Mercurial > repos > galaxyp > openms_featurefindermultiplex
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp |
|---|---|
| date | Fri, 14 Jun 2024 21:36:30 +0000 |
| parents | 9876bda3ec53 |
| children |
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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: [Quantitation]--> <tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Determination of peak ratios in LC-MS data</description> <macros> <token name="@EXECUTABLE@">FeatureFinderMultiplex</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($in.ext)' && #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out && #end if #if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_multiplets && #end if #if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_blacklist && #end if ## 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($in.ext)' #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out 'out/output.${gxy2omsext("featurexml")}' #end if #if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out_multiplets 'out_multiplets/output.${gxy2omsext("consensusxml")}' #end if #if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out_blacklist 'out_blacklist/output.${gxy2omsext("mzml")}' #end if #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' #end if ## Postprocessing #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out/output.${gxy2omsext("featurexml")}' '$out' #end if #if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out_multiplets/output.${gxy2omsext("consensusxml")}' '$out_multiplets' #end if #if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out_blacklist/output.${gxy2omsext("mzml")}' '$out_blacklist' #end if #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="mzml" label="LC-MS dataset in either centroid or profile mode" help=" select mzml data sets(s)"/> <section name="algorithm" title="algorithmic parameters" help="" expanded="false"> <param name="labels" argument="-algorithm:labels" type="text" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="If the sample is unlabelled (i.e. you want to detect only single peptide features) please leave this parameter empty. [...] specifies the labels for a single sample. For example. [][Lys8,Arg10] ... SILAC. [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC. [Dimethyl0][Dimethyl6] ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL"> <expand macro="list_string_san" name="labels"/> </param> <param name="charge" argument="-algorithm:charge" type="text" value="1:4" label="Range of charge states in the sample" help="i.e. min charge : max charge"> <expand macro="list_string_san" name="charge"/> </param> <param name="isotopes_per_peptide" argument="-algorithm:isotopes_per_peptide" type="text" value="3:6" label="Range of isotopes per peptide in the sample" help="For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. "> <expand macro="list_string_san" name="isotopes_per_peptide"/> </param> <param name="rt_typical" argument="-algorithm:rt_typical" type="float" min="0.0" value="40.0" label="Typical retention time [s] over which a characteristic peptide elutes" help="(This is not an upper bound. Peptides that elute for longer will be reported.)"/> <param name="rt_band" argument="-algorithm:rt_band" type="float" min="0.0" value="0.0" label="The algorithm searches for characteristic isotopic peak patterns, spectrum by spectrum" help="For some low-intensity peptides, an important peak might be missing in one spectrum but be present in one of the neighbouring ones. The algorithm takes a bundle of neighbouring spectra with width rt_band into account. For example with rt_band = 0, all characteristic isotopic peaks have to be present in one and the same spectrum. As rt_band increases, the sensitivity of the algorithm but also the likelihood of false detections increases"/> <param name="rt_min" argument="-algorithm:rt_min" type="float" min="0.0" value="2.0" label="Lower bound for the retention time [s]" help="(Any peptides seen for a shorter time period are not reported.)"/> <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="float" min="0.0" value="6.0" label="m/z tolerance for search of peak patterns" help=""/> <param name="mz_unit" argument="-algorithm:mz_unit" type="select" label="Unit of the 'mz_tolerance' paramete" help=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> <expand macro="list_string_san" name="mz_unit"/> </param> <param name="intensity_cutoff" argument="-algorithm:intensity_cutoff" type="float" min="0.0" value="1000.0" label="Lower bound for the intensity of isotopic peaks" help=""/> <param name="peptide_similarity" argument="-algorithm:peptide_similarity" type="float" min="-1.0" max="1.0" value="0.5" label="Two peptides in a multiplet are expected to have the same isotopic pattern" help="This parameter is a lower bound on their similarity"/> <param name="averagine_similarity" argument="-algorithm:averagine_similarity" type="float" min="-1.0" max="1.0" value="0.4" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position" help="This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model"/> <param name="averagine_similarity_scaling" argument="-algorithm:averagine_similarity_scaling" type="float" min="0.0" max="1.0" value="0.95" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -> p' = p and x = 1 -> p' = 1. (For knock_out = true, peptide doublets and singlets are detected simultaneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/> <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/> <param name="spectrum_type" argument="-algorithm:spectrum_type" type="select" label="Type of MS1 spectra in input mzML file" help="'automatic' determines the spectrum type directly from the input mzML file"> <option value="profile">profile</option> <option value="centroid">centroid</option> <option value="automatic" selected="true">automatic</option> <expand macro="list_string_san" name="spectrum_type"/> </param> <param name="averagine_type" argument="-algorithm:averagine_type" type="select" label="The type of averagine to use, currently RNA, DNA or peptide" help=""> <option value="peptide" selected="true">peptide</option> <option value="RNA">RNA</option> <option value="DNA">DNA</option> <expand macro="list_string_san" name="averagine_type"/> </param> <param name="knock_out" argument="-algorithm:knock_out" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Is it likely that knock-outs are present" help="(Supported for doublex, triplex and quadruplex experiments only.)"/> </section> <section name="labels" title="mass shifts for all possible labels" help="" expanded="false"> <param name="Arg6" argument="-labels:Arg6" type="float" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/> <param name="Arg10" argument="-labels:Arg10" type="float" min="0.0" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help=""/> <param name="Lys4" argument="-labels:Lys4" type="float" min="0.0" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help=""/> <param name="Lys6" argument="-labels:Lys6" type="float" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/> <param name="Lys8" argument="-labels:Lys8" type="float" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help=""/> <param name="Leu3" argument="-labels:Leu3" type="float" min="0.0" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help=""/> <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" min="0.0" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help=""/> <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" min="0.0" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help=""/> <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help=""/> <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help=""/> <param name="ICPL0" argument="-labels:ICPL0" type="float" min="0.0" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help=""/> <param name="ICPL4" argument="-labels:ICPL4" type="float" min="0.0" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help=""/> <param name="ICPL6" argument="-labels:ICPL6" type="float" min="0.0" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help=""/> <param name="ICPL10" argument="-labels:ICPL10" type="float" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help=""/> </section> <expand macro="adv_opts_macro"> <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="out_FLAG">out (Output file containing the individual peptide features)</option> <option value="out_multiplets_FLAG">out_multiplets (Optional output file containing all detected peptide groups)</option> <option value="out_blacklist_FLAG">out_blacklist (Optional output file containing all peaks which have been associated with a peptide feature (and subsequently blacklisted))</option> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> <outputs> <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"> <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> <data name="out_multiplets" label="${tool.name} on ${on_string}: out_multiplets" format="consensusxml"> <filter>OPTIONAL_OUTPUTS is not None and "out_multiplets_FLAG" in OPTIONAL_OUTPUTS</filter> </data> <data name="out_blacklist" label="${tool.name} on ${on_string}: out_blacklist" format="mzml"> <filter>OPTIONAL_OUTPUTS is not None and "out_blacklist_FLAG" in OPTIONAL_OUTPUTS</filter> </data> <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> <filter>OPTIONAL_OUTPUTS is None</filter> </data> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> <tests> <!-- TOPP_FeatureFinderMultiplex_1 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/> <output name="out" value="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <output name="out_multiplets" value="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="algorithm"> <param name="labels" value="[Dimethyl0][Dimethyl8]"/> <param name="charge" value="1:4"/> <param name="isotopes_per_peptide" value="3:6"/> <param name="rt_typical" value="90.0"/> <param name="rt_band" value="10.0"/> <param name="rt_min" value="5.0"/> <param name="mz_tolerance" value="40.0"/> <param name="mz_unit" value="ppm"/> <param name="intensity_cutoff" value="10.0"/> <param name="peptide_similarity" value="0.8"/> <param name="averagine_similarity" value="0.75"/> <param name="averagine_similarity_scaling" value="0.75"/> <param name="missed_cleavages" value="1"/> <param name="spectrum_type" value="automatic"/> <param name="averagine_type" value="peptide"/> <param name="knock_out" value="false"/> </section> <section name="labels"> <param name="Arg6" value="6.0201290268"/> <param name="Arg10" value="10.0082686"/> <param name="Lys4" value="4.0251069836"/> <param name="Lys6" value="6.0201290268"/> <param name="Lys8" value="8.0141988132"/> <param name="Leu3" value="3.01883"/> <param name="Dimethyl0" value="28.0313"/> <param name="Dimethyl4" value="32.056407"/> <param name="Dimethyl6" value="34.063117"/> <param name="Dimethyl8" value="36.07567"/> <param name="ICPL0" value="105.021464"/> <param name="ICPL4" value="109.046571"/> <param name="ICPL6" value="111.041593"/> <param name="ICPL10" value="115.0667"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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_FeatureFinderMultiplex_2 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/> <output name="out" value="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <output name="out_multiplets" value="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="algorithm"> <param name="labels" value="[][Lys8,Arg10]"/> <param name="charge" value="1:4"/> <param name="isotopes_per_peptide" value="3:6"/> <param name="rt_typical" value="40.0"/> <param name="rt_band" value="5.0"/> <param name="rt_min" value="2.0"/> <param name="mz_tolerance" value="6.0"/> <param name="mz_unit" value="ppm"/> <param name="intensity_cutoff" value="1000.0"/> <param name="peptide_similarity" value="0.5"/> <param name="averagine_similarity" value="0.4"/> <param name="averagine_similarity_scaling" value="0.75"/> <param name="missed_cleavages" value="0"/> <param name="spectrum_type" value="automatic"/> <param name="averagine_type" value="peptide"/> <param name="knock_out" value="false"/> </section> <section name="labels"> <param name="Arg6" value="6.0201290268"/> <param name="Arg10" value="10.0082686"/> <param name="Lys4" value="4.0251069836"/> <param name="Lys6" value="6.0201290268"/> <param name="Lys8" value="8.0141988132"/> <param name="Leu3" value="3.01883"/> <param name="Dimethyl0" value="28.0313"/> <param name="Dimethyl4" value="32.056407"/> <param name="Dimethyl6" value="34.063117"/> <param name="Dimethyl8" value="36.07567"/> <param name="ICPL0" value="105.021464"/> <param name="ICPL4" value="109.046571"/> <param name="ICPL6" value="111.041593"/> <param name="ICPL10" value="115.0667"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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_FeatureFinderMultiplex_3 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/> <output name="out" value="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <output name="out_multiplets" value="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="algorithm"> <param name="labels" value="[]"/> <param name="charge" value="5:15"/> <param name="isotopes_per_peptide" value="5:10"/> <param name="rt_typical" value="45.0"/> <param name="rt_band" value="5.0"/> <param name="rt_min" value="2.0"/> <param name="mz_tolerance" value="6.0"/> <param name="mz_unit" value="ppm"/> <param name="intensity_cutoff" value="200.0"/> <param name="peptide_similarity" value="0.5"/> <param name="averagine_similarity" value="0.4"/> <param name="averagine_similarity_scaling" value="0.75"/> <param name="missed_cleavages" value="0"/> <param name="spectrum_type" value="automatic"/> <param name="averagine_type" value="RNA"/> <param name="knock_out" value="false"/> </section> <section name="labels"> <param name="Arg6" value="6.0201290268"/> <param name="Arg10" value="10.0082686"/> <param name="Lys4" value="4.0251069836"/> <param name="Lys6" value="6.0201290268"/> <param name="Lys8" value="8.0141988132"/> <param name="Leu3" value="3.01883"/> <param name="Dimethyl0" value="28.0313"/> <param name="Dimethyl4" value="32.056407"/> <param name="Dimethyl6" value="34.063117"/> <param name="Dimethyl8" value="36.07567"/> <param name="ICPL0" value="105.021464"/> <param name="ICPL4" value="109.046571"/> <param name="ICPL6" value="111.041593"/> <param name="ICPL10" value="115.0667"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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_FeatureFinderMultiplex_4 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/> <output name="out" value="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <output name="out_multiplets" value="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="algorithm"> <param name="labels" value="[]"/> <param name="charge" value="5:15"/> <param name="isotopes_per_peptide" value="5:10"/> <param name="rt_typical" value="45.0"/> <param name="rt_band" value="5.0"/> <param name="rt_min" value="2.0"/> <param name="mz_tolerance" value="6.0"/> <param name="mz_unit" value="ppm"/> <param name="intensity_cutoff" value="200.0"/> <param name="peptide_similarity" value="0.5"/> <param name="averagine_similarity" value="0.4"/> <param name="averagine_similarity_scaling" value="0.75"/> <param name="missed_cleavages" value="0"/> <param name="spectrum_type" value="automatic"/> <param name="averagine_type" value="DNA"/> <param name="knock_out" value="false"/> </section> <section name="labels"> <param name="Arg6" value="6.0201290268"/> <param name="Arg10" value="10.0082686"/> <param name="Lys4" value="4.0251069836"/> <param name="Lys6" value="6.0201290268"/> <param name="Lys8" value="8.0141988132"/> <param name="Leu3" value="3.01883"/> <param name="Dimethyl0" value="28.0313"/> <param name="Dimethyl4" value="32.056407"/> <param name="Dimethyl6" value="34.063117"/> <param name="Dimethyl8" value="36.07567"/> <param name="ICPL0" value="105.021464"/> <param name="ICPL4" value="109.046571"/> <param name="ICPL6" value="111.041593"/> <param name="ICPL10" value="115.0667"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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_FeatureFinderMultiplex_5 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/> <output name="out" value="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <output name="out_multiplets" value="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="algorithm"> <param name="labels" value="[Dimethyl0][Dimethyl6]"/> <param name="charge" value="1:5"/> <param name="isotopes_per_peptide" value="3:6"/> <param name="rt_typical" value="50.0"/> <param name="rt_band" value="3.0"/> <param name="rt_min" value="8.0"/> <param name="mz_tolerance" value="10.0"/> <param name="mz_unit" value="ppm"/> <param name="intensity_cutoff" value="10000000.0"/> <param name="peptide_similarity" value="0.95"/> <param name="averagine_similarity" value="0.8"/> <param name="averagine_similarity_scaling" value="0.95"/> <param name="missed_cleavages" value="3"/> <param name="spectrum_type" value="profile"/> <param name="averagine_type" value="peptide"/> <param name="knock_out" value="false"/> </section> <section name="labels"> <param name="Arg6" value="6.0201290268"/> <param name="Arg10" value="10.0082686"/> <param name="Lys4" value="4.0251069836"/> <param name="Lys6" value="6.0201290268"/> <param name="Lys8" value="8.0141988132"/> <param name="Leu3" value="3.01883"/> <param name="Dimethyl0" value="28.0313"/> <param name="Dimethyl4" value="32.056407"/> <param name="Dimethyl6" value="34.063117"/> <param name="Dimethyl8" value="36.07567"/> <param name="ICPL0" value="105.021464"/> <param name="ICPL4" value="109.046571"/> <param name="ICPL6" value="111.041593"/> <param name="ICPL10" value="115.0667"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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_FeatureFinderMultiplex_6 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/> <output name="out" value="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <output name="out_multiplets" value="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="algorithm"> <param name="labels" value="[Dimethyl0][Dimethyl6]"/> <param name="charge" value="1:5"/> <param name="isotopes_per_peptide" value="3:6"/> <param name="rt_typical" value="50.0"/> <param name="rt_band" value="3.0"/> <param name="rt_min" value="8.0"/> <param name="mz_tolerance" value="10.0"/> <param name="mz_unit" value="ppm"/> <param name="intensity_cutoff" value="10000000.0"/> <param name="peptide_similarity" value="0.95"/> <param name="averagine_similarity" value="0.8"/> <param name="averagine_similarity_scaling" value="1.0"/> <param name="missed_cleavages" value="3"/> <param name="spectrum_type" value="profile"/> <param name="averagine_type" value="peptide"/> <param name="knock_out" value="false"/> </section> <section name="labels"> <param name="Arg6" value="6.0201290268"/> <param name="Arg10" value="10.0082686"/> <param name="Lys4" value="4.0251069836"/> <param name="Lys6" value="6.0201290268"/> <param name="Lys8" value="8.0141988132"/> <param name="Leu3" value="3.01883"/> <param name="Dimethyl0" value="28.0313"/> <param name="Dimethyl4" value="32.056407"/> <param name="Dimethyl6" value="34.063117"/> <param name="Dimethyl8" value="36.07567"/> <param name="ICPL0" value="105.021464"/> <param name="ICPL4" value="109.046571"/> <param name="ICPL6" value="111.041593"/> <param name="ICPL10" value="115.0667"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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_FeatureFinderMultiplex_7 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/> <output name="out" value="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <output name="out_multiplets" value="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="algorithm"> <param name="labels" value="[][Dimethyl4]"/> <param name="charge" value="1:4"/> <param name="isotopes_per_peptide" value="3:6"/> <param name="rt_typical" value="40.0"/> <param name="rt_band" value="5.0"/> <param name="rt_min" value="2.0"/> <param name="mz_tolerance" value="6.0"/> <param name="mz_unit" value="ppm"/> <param name="intensity_cutoff" value="1000.0"/> <param name="peptide_similarity" value="0.5"/> <param name="averagine_similarity" value="0.4"/> <param name="averagine_similarity_scaling" value="0.75"/> <param name="missed_cleavages" value="0"/> <param name="spectrum_type" value="automatic"/> <param name="averagine_type" value="peptide"/> <param name="knock_out" value="false"/> </section> <section name="labels"> <param name="Arg6" value="6.0201290268"/> <param name="Arg10" value="10.0082686"/> <param name="Lys4" value="4.0251069836"/> <param name="Lys6" value="6.0201290268"/> <param name="Lys8" value="8.0141988132"/> <param name="Leu3" value="3.01883"/> <param name="Dimethyl0" value="28.0313"/> <param name="Dimethyl4" value="31.0094"/> <param name="Dimethyl6" value="34.063117"/> <param name="Dimethyl8" value="36.07567"/> <param name="ICPL0" value="105.021464"/> <param name="ICPL4" value="109.046571"/> <param name="ICPL6" value="111.041593"/> <param name="ICPL10" value="115.0667"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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_FeatureFinderMultiplex_8 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/> <output name="out" value="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <output name="out_multiplets" value="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="algorithm"> <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/> <param name="charge" value="1:7"/> <param name="isotopes_per_peptide" value="3:8"/> <param name="rt_typical" value="50.0"/> <param name="rt_band" value="3.0"/> <param name="rt_min" value="8.0"/> <param name="mz_tolerance" value="10.0"/> <param name="mz_unit" value="ppm"/> <param name="intensity_cutoff" value="10.0"/> <param name="peptide_similarity" value="0.2"/> <param name="averagine_similarity" value="0.25"/> <param name="averagine_similarity_scaling" value="0.95"/> <param name="missed_cleavages" value="4"/> <param name="spectrum_type" value="automatic"/> <param name="averagine_type" value="peptide"/> <param name="knock_out" value="true"/> </section> <section name="labels"> <param name="Arg6" value="6.0201290268"/> <param name="Arg10" value="10.0082686"/> <param name="Lys4" value="4.0251069836"/> <param name="Lys6" value="6.0201290268"/> <param name="Lys8" value="8.0141988132"/> <param name="Leu3" value="3.01883"/> <param name="Dimethyl0" value="28.0313"/> <param name="Dimethyl4" value="32.056407"/> <param name="Dimethyl6" value="34.063117"/> <param name="Dimethyl8" value="36.07567"/> <param name="ICPL0" value="105.021464"/> <param name="ICPL4" value="109.046571"/> <param name="ICPL6" value="111.041593"/> <param name="ICPL10" value="115.0667"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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_FeatureFinderMultiplex_9 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/> <output name="out" value="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <output name="out_multiplets" value="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="algorithm"> <param name="labels" value="[0][6.03705]"/> <param name="charge" value="2:8"/> <param name="isotopes_per_peptide" value="3:8"/> <param name="rt_typical" value="40.0"/> <param name="rt_band" value="0.0"/> <param name="rt_min" value="4.0"/> <param name="mz_tolerance" value="10.0"/> <param name="mz_unit" value="ppm"/> <param name="intensity_cutoff" value="1000.0"/> <param name="peptide_similarity" value="0.5"/> <param name="averagine_similarity" value="0.4"/> <param name="averagine_similarity_scaling" value="0.95"/> <param name="missed_cleavages" value="0"/> <param name="spectrum_type" value="centroid"/> <param name="averagine_type" value="peptide"/> <param name="knock_out" value="false"/> </section> <section name="labels"> <param name="Arg6" value="6.0201290268"/> <param name="Arg10" value="10.0082686"/> <param name="Lys4" value="4.0251069836"/> <param name="Lys6" value="6.0201290268"/> <param name="Lys8" value="8.0141988132"/> <param name="Leu3" value="3.01883"/> <param name="Dimethyl0" value="28.0313"/> <param name="Dimethyl4" value="32.056407"/> <param name="Dimethyl6" value="34.063117"/> <param name="Dimethyl8" value="36.07567"/> <param name="ICPL0" value="105.021464"/> <param name="ICPL4" value="109.046571"/> <param name="ICPL6" value="111.041593"/> <param name="ICPL10" value="115.0667"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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_FeatureFinderMultiplex_10 --> <test expect_num_outputs="3"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/> <output name="out" value="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <output name="out_multiplets" value="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> <section name="algorithm"> <param name="labels" value="[Dimethyl0][Dimethyl6]"/> <param name="charge" value="1:7"/> <param name="isotopes_per_peptide" value="3:6"/> <param name="rt_typical" value="50.0"/> <param name="rt_band" value="5.0"/> <param name="rt_min" value="8.0"/> <param name="mz_tolerance" value="6.0"/> <param name="mz_unit" value="ppm"/> <param name="intensity_cutoff" value="10.0"/> <param name="peptide_similarity" value="0.4"/> <param name="averagine_similarity" value="0.5"/> <param name="averagine_similarity_scaling" value="0.95"/> <param name="missed_cleavages" value="3"/> <param name="spectrum_type" value="profile"/> <param name="averagine_type" value="peptide"/> <param name="knock_out" value="true"/> </section> <section name="labels"> <param name="Arg6" value="6.0201290268"/> <param name="Arg10" value="10.0082686"/> <param name="Lys4" value="4.0251069836"/> <param name="Lys6" value="6.0201290268"/> <param name="Lys8" value="8.0141988132"/> <param name="Leu3" value="3.01883"/> <param name="Dimethyl0" value="28.0313"/> <param name="Dimethyl4" value="32.056407"/> <param name="Dimethyl6" value="34.063117"/> <param name="Dimethyl8" value="36.07567"/> <param name="ICPL0" value="105.021464"/> <param name="ICPL4" value="109.046571"/> <param name="ICPL6" value="111.041593"/> <param name="ICPL10" value="115.0667"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_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_FeatureFinderMultiplex_11 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/> <output name="out" value="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> <section name="algorithm"> <param name="labels" value="[]"/> <param name="charge" value="1:4"/> <param name="isotopes_per_peptide" value="3:6"/> <param name="rt_typical" value="1e-05"/> <param name="rt_band" value="0.0"/> <param name="rt_min" value="0.0"/> <param name="mz_tolerance" value="10.0"/> <param name="mz_unit" value="ppm"/> <param name="intensity_cutoff" value="1000.0"/> <param name="peptide_similarity" value="0.5"/> <param name="averagine_similarity" value="0.7"/> <param name="averagine_similarity_scaling" value="0.95"/> <param name="missed_cleavages" value="0"/> <param name="spectrum_type" value="automatic"/> <param name="averagine_type" value="peptide"/> <param name="knock_out" value="false"/> </section> <section name="labels"> <param name="Arg6" value="6.0201290268"/> <param name="Arg10" value="10.0082686"/> <param name="Lys4" value="4.0251069836"/> <param name="Lys6" value="6.0201290268"/> <param name="Lys8" value="8.0141988132"/> <param name="Leu3" value="3.01883"/> <param name="Dimethyl0" value="28.0313"/> <param name="Dimethyl4" value="32.056407"/> <param name="Dimethyl6" value="34.063117"/> <param name="Dimethyl8" value="36.07567"/> <param name="ICPL0" value="105.021464"/> <param name="ICPL4" value="109.046571"/> <param name="ICPL6" value="111.041593"/> <param name="ICPL10" value="115.0667"/> </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> <assert_stdout> <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> </assert_stdout> </test> </tests> <help><![CDATA[Determination of peak ratios in LC-MS data For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderMultiplex.html]]></help> <expand macro="references"/> </tool>