="float" value="10.0" label="Mz tolerance for the resolution of overlapping m/z values for targets and decoys of one compound" help=""/> | ||
| <expand macro="adv_opts_macro"> | ||
| <param argument="-ambiguity_resolution_mz_tolerance_unit" type="select" label="Unit of the ambiguity_resolution_mz_tolerance" help=""> | ||
| <option value="ppm" selected="true">ppm</option> | ||
| <option value="Da">Da</option> | ||
| <expand macro="list_string_san" name="ambiguity_resolution_mz_tolerance_unit"/> | ||
| </param> | ||
| <param argument="-min_fragment_mz" type="float" value="0.0" label="Minimal m/z of a fragment ion choosen as a transition" help=""/> | ||
| <param argument="-max_fragment_mz" type="float" value="2000.0" label="Maximal m/z of a fragment ion choosen as a transition" help=""/> | ||
| <param argument="-decoy_resolution_mz_tolerance_unit" type="select" label="Unit of the decoy_resolution_mz_tolerance" help=""> | ||
| <option value="ppm" selected="true">ppm</option> | ||
| <option value="Da">Da</option> | ||
| <expand macro="list_string_san" name="decoy_resolution_mz_tolerance_unit"/> | ||
| </param> | ||
| <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" 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> | ||
| <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | ||
| <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | ||
| </param> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="out" label="${tool.name} on ${on_string}: out" format="pqp"> | ||
| <change_format> | ||
| <when input="out_type" value="traML" format="traml"/> | ||
| <when input="out_type" value="tsv" format="tabular"/> | ||
| </change_format> | ||
| </data> | ||
| <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | ||
| <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | ||
| </data> | ||
| </outputs> | ||
| <tests> | ||
| <!-- TOPP_AssayGeneratorMetaboSirius_1 --> | ||
| <test expect_num_outputs="2"> | ||
| <section name="adv_opts"> | ||
| <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/> | ||
| <param name="min_fragment_mz" value="0.0"/> | ||
| <param name="max_fragment_mz" value="2000.0"/> | ||
| <param name="decoy_resolution_mz_tolerance_unit" value="ppm"/> | ||
| <param name="force" value="false"/> | ||
| <param name="test" value="true"/> | ||
| </section> | ||
| <param name="in" value="AssayGeneratorMetabo-in-SIRIUS-project"/> | ||
| <param name="in_compoundinfo" value="SiriusExport_2_output_compoundinfo.tsv" ftype="tabular"/> | ||
| <param name="out_type" value="tsv"/> | ||
| <output name="out" value="AssayGeneratorMetaboSirius_output_1.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> | ||
| <param name="ambiguity_resolution_mz_tolerance" value="10.0"/> | ||
| <param name="ambiguity_resolution_rt_tolerance" value="10.0"/> | ||
| <param name="total_occurrence_filter" value="0.1"/> | ||
| <param name="fragment_annotation_score_threshold" value="0.8"/> | ||
| <param name="method" value="highest_intensity"/> | ||
| <param name="use_exact_mass" value="false"/> | ||
| <param name="exclude_ms2_precursor" value="true"/> | ||
| <param name="use_known_unknowns" value="false"/> | ||
| <param name="min_transitions" value="3"/> | ||
| <param name="max_transitions" value="3"/> | ||
| <param name="transition_threshold" value="5.0"/> | ||
| <param name="decoy_generation" value="false"/> | ||
| <param name="decoy_generation_method" value="original"/> | ||
| <param name="decoy_resolution_mz_tolerance" value="10.0"/> | ||
| <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | ||
| <output name="ctd_out" ftype="xml"> | ||
| <assert_contents> | ||
| <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> | ||
| <!-- TOPP_AssayGeneratorMetaboSirius_2 --> | ||
| <test expect_num_outputs="2"> | ||
| <section name="adv_opts"> | ||
| <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/> | ||
| <param name="min_fragment_mz" value="0.0"/> | ||
| <param name="max_fragment_mz" value="2000.0"/> | ||
| <param name="decoy_resolution_mz_tolerance_unit" value="ppm"/> | ||
| <param name="force" value="false"/> | ||
| <param name="test" value="true"/> | ||
| </section> | ||
| <param name="in" value="AssayGeneratorMetabo-in-SIRIUS-project"/> | ||
| <param name="in_compoundinfo" value="SiriusExport_2_output_compoundinfo.tsv" ftype="tabular"/> | ||
| <param name="out_type" value="tsv"/> | ||
| <output name="out" value="AssayGeneratorMetaboSirius_output_2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> | ||
| <param name="ambiguity_resolution_mz_tolerance" value="10.0"/> | ||
| <param name="ambiguity_resolution_rt_tolerance" value="10.0"/> | ||
| <param name="total_occurrence_filter" value="0.1"/> | ||
| <param name="fragment_annotation_score_threshold" value="0.8"/> | ||
| <param name="method" value="highest_intensity"/> | ||
| <param name="use_exact_mass" value="false"/> | ||
| <param name="exclude_ms2_precursor" value="true"/> | ||
| <param name="use_known_unknowns" value="true"/> | ||
| <param name="min_transitions" value="3"/> | ||
| <param name="max_transitions" value="3"/> | ||
| <param name="transition_threshold" value="5.0"/> | ||
| <param name="decoy_generation" value="false"/> | ||
| <param name="decoy_generation_method" value="original"/> | ||
| <param name="decoy_resolution_mz_tolerance" value="10.0"/> | ||
| <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | ||
| <output name="ctd_out" ftype="xml"> | ||
| <assert_contents> | ||
| <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> | ||
| <!-- TOPP_AssayGeneratorMetaboSirius_3 --> | ||
| <test expect_num_outputs="2"> | ||
| <section name="adv_opts"> | ||
| <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/> | ||
| <param name="min_fragment_mz" value="0.0"/> | ||
| <param name="max_fragment_mz" value="2000.0"/> | ||
| <param name="decoy_resolution_mz_tolerance_unit" value="ppm"/> | ||
| <param name="force" value="false"/> | ||
| <param name="test" value="true"/> | ||
| </section> | ||
| <param name="in" value="AssayGeneratorMetabo-in-SIRIUS-project"/> | ||
| <param name="in_compoundinfo" value="SiriusExport_2_output_compoundinfo.tsv" ftype="tabular"/> | ||
| <param name="out_type" value="tsv"/> | ||
| <output name="out" value="AssayGeneratorMetaboSirius_output_3.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> | ||
| <param name="ambiguity_resolution_mz_tolerance" value="10.0"/> | ||
| <param name="ambiguity_resolution_rt_tolerance" value="10.0"/> | ||
| <param name="total_occurrence_filter" value="0.1"/> | ||
| <param name="fragment_annotation_score_threshold" value="0.8"/> | ||
| <param name="method" value="highest_intensity"/> | ||
| <param name="use_exact_mass" value="false"/> | ||
| <param name="exclude_ms2_precursor" value="true"/> | ||
| <param name="use_known_unknowns" value="false"/> | ||
| <param name="min_transitions" value="3"/> | ||
| <param name="max_transitions" value="3"/> | ||
| <param name="transition_threshold" value="5.0"/> | ||
| <param name="decoy_generation" value="true"/> | ||
| <param name="decoy_generation_method" value="resolve_overlap"/> | ||
| <param name="decoy_resolution_mz_tolerance" value="10.0"/> | ||
| <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | ||
| <output name="ctd_out" ftype="xml"> | ||
| <assert_contents> | ||
| <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[Assay library generation from a SIRIUS project directory (Metabolomics) | ||
| For more information, visit https://openms.de/doxygen/release/3.2.0/html/TOPP_AssayGeneratorMetaboSirius.html]]></help> | ||
| <expand macro="references"/> | ||
| </tool> |
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