Mercurial > repos > galaxyp > openms_featurefindermultiplex
changeset 16:9876bda3ec53 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 18:59:52 +0000 |
| parents | 5e948629bc73 |
| children | c9b2a5022d9e |
| files | 404-urls.patch FeatureFinderMultiplex.xml OMSSAAdapter.patch PepNovoAdapter.patch filetypes.txt fill_ctd.py fill_ctd_clargs.py generate-foo.sh generate.sh hardcoded_params.json macros.xml macros_autotest.xml macros_discarded_auto.xml macros_test.xml prepare_test_data_manual.sh readme.md test-data.sh test-data/pepnovo_models.loc test-data/random.fa test-data/random_RNA.fa tools_blacklist.txt |
| diffstat | 21 files changed, 820 insertions(+), 28803 deletions(-) [+] |
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--- a/404-urls.patch Fri Nov 06 19:42:25 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -diff -ruN FeatureFinderSuperHirn.xml FeatureFinderSuperHirn.xml ---- FeatureFinderSuperHirn.xml 2020-10-02 12:06:56.398572301 +0200 -+++ FeatureFinderSuperHirn.xml 2020-10-02 12:07:31.511153834 +0200 -@@ -105,6 +105,6 @@ - <help><![CDATA[Finds mass spectrometric features in mass spectra. - - --For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderSuperHirn.html]]></help> -+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.6.0/html/UTILS_FeatureFinderSuperHirn.html]]></help> - <expand macro="references"/> - </tool>
--- a/FeatureFinderMultiplex.xml Fri Nov 06 19:42:25 2020 +0000 +++ b/FeatureFinderMultiplex.xml Thu Dec 01 18:59:52 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: [Quantitation]--> -<tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<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> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -70,42 +68,42 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="mzml" optional="false" label="LC-MS dataset in either centroid or profile mode" help=" select mzml data sets(s)"/> + <param argument="-in" type="data" format="mzml" optional="false" 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" optional="true" 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"/> + <param name="labels" argument="-algorithm:labels" type="text" optional="true" 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" optional="true" value="1:4" label="Range of charge states in the sample" help="i.e. min charge : max charge"> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="charge"/> </param> <param name="isotopes_per_peptide" argument="-algorithm:isotopes_per_peptide" type="text" optional="true" 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"/> + <expand macro="list_string_san" name="isotopes_per_peptide"/> </param> <param name="rt_typical" argument="-algorithm:rt_typical" type="float" optional="true" 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" optional="true" 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" optional="true" 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" optional="true" min="0.0" value="6.0" label="m/z tolerance for search of peak patterns" help=""/> - <param name="mz_unit" argument="-algorithm:mz_unit" display="radio" type="select" optional="false" label="Unit of the 'mz_tolerance' paramete" help=""> + <param name="mz_unit" argument="-algorithm:mz_unit" type="select" optional="true" 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"/> + <expand macro="list_string_san" name="mz_unit"/> </param> <param name="intensity_cutoff" argument="-algorithm:intensity_cutoff" type="float" optional="true" 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" optional="true" 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" optional="true" 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" optional="true" 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 simulataneously. 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="averagine_similarity_scaling" argument="-algorithm:averagine_similarity_scaling" type="float" optional="true" 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" optional="true" 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" display="radio" type="select" optional="false" label="Type of MS1 spectra in input mzML file" help="'automatic' determines the spectrum type directly from the input mzML file"> + <param name="spectrum_type" argument="-algorithm:spectrum_type" type="select" optional="true" 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"/> + <expand macro="list_string_san" name="spectrum_type"/> </param> - <param name="averagine_type" argument="-algorithm:averagine_type" display="radio" type="select" optional="false" label="The type of averagine to use, currently RNA, DNA or peptide" help=""> + <param name="averagine_type" argument="-algorithm:averagine_type" type="select" optional="true" 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"/> + <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> @@ -126,9 +124,9 @@ <param name="ICPL10" argument="-labels:ICPL10" type="float" optional="true" 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 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"> @@ -155,13 +153,559 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_FeatureFinderMultiplex"/> - <expand macro="manutest_FeatureFinderMultiplex"/> + <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" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out_multiplets" file="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> + </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" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out_multiplets" file="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> + </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" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out_multiplets" file="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> + </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" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out_multiplets" file="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> + </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" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out_multiplets" file="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> + </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" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out_multiplets" file="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> + </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" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out_multiplets" file="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> + </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" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out_multiplets" file="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> + </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" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out_multiplets" file="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> + </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" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/> + <output name="out_multiplets" file="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> + </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" file="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> + </test> </tests> <help><![CDATA[Determination of peak ratios in LC-MS data -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderMultiplex.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderMultiplex.html]]></help> <expand macro="references"/> </tool>
--- a/OMSSAAdapter.patch Fri Nov 06 19:42:25 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ ---- OMSSAAdapter.xml 2020-06-16 15:51:40.315400730 +0200 -+++ /tmp/OMSSAAdapter.xml 2020-06-16 15:50:23.536086074 +0200 -@@ -22,6 +22,7 @@ - mkdir database && - ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && - -+makeblastdb -dbtype prot -in 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && - ## Main program call - - set -o pipefail &&
--- a/PepNovoAdapter.patch Fri Nov 06 19:42:25 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ ---- PepNovoAdapter.xml 2020-05-12 15:55:24.712831518 +0200 -+++ /tmp/PepNovoAdapter.xml 2020-05-12 15:36:31.267276757 +0200 -@@ -42,8 +42,13 @@ - </configfiles> - <inputs> - <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> -- <param name="model_directory" argument="-model_directory" type="text" optional="false" value="" label="Name of the directory where the model files are kept" help=""> -- <expand macro="list_string_san"/> -+ <param name="model_directory" argument="-model_directory" type="select" optional="false" label="Name of the directory where the model files are kept" help=""> -+ <options from_data_table="pepnovo_models"> -+ <column name="name" index="0"/> -+ <column name="value" index="2"/> -+ <filter type="unique_value" name="unique_set" column="0"/> -+ <validator type="no_options" message="No model directory available"/> -+ </options> - </param> - <param name="correct_pm" argument="-correct_pm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find optimal precursor mass and charge values" help=""/> - <param name="use_spectrum_charge" argument="-use_spectrum_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct charge" help=""/> -@@ -51,8 +56,14 @@ - <param name="no_quality_filter" argument="-no_quality_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not remove low quality spectra" help=""/> - <param name="fragment_tolerance" argument="-fragment_tolerance" type="float" optional="true" value="-1.0" label="The fragment tolerance (between 0 and 0.75 Da" help="Set to -1.0 to use model's default setting)"/> - <param name="pm_tolerance" argument="-pm_tolerance" type="float" optional="true" value="-1.0" label="The precursor mass tolerance (between 0 and 5.0 Da" help="Set to -1.0 to use model's default setting)"/> -- <param name="model" argument="-model" type="text" optional="true" value="CID_IT_TRYP" label="Name of the model that should be used" help=""> -- <expand macro="list_string_san"/> -+ <param name="model" argument="-model" type="select" label="Name of the model that should be used" help=""> -+ <options from_data_table="pepnovo_models"> -+ <column name="name" index="1"/> -+ <column name="value" index="1"/> -+ <filter type="param_value" ref="model_directory" column="2"/> -+ <filter type="unique_value" column="1"/> -+ <validator type="no_options" message="No model available"/> -+ </options> - </param> - <param name="digest" argument="-digest" display="radio" type="select" optional="false" label="Enzyme used for digestion (default TRYPSIN)" help=""> - <option value="TRYPSIN" selected="true">TRYPSIN</option>
--- a/filetypes.txt Fri Nov 06 19:42:25 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,85 +0,0 @@ -# CTD type # Galaxy type -# the following lines need to be at the top in order to ensure -# correct translation Galaxy->CTD type for the ambiguous cases -# (should only be relevant for the autogenerated tests [which -# do not set the ftype of the inputs]) -txt txt -tsv tabular - -##analysisXML -# XTandemAdapter output is named xml in OMS (which is to unspecific) and bioml in Galaxy .. so this is renamed via hardcoded parameters -bioml xml -consensusXML consensusxml -# TODO csv is problematic, since csv often actually means tsv .. but not always -csv csv -##dat -dta dta -dta2d dta2d -edta edta -fa fasta -fas fasta -fasta fasta -FASTA fasta -featureXML featurexml -featurexml featurexml -# fid -html html -HTML html -idXML idxml -##ini txt -json json -kroenik kroenik -mascotXML mascotxml -mgf mgf -mrm mrm -ms sirius.ms -ms2 ms2 -msp msp -mzData mzdata -mzid mzid -# important to have mzML first, since LuciphorAdapter is case sensitive https://github.com/OpenMS/OpenMS/issues/4444 -mzML mzml -mzml mzml -mzq mzq -mzTab mztab -mzXML mzxml -novor txt -obo obo -# I guess this is the idXML output of omssa -omssaXML idxml -osw osw -OSW osw -params txt -paramXML paramxml -fasta peff -peplist peplist -# TODO pep.xml should be removed with OMS 2.6 https://github.com/OpenMS/OpenMS/pull/4541 .. but still in the tests -pep.xml pepxml -pepXML pepxml -png png -PNG png -protXML protxml -psms psms -# TODO implement or use -# psq -pqp pqp -qcML qcml -spec.xml spec.xml -splib splib -sqMass sqmass -tandem.xml tandem -trafoXML trafoxml -traML traml -TraML traml -tab tabular -## MOVED TO TOP txt txt -raw thermo.raw -## xls: SpectraSTSearchAdapter https://github.com/OpenMS/OpenMS/pull/4419 -xls tsv -XML xml -xml xml -xquest.xml xquest.xml -xsd xml - -# TODO needs to be implemented, needs to be below xml in order that Galaxy->OMS mapping gives xml -# cachedMzML xml
--- a/fill_ctd.py Fri Nov 06 19:42:25 2020 +0000 +++ b/fill_ctd.py Thu Dec 01 18:59:52 2022 +0000 @@ -32,7 +32,7 @@ for k, v in e.items(): if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)): mergeDicts(d[k], e[k]) - elif k not in d and not isinstance(e[k], collections.abc.Mapping): + elif k not in d: d[k] = e[k] else: sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e)) @@ -135,9 +135,10 @@ # insert the hc_args into the args mergeDicts(args, hc_args) -if "adv_opts_cond" in args: - args.update(args["adv_opts_cond"]) - del args["adv_opts_cond"] +# put the contents of the advanced options section into the main dict +if "adv_opts" in args: + args.update(args["adv_opts"]) + del args["adv_opts"] # IDMapper has in and spectra:in params, in is used in out as format_source", # which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493"
--- a/fill_ctd_clargs.py Fri Nov 06 19:42:25 2020 +0000 +++ b/fill_ctd_clargs.py Thu Dec 01 18:59:52 2022 +0000 @@ -1,40 +1,70 @@ #!/usr/bin/env python3 + +import operator from argparse import ArgumentParser +from functools import reduce # forward compatibility for Python 3 from io import StringIO from CTDopts.CTDopts import ( + _Null, CTDModel, ModelTypeError, Parameters ) + +def getFromDict(dataDict, mapList): + return reduce(operator.getitem, mapList, dataDict) + + +def setInDict(dataDict, mapList, value): + getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value + + if __name__ == "__main__": # note add_help=False since otherwise arguments starting with -h will # trigger an error (despite allow_abbreviate) parser = ArgumentParser(prog="fill_ctd_clargs", description="fill command line arguments" - "into a CTD file and write the CTD file to", + "into a CTD file and write the CTD file to stdout", add_help=False, allow_abbrev=False) - parser.add_argument("--ctd", dest="ctd", help="input ctd file", - metavar='CTD', default=None, required=True) + parser.add_argument("--ini_file", dest="ini_file", help="input ini file", + metavar='INI', default=None, required=True) + parser.add_argument("--ctd_file", dest="ctd_file", help="input ctd file" + "if given then optional parameters from the ini file" + "will be filled with the defaults from this CTD file", + metavar='CTD', default=None, required=False) args, cliargs = parser.parse_known_args() + # load CTDModel - model = None + ini_model = None try: - model = CTDModel(from_file=args.ctd) + ini_model = CTDModel(from_file=args.ini_file) except ModelTypeError: pass try: - model = Parameters(from_file=args.ctd) + ini_model = Parameters(from_file=args.ini_file) except ModelTypeError: pass - assert model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ctd) + assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ini_file) # get a dictionary of the ctd arguments where the values of the parameters # given on the command line are overwritten - margs = model.parse_cl_args(cl_args=cliargs, ignore_required=True) + ini_values = ini_model.parse_cl_args(cl_args=cliargs, ignore_required=True) + + if args.ctd_file: + ctd_model = CTDModel(from_file=args.ctd_file) + ctd_values = ctd_model.get_defaults() + for param in ini_model.get_parameters(): + if not param.required and (param.default is None or type(param.default) is _Null): + lineage = param.get_lineage(name_only=True) + try: + default = getFromDict(ctd_values, lineage) + except KeyError: + continue + setInDict(ini_values, lineage, default) # write the ctd with the values taken from the dictionary out = StringIO() - ctd_tree = model.write_ctd(out, margs) + ctd_tree = ini_model.write_ctd(out, ini_values) print(out.getvalue())
--- a/generate-foo.sh Fri Nov 06 19:42:25 2020 +0000 +++ b/generate-foo.sh Thu Dec 01 18:59:52 2022 +0000 @@ -8,17 +8,15 @@ # get the tests from the CMakeLists.txt # 1st remove some tests - # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399 + # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399 # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt # - several tools with duplicated input (leads to conflict when linking) - # - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525 # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456) # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed) # - some input files are originally in a subdir (degenerated cases/), but not in test-data - # - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404 # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet) - # - FeatureFinderIdentification name clash of two tests https://github.com/OpenMS/OpenMS/pull/5002 - # - TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010 + # - SiriusAdapter_4 depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 + # - SiriusAdapter_10 should work in >2.8 https://github.com/OpenMS/OpenMS/issues/5869 CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's@${DATA_DIR_SHARE}/@@g' | grep -v 'OpenSwathMzMLFileCacher .*-convert_back' | @@ -26,19 +24,9 @@ grep -v "MaRaClusterAdapter.*-consensus_out"| grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " | sed 's@degenerate_cases/@@g' | - grep -v 'TOPP_SeedListGenerator_3"' | egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' | - egrep -v '"TOPP_FeatureFinderIdentification_4"' | - sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/') - - -# grep -v 'FileFilter.*-spectra:select_polarity ""' | -# grep -v 'MassTraceExtractor_2.ini ' | -# grep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" | -# grep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" | -# grep -v "degenerated_empty.idXML.*degenerated_empty.idXML" | -# grep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" | -# grep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" | + sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | + grep -v '"TOPP_SiriusAdapter_10"') # 1st part is a dirty hack to join lines containing a single function call, e.g. # addtest(.... @@ -50,6 +38,7 @@ # >&2 echo $line test_id=$(echo "$line" | cut -d" " -f 1) tool_id=$(echo "$line" | cut -d" " -f 2) + # >&2 echo "test_id $test_id" if [[ $test_id =~ _out_?[0-9]? ]]; then >&2 echo " skip $test_id $line" continue @@ -67,7 +56,7 @@ tes=" <test>\n" line=$(fix_tmp_files "$line") line=$(unique_files "$line") - # >&2 echo $line + # >&2 echo LINE $line #if there is an ini file then we use this to generate the test #otherwise the ctd file is used #other command line parameters are inserted later into this xml @@ -77,19 +66,23 @@ else ini="ctd/$tool_id.ctd" fi + # >&2 echo "========================================================" + # >&2 echo "USING ini $ini" cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//') ctdtmp=$(mktemp) - #echo python3 fill_ctd_clargs.py --ctd $ini $cli # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"]) - # >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli" - eval "python3 fill_ctd_clargs.py --ctd $ini $cli" > "$ctdtmp" - # echo $ctdtmp + # >&2 echo "python3 fill_ctd_clargs.py --ini_file $ini $cli" + eval "python3 fill_ctd_clargs.py --ini_file $ini $cli" > "$ctdtmp" + # >&2 echo $ctdtmp # >&2 cat $ctdtmp testtmp=$(mktemp) - python3 $CTDCONVERTER/convert.py galaxy -i $ctdtmp -o $testtmp -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib > /dev/null + # >&2 echo CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" + CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" > /dev/null + echo "<!-- $test_id -->" cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/' - rm $ctdtmp $testtmp + + rm "$ctdtmp" "$testtmp" #> /dev/null @@ -130,23 +123,23 @@ #(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt) #this function replaces the tmp file by the expected file. function fix_tmp_files { -# >&2 echo "FIX $line" + # >&2 echo "FIX $line" ret="" for a in $@; do - if [[ ! $a =~ .tmp$ ]]; then + # >&2 echo " a "$a + if [[ ! $a =~ .tmp$ ]] && [[ ! $a =~ _tmp_ ]]; then ret="$ret $a" continue fi -# >&2 echo " a "$a - g=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a") -# >&2 echo " g "$g - in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$g) + diff_line=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a") + # >&2 echo " diff_line "$diff_line + in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$diff_line) # >&2 echo " in1 "$in1 if [[ "$a" != "$in1" ]]; then ret="$ret $a" continue fi - in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$g) + in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$diff_line) in2=$(basename $in2 | sed 's/)$//') # >&2 echo " in2 "$in2 if [[ -f "test-data/$in2" ]]; then @@ -176,11 +169,11 @@ fi ln -f -s $in1 test-data/$in2 done - for i in test-data/*.tmp - do + + find test-data/ -name "*.tmp" -print0 | + while IFS= read -r -d '' i; do if [ ! -e test-data/$(basename $i .tmp) ]; then ln -s $(basename $i) test-data/$(basename $i .tmp) - #ln -s $(basename $i) test-data/$(basename $i .tmp) else ln -fs $(basename $i) test-data/$(basename $i .tmp) fi @@ -194,14 +187,14 @@ # id=$1 # | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?" -# TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010 + # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010 cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' | grep -v "^$" | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | sed 's/degenerate_cases\///' | egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | grep add_test | egrep "TOPP|UTILS" | sed 's@${DATA_DIR_SHARE}/@@g;'| - sed 's@${TMP_RIP_PATH}@dummy2.tmp@g'| + sed 's@${TMP_RIP_PATH}@./@g'| sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' | while read line
--- a/generate.sh Fri Nov 06 19:42:25 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -#!/usr/bin/env bash - -VERSION=2.6 -FILETYPES="filetypes.txt" -PROFILE="20.05" -## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g') - -export tmp=$(mktemp -d) -export CTDCONVERTER="$tmp/CTDConverter" - -############################################################################### -## reset old data -############################################################################### -# rm $(ls *xml |grep -v macros) -# rm -rf ctd -# mkdir -p ctd -# echo "" > prepare_test_data.sh - -############################################################################### -## generate tests -## also creates -## - conda environment (for executing the binaries) and -## - the git clone of OpenMS (for generating the tests) -## - ctd files -############################################################################### -bash ./test-data.sh ./macros_autotest.xml - -############################################################################### -## get the -## - conda package (for easy access and listing of the OpenMS binaries), -############################################################################### -# if [ ! -d $OPENMSPKG ]; then -# mkdir $OPENMSPKG/ -# wget -P $OPENMSPKG/ "$CONDAPKG" -# tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C OpenMS$VERSION-pkg/ -# rm $OPENMSPKG/"$(basename $CONDAPKG)" -# fi - -############################################################################### -## Get python libaries for CTD -> Galaxy conversion -## TODO fix to main repo OR conda packkage if PRs are merged -############################################################################### -# if [ ! -d CTDopts ]; then -# # git clone https://github.com/genericworkflownodes/CTDopts CTDopts -# git clone -b topic/no-1-2x https://github.com/bernt-matthias/CTDopts CTDopts -# fi -if [ ! -d $CTDCONVERTER ]; then - #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter - git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER -fi -# export PYTHONPATH=$(pwd)/CTDopts -############################################################################### -## conversion ctd->xml -############################################################################### - -find . -maxdepth 0 -name "[A-Z]*xml" -delete -source $(dirname $(which conda))/../etc/profile.d/conda.sh -conda activate $tmp/OpenMS$VERSION-env -python $CTDCONVERTER/convert.py galaxy -i ctd/*ctd -o ./ -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf -p hardcoded_params.json --test-macros macros_autotest.xml --test-macros-prefix autotest_ --test-macros macros_test.xml --test-macros-prefix manutest_ --tool-version $VERSION --tool-profile $PROFILE > convert.out 2> convert.err -if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi -conda deactivate - -patch PepNovoAdapter.xml < PepNovoAdapter.patch -patch OMSSAAdapter.xml < OMSSAAdapter.patch - -# https://github.com/OpenMS/OpenMS/pull/4984 -sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml -# https://github.com/OpenMS/OpenMS/pull/4984#issuecomment-702641976 -patch -p0 <404-urls.patch - -# #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool - -# for i in A-E F-H I-L M-N O-P Q-Z -# do -# planemo t [$i]*xml --galaxy_branch release_20.05 --galaxy_python_version 3.7 --test_output $i.html --test_output_json $i.json & -# done
--- a/hardcoded_params.json Fri Nov 06 19:42:25 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,236 +0,0 @@ -{ - "#": "blacklist parameters", - - "version": [{"value": "@"}], - "debug": [{"value": "@"}], - "algorithm:debug": [{"value": "@"}], - "java_memory": [{"value": "@"}], - "java_permgen": [{"value": "@"}], - "#": "type of input is always determined from the file extension ", - "in_type": [{"value": "@"}], - - "#": "tool specific blacklist parameters", - - "convert_back": [{"value": "@", "tools": ["OpenSwathMzMLFileCacher"]}], - "NET_executable": [{ - "value": "@", - "tools": ["FileConverter"] - }], - - - "params_file": [{"value": "@", "tools": ["SpectraSTSearchAdapter"]}], - - "#": "TODO not usable in 2.5 https://github.com/OpenMS/OpenMS/issues/4456, corresponding test currently disabled", - "consensus_out": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], - "#": "TODO would need treatment as prefix-output", - "output_directory": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], - - "#": "hardcode parameter values", - - "comet_version": [{ - "value":"2016.01 rev. 3" - }], - "comet_executable": [{ - "value":"comet" - }], - "crux_executable": [{ - "value": "crux" - }], - "fido_executable": [{ - "value":"Fido" - }], - "fidocp_executable": [{ - "value":"FidoChooseParameters" - }], - "maracluster_executable": [{ - "value":"/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster" - }], - "mascot_directory": [{ - "value":"TODO" - }], - "myrimatch_executable": [{ - "value":"myrimatch" - }], - "omssa_executable": [{ - "value":"$(dirname $(realpath $(which omssacl)))/omssacl" - }], - "ThermoRaw_executable": [{ - "value": "ThermoRawFileParser.exe", - "tools": ["FileConverter"] - }], - "pepnovo_executable": [{ - "value":"pepnovo" - }], - "percolator_executable": [{ - "value":"percolator" - }], - "xtandem_executable": [{ - "value":"xtandem" - }], - "executable": [ - { - "value":"$(dirname $(realpath $(which luciphor2)))/luciphor2.jar", - "tools": ["LuciphorAdapter"] - }, { - "value":"/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar", - "tools": ["MSFraggerAdapter"] - }, { - "value":"$(msgf_plus -get_jar_path)", - "tools": ["MSGFPlusAdapter"] - }, { - "value": "/home/berntm/Downloads/novor/lib/novor.jar", - "tools": ["NovorAdapter"] - }, { - "value":"$(which sirius)", - "tools": ["SiriusAdapter", "AssayGeneratorMetabo"] - }, { - "value":"spectrast", - "tools": ["SpectraSTSearchAdapter"] - } - ], - "r_executable": [{ - "value":"R" - }], - "rscript_executable": [{ - "value":"Rscript" - }], - "java_executable": [{ - "value":"java" - }], - "log": [{ - "value":"log.txt" - }], - "tempDirectory": [{ - "value":"$TMP_DIR" - }], - "temp_data_directory": [{ - "value":"$TMP_DIR" - }], - "algorithm:Preprocessing:tmp_dir": [{ - "value":"$TMP_DIR" - }], - "no_progress": [{ - "value": true - }], - "#": "only used in LuciphorAdapter at the moment, inconsistency will be fixed", - "num_threads": [{ - "value":"${GALAXY_SLOTS:-1}" - }], - "threads": [{ - "value": "${GALAXY_SLOTS:-1}" - }], - "sirius:cores": [{ - "value": "${GALAXY_SLOTS:-1}" - }], - - "#": "hardcode the outer loop threads for OpenSwathWorkflow", - "outer_loop_threads": [{ - "value": "1", - "tools": ["OpenSwathWorkflow"] - }], - "separator": [{ - "value": ",", - "tools": ["IDMassAccuracy"] - }], - - "#": "don't alow to copy data internally to save computation time for reloading", - "copy_data": [{ - "value": "false", - "tools": ["MapAlignerTreeGuided"] - }], - - "#": "overwrite/add Galaxy xml attributes of some parameters (names need to start with param_)", - - "#": "test is not a hardcoded value since we need to set it in the tool tests", - "test": [{ - "CTD:type": "text", - "XML:type": "hidden" - }], - - "#": "overwrite CTD attributes of some parameters (some are not possible, e.g. type)", - - "#": "for some tools the user needs to select the desired output type since detection by extension makes no sense for galaxy tools", - "out_type": [{ - "CTD:required": true, - "CTD:advanced": false - }], - - "#": "SeedListGenerator with consensusXML input needs a dynamic number of outputs that depends on the content of the input, so we remove this options at the moment because its hard or impossible to implement in Galaxy, https://github.com/OpenMS/OpenMS/issues/4404 .. see also in parameter", - "#": "FileInfo, MapStatistics, SequenceCoverageCalculator wo -out just writes to stdout. not wanted here", - "#": "MzMLSplitter output prefix https://github.com/OpenMS/OpenMS/issues/4404", - "#": "IDRipper: blacklist out (is doing the same as the output-prefix out-path)", - "out": [{ - "CTD:is_list": false, - "tools": ["SeedListGenerator"] - }, { - "CTD:required": true, - "tools": ["FileInfo", "MapStatistics", "SequenceCoverageCalculator"] - }, { - "CTD:type": "output-prefix", - "CTD:required": true, - "CTD:restrictions": "mzml", - "tools": ["MzMLSplitter"] - }, { - "value": "@", - "tools": ["IDRipper"] - }], - - "#": "Try to remove xml data type whereever possible", - "#": "XTandem Adapter output is called .xml in OMS which is to unspecific -> use Galaxy's bioml", - "xml_out": [{ - "CTD:restrictions": "bioml", - "tools": ["XTandemAdapter"] - }], - - "#": "IDFileConverter remove xml", - "#": "OpenSwathWorkflow make in single file input and all outputs non-optional", - "#": "XFDR does not need xml .. redundant with xquest.xml TODO check if list is up to date with each new release", - "#": "SeedListGenerator: remove consensusXML https://github.com/OpenMS/OpenMS/issues/4404 .. see also out parameter", - "in": [{ - "CTD:restrictions": "pepXML,protXML,mascotXML,omssaXML,bioml,psms,tsv,idXML,mzid,xquest.xml", - "tools": ["IDFileConverter"] - }, { - "CTD:is_list": false, - "tools": ["OpenSwathWorkflow"] - }, { - "CTD:restrictions": "idXML,mzid,xquest.xml", - "tools": ["XFDR"] - }, { - "CTD:restrictions": "mzML,idXML,featureXML", - "tools": ["SeedListGenerator"] - }], - - "#": "IDMapper has in and spectra:in params, in is used in out as format_source", - "#": "which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493", - "spectra:in": [{ - "CTD:name": "_in", - "tools": ["IDMapper"] - }], - - "#": "hardcoding prefix parameters which are not yet available in OMS but in CTDOpts https://github.com/OpenMS/OpenMS/pull/4527", - "#": "output-prefix", - "out_path": [{ - "CTD:type": "output-prefix", - "CTD:required": true, - "CTD:restrictions": "idXML", - "tools": ["IDRipper"] - }], - "outputDirectory": [{ - "CTD:type": "output-prefix", - "CTD:advanced": false, - "CTD:required": true, - "CTD:restrictions": "mzml", - "tools": ["OpenSwathFileSplitter"] - }], - - "#": "OpenSwathDIAPreScoring: https://github.com/OpenMS/OpenMS/pull/4443", - "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release", - "output_files": [{ - "CTD:required": true, - "tools": ["OpenSwathDIAPreScoring"] - }, { - "CTD:restrictions": "txt,tsv,pep.xml,pepXML,html", - "tools": ["SpectraSTSearchAdapter"] - - }] -}
--- a/macros.xml Fri Nov 06 19:42:25 2020 +0000 +++ b/macros.xml Thu Dec 01 18:59:52 2022 +0000 @@ -3,14 +3,15 @@ You can edit this file to add your own macros, if you so desire, or you can add additional macro files using the m/macros parameter --> <macros> - <token name="@TOOL_VERSION@">2.6</token> - <token name="@GALAXY_VERSION@">0</token> + <token name="@TOOL_VERSION@">2.8</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">openms</requirement> <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement> - <!-- makeblastdb for OMSSAAdapter --> - <requirement type="package" version="2.9.0">blast</requirement> + <!-- omssa (which has been excluded from 3rdparty) and makeblastdb for OMSSAAdapter --> + <requirement type="package" version="2.1.9">omssa</requirement> + <requirement type="package" version="2.13.0">blast</requirement> <!--<requirement type="package" version="5.0.0">tpp</requirement>--> <!-- for realpath (used e.g. in LuciphorAdapter) --> <!--<requirement type="package" version="8.25">coreutils</requirement>--> @@ -21,6 +22,7 @@ <xml name="stdio"> <stdio> <regex match="std::bad_alloc" level="fatal_oom" description="Could not allocate memory"/> + <regex match="OutOfMemoryError" level="fatal_oom" description="Could not allocate memory"/> <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/> <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/> <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/> @@ -32,23 +34,15 @@ </citations> </xml> <xml name="adv_opts_macro"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic"/> - <when value="advanced"> - <yield/> - </when> - </conditional> + <section name="adv_opts" title="Advanced Options" expanded="false"> + <yield/> + </section> </xml> <!-- sanitizers and validators --> - <xml name="list_string_val"> - <validator type="regex" message="parameter must not start with $">^[^$]</validator> - - <validator type="regex" message="a space separated list of string is needed (strings that contain spaces can be quoted with ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> + <xml name="list_string_val" token_name=""> + <validator type="regex" message="parameter @NAME@: must not start with $">^[^$]</validator> + <validator type="regex" message="parameter @NAME@: a space separated list of string is needed (strings that contain spaces can be quoted with ")">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator> </xml> <xml name="list_string_san"> <sanitizer> @@ -64,8 +58,8 @@ </valid> </sanitizer> </xml> - <xml name="list_float_valsan"> - <validator type="regex" message="a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator> + <xml name="list_float_valsan" token_name=""> + <validator type="regex" message="parameter @NAME@: a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator> <yield/> <sanitizer> <valid initial="string.digits"> @@ -78,8 +72,8 @@ </valid> </sanitizer> </xml> - <xml name="list_integer_valsan"> - <validator type="regex" message="a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator> + <xml name="list_integer_valsan" token_name=""> + <validator type="regex" message="parameter @NAME@: a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator> <yield/> <sanitizer> <valid initial="string.digits"> @@ -119,11 +113,11 @@ </token> <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o) - #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} + #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} #return m[o] #end def #def gxy2omsext(g) - #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} + #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} #return m[g] #end def ]]></token></macros>
--- a/macros_autotest.xml Fri Nov 06 19:42:25 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27205 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<macros> - <xml name="autotest_AccurateMassSearch"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/> - <output name="out" file="AccurateMassSearch_1_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/> - <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/> - <section name="db"> - <param name="mapping" value="CHEMISTRY/HMDBMappingFile.tsv" ftype="tabular"/> - <param name="struct" value="CHEMISTRY/HMDB2StructMapping.tsv" ftype="tabular"/> - </section> - <section name="algorithm"> - <param name="mass_error_value" value="5.0"/> - <param name="mass_error_unit" value="ppm"/> - <param name="ionization_mode" value="positive"/> - <param name="isotopic_similarity" value="false"/> - <param name="use_feature_adducts" value="false"/> - <param name="keep_unidentified_masses" value="false"/> - <section name="mzTab"> - <param name="exportIsotopeIntensities" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AccurateMassSearch_2_input.featureXML"/> - <output name="out" file="AccurateMassSearch_2_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/> - <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/> - <section name="db"> - <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/> - <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/> - </section> - <section name="algorithm"> - <param name="mass_error_value" value="5.0"/> - <param name="mass_error_unit" value="ppm"/> - <param name="ionization_mode" value="positive"/> - <param name="isotopic_similarity" value="false"/> - <param name="use_feature_adducts" value="false"/> - <param name="keep_unidentified_masses" value="false"/> - <section name="mzTab"> - <param name="exportIsotopeIntensities" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AccurateMassSearch_2_input.featureXML"/> - <output name="out" file="AccurateMassSearch_3_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/> - <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/> - <section name="db"> - <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/> - <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/> - </section> - <section name="algorithm"> - <param name="mass_error_value" value="5.0"/> - <param name="mass_error_unit" value="ppm"/> - <param name="ionization_mode" value="positive"/> - <param name="isotopic_similarity" value="false"/> - <param name="use_feature_adducts" value="false"/> - <param name="keep_unidentified_masses" value="false"/> - <section name="mzTab"> - <param name="exportIsotopeIntensities" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_AssayGeneratorMetabo"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ffm_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="consensus_spectrum"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="consensus_spectrum"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="none"/> - <param name="method" value="consensus_spectrum"/> - <param name="use_exact_mass" value="false"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="true"/> - <param name="min_transitions" value="1"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="5.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_sirius_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="sirius"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="true"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="2"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="10.0"/> - <param name="precursor_mz_tolerance_unit" value="ppm"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="100"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="sirius"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="true"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="true"/> - <param name="min_transitions" value="2"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="10.0"/> - <param name="precursor_mz_tolerance_unit" value="ppm"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="100"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="0.0"/> - <param name="max_fragment_mz" value="2000.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_intsort_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_intsort_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="sirius"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="true"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="2"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="10.0"/> - <param name="precursor_mz_tolerance_unit" value="ppm"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="100"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="precursor_recalibration_window" value="0.1"/> - <param name="precursor_recalibration_window_unit" value="Da"/> - <param name="min_fragment_mz" value="100.0"/> - <param name="max_fragment_mz" value="900.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_input.mzML"/> - <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/> - <param name="out_type" value="tsv"/> - <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_annotation" value="sirius"/> - <param name="method" value="highest_intensity"/> - <param name="use_exact_mass" value="true"/> - <param name="exclude_ms2_precursor" value="false"/> - <param name="precursor_mz_distance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <param name="use_known_unknowns" value="false"/> - <param name="min_transitions" value="2"/> - <param name="max_transitions" value="3"/> - <param name="cosine_similarity_threshold" value="0.98"/> - <param name="transition_threshold" value="3.0"/> - <param name="out_workspace_directory" value=""/> - <section name="deisotoping"> - <param name="use_deisotoper" value="false"/> - <param name="fragment_tolerance" value="1.0"/> - <param name="fragment_unit" value="ppm"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="1"/> - <param name="min_isopeaks" value="2"/> - <param name="max_isopeaks" value="3"/> - <param name="keep_only_deisotoped" value="false"/> - <param name="annotate_charge" value="false"/> - </section> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="10.0"/> - <param name="precursor_mz_tolerance_unit" value="ppm"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="100"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_BaselineFilter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="BaselineFilter_input.mzML"/> - <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="struc_elem_length" value="1.5"/> - <param name="struc_elem_unit" value="Thomson"/> - <param name="method" value="tophat"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ClusterMassTracesByPrecursor"> -</xml> - <xml name="autotest_ClusterMassTraces"> -</xml> - <xml name="autotest_CometAdapter"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_A_ions" value="false"/> - <param name="use_B_ions" value="true"/> - <param name="use_C_ions" value="false"/> - <param name="use_X_ions" value="false"/> - <param name="use_Y_ions" value="true"/> - <param name="use_Z_ions" value="false"/> - <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> - <param name="digest_mass_range" value="600:5000"/> - <param name="max_precursor_charge" value="5"/> - <param name="spectrum_batch_size" value="1000"/> - <param name="mass_offsets" value="0.0"/> - <param name="minimum_peaks" value="10"/> - <param name="minimum_intensity" value="0.0"/> - <param name="remove_precursor_peak" value="no"/> - <param name="remove_precursor_tolerance" value="1.5"/> - <param name="clear_mz_range" value="0:0"/> - <param name="max_variable_mods_in_peptide" value="5"/> - <param name="require_variable_mod" value="false"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra_comet.mzML"/> - <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="precursor_mass_tolerance" value="3.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="isotope_error" value="off"/> - <param name="fragment_mass_tolerance" value="0.50025"/> - <param name="fragment_error_units" value="Da"/> - <param name="fragment_bin_offset" value="0.25"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin"/> - <param name="num_enzyme_termini" value="fully"/> - <param name="missed_cleavages" value="1"/> - <param name="min_peptide_length" value="5"/> - <param name="max_peptide_length" value="63"/> - <param name="num_hits" value="5"/> - <param name="precursor_charge" value="0:0"/> - <param name="override_charge" value="keep any known"/> - <param name="ms_level" value="2"/> - <param name="activation_method" value="ALL"/> - <param name="max_fragment_charge" value="3"/> - <param name="clip_nterm_methionine" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="binary_modifications" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_A_ions" value="false"/> - <param name="use_B_ions" value="true"/> - <param name="use_C_ions" value="false"/> - <param name="use_X_ions" value="false"/> - <param name="use_Y_ions" value="true"/> - <param name="use_Z_ions" value="false"/> - <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> - <param name="digest_mass_range" value="600:5000"/> - <param name="max_precursor_charge" value="5"/> - <param name="spectrum_batch_size" value="1000"/> - <param name="mass_offsets" value="0.0"/> - <param name="minimum_peaks" value="10"/> - <param name="minimum_intensity" value="0.0"/> - <param name="remove_precursor_peak" value="no"/> - <param name="remove_precursor_tolerance" value="1.5"/> - <param name="clear_mz_range" value="0:0"/> - <param name="max_variable_mods_in_peptide" value="5"/> - <param name="require_variable_mod" value="false"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="CometAdapter_2_prepared.mzML"/> - <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="CometAdapter_2_in.fasta"/> - <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="precursor_mass_tolerance" value="3.0"/> - <param name="precursor_error_units" value="Da"/> - <param name="isotope_error" value="off"/> - <param name="fragment_mass_tolerance" value="0.50025"/> - <param name="fragment_error_units" value="Da"/> - <param name="fragment_bin_offset" value="0.25"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin"/> - <param name="num_enzyme_termini" value="fully"/> - <param name="missed_cleavages" value="1"/> - <param name="min_peptide_length" value="5"/> - <param name="max_peptide_length" value="63"/> - <param name="num_hits" value="5"/> - <param name="precursor_charge" value="0:0"/> - <param name="override_charge" value="keep any known"/> - <param name="ms_level" value="2"/> - <param name="activation_method" value="ALL"/> - <param name="max_fragment_charge" value="3"/> - <param name="clip_nterm_methionine" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="binary_modifications" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_A_ions" value="false"/> - <param name="use_B_ions" value="true"/> - <param name="use_C_ions" value="false"/> - <param name="use_X_ions" value="false"/> - <param name="use_Y_ions" value="true"/> - <param name="use_Z_ions" value="false"/> - <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> - <param name="digest_mass_range" value="600:5000"/> - <param name="max_precursor_charge" value="5"/> - <param name="spectrum_batch_size" value="20000"/> - <param name="mass_offsets" value="0.0"/> - <param name="minimum_peaks" value="10"/> - <param name="minimum_intensity" value="0.0"/> - <param name="remove_precursor_peak" value="no"/> - <param name="remove_precursor_tolerance" value="1.5"/> - <param name="clear_mz_range" value="0:0"/> - <param name="max_variable_mods_in_peptide" value="3"/> - <param name="require_variable_mod" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="CometAdapter_3.mzML"/> - <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="CometAdapter_3.fasta"/> - <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="isotope_error" value="off"/> - <param name="fragment_mass_tolerance" value="0.01"/> - <param name="fragment_error_units" value="Da"/> - <param name="fragment_bin_offset" value="0.0"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin"/> - <param name="num_enzyme_termini" value="fully"/> - <param name="missed_cleavages" value="3"/> - <param name="min_peptide_length" value="5"/> - <param name="max_peptide_length" value="63"/> - <param name="num_hits" value="5"/> - <param name="precursor_charge" value="0:0"/> - <param name="override_charge" value="keep known search unknown"/> - <param name="ms_level" value="2"/> - <param name="activation_method" value="ALL"/> - <param name="max_fragment_charge" value="3"/> - <param name="clip_nterm_methionine" value="false"/> - <param name="fixed_modifications" value="Carbamidomethyl (C)"/> - <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/> - <param name="binary_modifications" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_A_ions" value="false"/> - <param name="use_B_ions" value="true"/> - <param name="use_C_ions" value="false"/> - <param name="use_X_ions" value="false"/> - <param name="use_Y_ions" value="true"/> - <param name="use_Z_ions" value="false"/> - <param name="use_NL_ions" value="false"/> - <param name="second_enzyme" value=""/> - <param name="digest_mass_range" value="600:1200"/> - <param name="max_precursor_charge" value="5"/> - <param name="spectrum_batch_size" value="20000"/> - <param name="mass_offsets" value="0.0"/> - <param name="minimum_peaks" value="10"/> - <param name="minimum_intensity" value="0.0"/> - <param name="remove_precursor_peak" value="no"/> - <param name="remove_precursor_tolerance" value="1.5"/> - <param name="clear_mz_range" value="0:0"/> - <param name="max_variable_mods_in_peptide" value="3"/> - <param name="require_variable_mod" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/> - <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="isotope_error" value="off"/> - <param name="fragment_mass_tolerance" value="0.01"/> - <param name="fragment_error_units" value="Da"/> - <param name="fragment_bin_offset" value="0.0"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin"/> - <param name="num_enzyme_termini" value="fully"/> - <param name="missed_cleavages" value="3"/> - <param name="min_peptide_length" value="5"/> - <param name="max_peptide_length" value="63"/> - <param name="num_hits" value="5"/> - <param name="precursor_charge" value="0:0"/> - <param name="override_charge" value="keep known search unknown"/> - <param name="ms_level" value="2"/> - <param name="activation_method" value="ALL"/> - <param name="max_fragment_charge" value="3"/> - <param name="clip_nterm_methionine" value="false"/> - <param name="fixed_modifications" value="Carbamidomethyl (C)"/> - <param name="variable_modifications" value="Met-loss (Protein N-term M)"/> - <param name="binary_modifications" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_CompNovoCID"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="CompNovoCID_1_input.mzML"/> - <output name="out" file="CompNovoCID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="algorithm"> - <param name="max_number_aa_per_decomp" value="4"/> - <param name="tryptic_only" value="true"/> - <param name="precursor_mass_tolerance" value="0.3"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="max_number_pivot" value="9"/> - <param name="max_subscore_number" value="40"/> - <param name="decomp_weights_precision" value="0.01"/> - <param name="double_charged_iso_threshold" value="0.6"/> - <param name="max_mz" value="2000.0"/> - <param name="min_mz" value="200.0"/> - <param name="max_isotope_to_score" value="3"/> - <param name="max_decomp_weight" value="450.0"/> - <param name="max_isotope" value="3"/> - <param name="missed_cleavages" value="1"/> - <param name="number_of_hits" value="1"/> - <param name="estimate_precursor_mz" value="true"/> - <param name="number_of_prescoring_hits" value="250"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="residue_set" value="Natural19WithoutI"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_CompNovo"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="CompNovo_1_input.mzML"/> - <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="algorithm"> - <param name="max_number_aa_per_decomp" value="4"/> - <param name="tryptic_only" value="true"/> - <param name="precursor_mass_tolerance" value="0.3"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="max_number_pivot" value="9"/> - <param name="max_subscore_number" value="40"/> - <param name="decomp_weights_precision" value="0.01"/> - <param name="double_charged_iso_threshold" value="0.6"/> - <param name="max_mz" value="2000.0"/> - <param name="min_mz" value="200.0"/> - <param name="max_isotope_to_score" value="3"/> - <param name="max_decomp_weight" value="450.0"/> - <param name="max_isotope" value="3"/> - <param name="missed_cleavages" value="1"/> - <param name="number_of_hits" value="1"/> - <param name="estimate_precursor_mz" value="true"/> - <param name="number_of_prescoring_hits" value="250"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="residue_set" value="Natural19WithoutI"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ConsensusID"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_1_input.idXML"/> - <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="PEPMatrix"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="PAM30MS"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_2_input.featureXML"/> - <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="average"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_3_input.consensusXML"/> - <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="best"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_1_input.idXML"/> - <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="PEPMatrix"/> - <section name="filter"> - <param name="considered_hits" value="6"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_1_input.idXML"/> - <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="PEPIons"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_1_input.idXML"/> - <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="false"/> - <param name="algorithm" value="best"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.5"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="false"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_6_input.idXML"/> - <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="true"/> - <param name="algorithm" value="best"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="true"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusID_8_input.idXML"/> - <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="rt_delta" value="0.1"/> - <param name="mz_delta" value="0.1"/> - <param name="per_spectrum" value="true"/> - <param name="algorithm" value="best"/> - <section name="filter"> - <param name="considered_hits" value="0"/> - <param name="min_support" value="0.0"/> - <param name="count_empty" value="false"/> - <param name="keep_old_scores" value="true"/> - </section> - <section name="PEPIons"> - <param name="mass_tolerance" value="0.5"/> - <param name="min_shared" value="2"/> - </section> - <section name="PEPMatrix"> - <param name="matrix" value="identity"/> - <param name="penalty" value="5"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ConsensusMapNormalizer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="accession_filter" value=""/> - <param name="description_filter" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/> - <output name="out" file="ConsensusMapNormalizer_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="algorithm_type" value="robust_regression"/> - <param name="ratio_threshold" value="0.67"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_CruxAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="custom_enzyme" value=""/> - <param name="decoy_prefix" value="decoy_"/> - <param name="deisotope" value="false"/> - <param name="report_decoys" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra_comet.mzML"/> - <output name="out" file="CruxAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <param name="extra_index_args" value=""/> - <param name="extra_search_args" value=""/> - <param name="extra_percolator_args" value=""/> - <param name="precursor_mass_tolerance" value="10.0"/> - <param name="precursor_mass_units" value="ppm"/> - <param name="fragment_bin_offset" value="0.0"/> - <param name="fragment_bin_width" value="0.02"/> - <param name="isotope_error" value=""/> - <param name="run_percolator" value="false"/> - <param name="enzyme" value="trypsin"/> - <param name="digestion" value="full-digest"/> - <param name="allowed_missed_cleavages" value="0"/> - <param name="decoy_format" value="peptide-reverse"/> - <param name="keep_terminal_aminos" value="NC"/> - <param name="cterm_modifications" value=""/> - <param name="nterm_modifications" value=""/> - <param name="modifications" value=""/> - <param name="test_fdr" value="0.01"/> - <param name="train_fdr" value="0.01"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_CVInspector"> -</xml> - <xml name="autotest_DatabaseFilter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DatabaseFilter_1.fasta"/> - <param name="id" value="DatabaseFilter_1.idXML"/> - <param name="method" value="whitelist"/> - <output name="out" file="DatabaseFilter_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DatabaseFilter_1.fasta"/> - <param name="id" value="DatabaseFilter_1.idXML"/> - <param name="method" value="blacklist"/> - <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DatabaseFilter_3.fasta"/> - <param name="id" value="DatabaseFilter_3.mzid"/> - <param name="method" value="whitelist"/> - <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DatabaseFilter_3.fasta"/> - <param name="id" value="DatabaseFilter_3.mzid"/> - <param name="method" value="blacklist"/> - <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_DatabaseSuitability"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_id" value="DatabaseSuitability_in_id.idXML"/> - <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/> - <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> - <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="algorithm"> - <param name="no_rerank" value="false"/> - <param name="reranking_cutoff_percentile" value="0.01"/> - <param name="FDR" value="0.8"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_id" value="DatabaseSuitability_in_id.idXML"/> - <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/> - <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> - <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="algorithm"> - <param name="no_rerank" value="false"/> - <param name="reranking_cutoff_percentile" value="0.9"/> - <param name="FDR" value="1.0"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_id" value="DatabaseSuitability_in_id.idXML"/> - <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/> - <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/> - <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="algorithm"> - <param name="no_rerank" value="true"/> - <param name="reranking_cutoff_percentile" value="0.01"/> - <param name="FDR" value="0.9"/> - </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> - </xml> - <xml name="autotest_Decharger"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Decharger_input.featureXML"/> - <output name="out_cm" file="Decharger_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_fm" file="Decharger_output_fm.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="outpairs" file="Decharger_p_output.tmp" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <section name="FeatureDeconvolution"> - <param name="charge_min" value="1"/> - <param name="charge_max" value="10"/> - <param name="charge_span_max" value="4"/> - <param name="q_try" value="feature"/> - <param name="retention_max_diff" value="1.0"/> - <param name="retention_max_diff_local" value="1.0"/> - <param name="mass_max_diff" value="0.1"/> - <param name="potential_adducts" value=""H:+:0.7" "Na:+:0.1" "(2)H4H-4:0:0.1:-2:heavy""/> - <param name="max_neutrals" value="0"/> - <param name="max_minority_bound" value="2"/> - <param name="min_rt_overlap" value="0.66"/> - <param name="intensity_filter" value="false"/> - <param name="negative_mode" value="false"/> - <param name="default_map_label" value="decharged features"/> - <param name="verbose_level" value="0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG,outpairs_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_DecoyDatabase"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="seed" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DecoyDatabase_1.fasta"/> - <output name="out" file="DecoyDatabase_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="decoy_string" value="DECOY_"/> - <param name="decoy_string_position" value="prefix"/> - <param name="only_decoy" value="true"/> - <param name="type" value="protein"/> - <param name="method" value="reverse"/> - <param name="enzyme" value="Trypsin"/> - <section name="Decoy"> - <param name="non_shuffle_pattern" value=""/> - <param name="keepPeptideNTerm" value="true"/> - <param name="keepPeptideCTerm" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="seed" value="42"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DecoyDatabase_1.fasta"/> - <output name="out" file="DecoyDatabase_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="decoy_string" value="blabla"/> - <param name="decoy_string_position" value="prefix"/> - <param name="only_decoy" value="false"/> - <param name="type" value="protein"/> - <param name="method" value="shuffle"/> - <param name="enzyme" value="Trypsin"/> - <section name="Decoy"> - <param name="non_shuffle_pattern" value="KRP"/> - <param name="keepPeptideNTerm" value="true"/> - <param name="keepPeptideCTerm" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="seed" value="42"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DecoyDatabase_1.fasta"/> - <output name="out" file="DecoyDatabase_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="decoy_string" value="blabla"/> - <param name="decoy_string_position" value="prefix"/> - <param name="only_decoy" value="false"/> - <param name="type" value="protein"/> - <param name="method" value="shuffle"/> - <param name="enzyme" value="Chymotrypsin"/> - <section name="Decoy"> - <param name="non_shuffle_pattern" value="KR"/> - <param name="keepPeptideNTerm" value="true"/> - <param name="keepPeptideCTerm" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="seed" value="42"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DecoyDatabase_4.fasta"/> - <output name="out" file="DecoyDatabase_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="decoy_string" value="blabla"/> - <param name="decoy_string_position" value="prefix"/> - <param name="only_decoy" value="false"/> - <param name="type" value="RNA"/> - <param name="method" value="reverse"/> - <param name="enzyme" value="Trypsin"/> - <section name="Decoy"> - <param name="non_shuffle_pattern" value=""/> - <param name="keepPeptideNTerm" value="true"/> - <param name="keepPeptideCTerm" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_DeMeanderize"> -</xml> - <xml name="autotest_DigestorMotif"> -</xml> - <xml name="autotest_Digestor"> -</xml> - <xml name="autotest_DTAExtractor"> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DTAExtractor_1_input.mzML"/> - <param name="out" value="DTAExtractor"/> - <param name="mz" value=":"/> - <param name="rt" value=":61"/> - <param name="level" value="1,2,3"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DTAExtractor_1_input.mzML"/> - <param name="out" value="DTAExtractor"/> - <param name="mz" value=":"/> - <param name="rt" value=":"/> - <param name="level" value="1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="DTAExtractor_1_input.mzML"/> - <param name="out" value="DTAExtractor"/> - <param name="mz" value=":1000"/> - <param name="rt" value=":"/> - <param name="level" value="2"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_EICExtractor"> -</xml> - <xml name="autotest_Epifany"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="conservative_fdr" value="true"/> - <param name="min_psms_extreme_probability" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idxml"/> - <param name="protein_fdr" value="false"/> - <param name="greedy_group_resolution" value="none"/> - <param name="max_psms_extreme_probability" value="1.0"/> - <section name="algorithm"> - <param name="psm_probability_cutoff" value="0.001"/> - <param name="top_PSMs" value="1"/> - <param name="keep_best_PSM_only" value="true"/> - <param name="update_PSM_probabilities" value="true"/> - <param name="user_defined_priors" value="false"/> - <param name="annotate_group_probabilities" value="true"/> - <param name="use_ids_outside_features" value="false"/> - <section name="model_parameters"> - <param name="prot_prior" value="0.7"/> - <param name="pep_emission" value="0.1"/> - <param name="pep_spurious_emission" value="0.001"/> - <param name="pep_prior" value="0.1"/> - <param name="regularize" value="false"/> - <param name="extended_model" value="false"/> - </section> - <section name="loopy_belief_propagation"> - <param name="scheduling_type" value="priority"/> - <param name="convergence_threshold" value="1e-05"/> - <param name="dampening_lambda" value="0.001"/> - <param name="max_nr_iterations" value="2147483647"/> - <param name="p_norm_inference" value="1.0"/> - </section> - <section name="param_optimize"> - <param name="aucweight" value="0.3"/> - <param name="conservative_fdr" value="true"/> - <param name="regularized_fdr" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="conservative_fdr" value="true"/> - <param name="min_psms_extreme_probability" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Epifany_2_input.consensusXML"/> - <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="protein_fdr" value="false"/> - <param name="greedy_group_resolution" value="none"/> - <param name="max_psms_extreme_probability" value="1.0"/> - <section name="algorithm"> - <param name="psm_probability_cutoff" value="0.001"/> - <param name="top_PSMs" value="1"/> - <param name="keep_best_PSM_only" value="true"/> - <param name="update_PSM_probabilities" value="true"/> - <param name="user_defined_priors" value="false"/> - <param name="annotate_group_probabilities" value="true"/> - <param name="use_ids_outside_features" value="false"/> - <section name="model_parameters"> - <param name="prot_prior" value="0.7"/> - <param name="pep_emission" value="0.1"/> - <param name="pep_spurious_emission" value="0.001"/> - <param name="pep_prior" value="0.1"/> - <param name="regularize" value="false"/> - <param name="extended_model" value="false"/> - </section> - <section name="loopy_belief_propagation"> - <param name="scheduling_type" value="priority"/> - <param name="convergence_threshold" value="1e-05"/> - <param name="dampening_lambda" value="0.001"/> - <param name="max_nr_iterations" value="2147483647"/> - <param name="p_norm_inference" value="1.0"/> - </section> - <section name="param_optimize"> - <param name="aucweight" value="0.3"/> - <param name="conservative_fdr" value="true"/> - <param name="regularized_fdr" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="conservative_fdr" value="true"/> - <param name="min_psms_extreme_probability" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Epifany_2_input.consensusXML"/> - <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="protein_fdr" value="false"/> - <param name="greedy_group_resolution" value="none"/> - <param name="max_psms_extreme_probability" value="1.0"/> - <section name="algorithm"> - <param name="psm_probability_cutoff" value="0.001"/> - <param name="top_PSMs" value="1"/> - <param name="keep_best_PSM_only" value="false"/> - <param name="update_PSM_probabilities" value="true"/> - <param name="user_defined_priors" value="false"/> - <param name="annotate_group_probabilities" value="true"/> - <param name="use_ids_outside_features" value="false"/> - <section name="model_parameters"> - <param name="prot_prior" value="0.7"/> - <param name="pep_emission" value="0.1"/> - <param name="pep_spurious_emission" value="0.001"/> - <param name="pep_prior" value="0.1"/> - <param name="regularize" value="false"/> - <param name="extended_model" value="false"/> - </section> - <section name="loopy_belief_propagation"> - <param name="scheduling_type" value="priority"/> - <param name="convergence_threshold" value="1e-05"/> - <param name="dampening_lambda" value="0.001"/> - <param name="max_nr_iterations" value="2147483647"/> - <param name="p_norm_inference" value="1.0"/> - </section> - <section name="param_optimize"> - <param name="aucweight" value="0.3"/> - <param name="conservative_fdr" value="true"/> - <param name="regularized_fdr" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ERPairFinder"> -</xml> - <xml name="autotest_ExternalCalibration"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ExternalCalibration_1_input.mzML"/> - <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="offset" value="-5.5"/> - <param name="slope" value="0.0001"/> - <param name="power" value="0.0"/> - <param name="ms_level" value="1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ExternalCalibration_1_input.mzML"/> - <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="offset" value="-5.5"/> - <param name="slope" value="0.0001"/> - <param name="power" value="0.0"/> - <param name="ms_level" value="2"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FalseDiscoveryRate"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> - <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> - <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="true"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/> - <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="true"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/> - <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="true"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_5_input.idXML"/> - <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="false"/> - <param name="protein" value="true"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="true"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_6_input.idXML"/> - <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="true"/> - <param name="protein" value="false"/> - <section name="FDR"> - <param name="PSM" value="0.05"/> - <param name="protein" value="1.0"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FalseDiscoveryRate_7_input.idXML"/> - <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="PSM" value="false"/> - <param name="protein" value="true"/> - <section name="FDR"> - <param name="PSM" value="1.0"/> - <param name="protein" value="0.3"/> - <section name="cleanup"> - <param name="remove_proteins_without_psms" value="true"/> - <param name="remove_psms_without_proteins" value="true"/> - <param name="remove_spectra_without_psms" value="true"/> - </section> - </section> - <section name="algorithm"> - <param name="no_qvalues" value="false"/> - <param name="use_all_hits" value="false"/> - <param name="split_charge_variants" value="false"/> - <param name="treat_runs_separately" value="false"/> - <param name="add_decoy_peptides" value="false"/> - <param name="add_decoy_proteins" value="false"/> - <param name="conservative" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderCentroided"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - <param name="pseudo_rt_shift" value="500.0"/> - </conditional> - <param name="in" value="FeatureFinderCentroided_1_input.mzML"/> - <output name="out" file="FeatureFinderCentroided_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="intensity"> - <param name="bins" value="1"/> - </section> - <section name="mass_trace"> - <param name="mz_tolerance" value="0.02"/> - <param name="min_spectra" value="14"/> - <param name="max_missing" value="1"/> - <param name="slope_bound" value="0.1"/> - </section> - <section name="isotopic_pattern"> - <param name="charge_low" value="2"/> - <param name="charge_high" value="2"/> - <param name="mz_tolerance" value="0.02"/> - <param name="intensity_percentage" value="10.0"/> - <param name="intensity_percentage_optional" value="0.1"/> - <param name="optional_fit_improvement" value="2.0"/> - <param name="mass_window_width" value="100.0"/> - <param name="abundance_12C" value="98.93"/> - <param name="abundance_14N" value="99.632"/> - </section> - <section name="seed"> - <param name="min_score" value="0.8"/> - </section> - <section name="fit"> - <param name="max_iterations" value="500"/> - </section> - <section name="feature"> - <param name="min_score" value="0.7"/> - <param name="min_isotope_fit" value="0.8"/> - <param name="min_trace_score" value="0.5"/> - <param name="min_rt_span" value="0.333"/> - <param name="max_rt_span" value="2.5"/> - <param name="rt_shape" value="symmetric"/> - <param name="max_intersection" value="0.35"/> - <param name="reported_mz" value="monoisotopic"/> - </section> - <section name="user-seed"> - <param name="rt_tolerance" value="5.0"/> - <param name="mz_tolerance" value="1.1"/> - <param name="min_score" value="0.5"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderIdentification"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> - <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> - <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="extract"> - <param name="batch_size" value="1000"/> - <param name="mz_window" value="0.1"/> - <param name="n_isotopes" value="2"/> - <param name="isotope_pmin" value="0.0"/> - <param name="rt_quantile" value="0.95"/> - <param name="rt_window" value="0.0"/> - </section> - <section name="detect"> - <param name="peak_width" value="60.0"/> - <param name="min_peak_width" value="0.2"/> - <param name="signal_to_noise" value="0.8"/> - <param name="mapping_tolerance" value="0.0"/> - </section> - <section name="svm"> - <param name="samples" value="0"/> - <param name="no_selection" value="false"/> - <param name="kernel" value="RBF"/> - <param name="xval" value="5"/> - <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/> - <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/> - <param name="epsilon" value="0.001"/> - <param name="cache_size" value="100.0"/> - <param name="no_shrinking" value="false"/> - <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/> - <param name="min_prob" value="0.0"/> - </section> - <section name="model"> - <param name="type" value="none"/> - <param name="add_zeros" value="0.2"/> - <param name="unweighted_fit" value="false"/> - <param name="no_imputation" value="false"/> - <param name="each_trace" value="false"/> - <section name="check"> - <param name="min_area" value="1.0"/> - <param name="boundaries" value="0.5"/> - <param name="width" value="10.0"/> - <param name="asymmetry" value="10.0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderIdentification_1_input.mzML"/> - <param name="id" value="FeatureFinderIdentification_1_input.idXML"/> - <output name="out" file="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="extract"> - <param name="batch_size" value="1000"/> - <param name="mz_window" value="0.1"/> - <param name="n_isotopes" value="2"/> - <param name="isotope_pmin" value="0.0"/> - <param name="rt_quantile" value="0.95"/> - <param name="rt_window" value="0.0"/> - </section> - <section name="detect"> - <param name="peak_width" value="60.0"/> - <param name="min_peak_width" value="0.2"/> - <param name="signal_to_noise" value="0.8"/> - <param name="mapping_tolerance" value="0.0"/> - </section> - <section name="svm"> - <param name="samples" value="0"/> - <param name="no_selection" value="false"/> - <param name="kernel" value="RBF"/> - <param name="xval" value="5"/> - <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/> - <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/> - <param name="epsilon" value="0.001"/> - <param name="cache_size" value="100.0"/> - <param name="no_shrinking" value="false"/> - <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/> - <param name="min_prob" value="0.0"/> - </section> - <section name="model"> - <param name="type" value="symmetric"/> - <param name="add_zeros" value="0.2"/> - <param name="unweighted_fit" value="false"/> - <param name="no_imputation" value="false"/> - <param name="each_trace" value="false"/> - <section name="check"> - <param name="min_area" value="1.0"/> - <param name="boundaries" value="0.5"/> - <param name="width" value="10.0"/> - <param name="asymmetry" value="10.0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderIsotopeWavelet"> -</xml> - <xml name="autotest_FeatureFinderMetaboIdent"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/> - <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/> - <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="extract"> - <param name="mz_window" value="5.0"/> - <param name="n_isotopes" value="2"/> - <param name="isotope_pmin" value="0.0"/> - <param name="rt_window" value="20.0"/> - </section> - <section name="detect"> - <param name="peak_width" value="3.0"/> - <param name="min_peak_width" value="0.2"/> - <param name="signal_to_noise" value="0.8"/> - </section> - <section name="model"> - <param name="type" value="symmetric"/> - <param name="add_zeros" value="0.2"/> - <param name="unweighted_fit" value="false"/> - <param name="no_imputation" value="false"/> - <param name="each_trace" value="false"/> - <section name="check"> - <param name="min_area" value="1.0"/> - <param name="boundaries" value="0.5"/> - <param name="width" value="10.0"/> - <param name="asymmetry" value="10.0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderMetabo"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_1_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="20.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="300.0"/> - </section> - <section name="epd"> - <param name="enabled" value="true"/> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="6.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="true"/> - <param name="isotope_filtering_model" value="metabolites (5% RMS)"/> - <param name="mz_scoring_13C" value="true"/> - <param name="use_smoothed_intensities" value="true"/> - <param name="report_convex_hulls" value="false"/> - <param name="remove_single_traces" value="false"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_2_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="100.0"/> - <param name="chrom_peak_snr" value="0.0"/> - <param name="chrom_fwhm" value="100.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="5.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="median"/> - <param name="trace_termination_criterion" value="sample_rate"/> - <param name="trace_termination_outliers" value="2"/> - <param name="min_sample_rate" value="0.01"/> - <param name="min_trace_length" value="30.0"/> - <param name="max_trace_length" value="3000.0"/> - </section> - <section name="epd"> - <param name="enabled" value="false"/> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="10.0"/> - <param name="max_fwhm" value="80.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="4.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="false"/> - <param name="isotope_filtering_model" value="none"/> - <param name="mz_scoring_13C" value="false"/> - <param name="use_smoothed_intensities" value="false"/> - <param name="report_convex_hulls" value="true"/> - <param name="remove_single_traces" value="false"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="5.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="-1.0"/> - </section> - <section name="epd"> - <param name="enabled" value="true"/> - <param name="width_filtering" value="fixed"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="6.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="true"/> - <param name="isotope_filtering_model" value="none"/> - <param name="mz_scoring_13C" value="true"/> - <param name="use_smoothed_intensities" value="true"/> - <param name="report_convex_hulls" value="true"/> - <param name="remove_single_traces" value="false"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_3_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="5.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="-1.0"/> - </section> - <section name="epd"> - <param name="enabled" value="true"/> - <param name="width_filtering" value="fixed"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="6.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="true"/> - <param name="isotope_filtering_model" value="none"/> - <param name="mz_scoring_13C" value="true"/> - <param name="use_smoothed_intensities" value="true"/> - <param name="report_convex_hulls" value="true"/> - <param name="remove_single_traces" value="true"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMetabo_1_input.mzML"/> - <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="20.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="max_height"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="300.0"/> - </section> - <section name="epd"> - <param name="enabled" value="true"/> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - </section> - <section name="ffm"> - <param name="local_rt_range" value="10.0"/> - <param name="local_mz_range" value="6.5"/> - <param name="charge_lower_bound" value="1"/> - <param name="charge_upper_bound" value="3"/> - <param name="report_summed_ints" value="false"/> - <param name="enable_RT_filtering" value="true"/> - <param name="isotope_filtering_model" value="metabolites (5% RMS)"/> - <param name="mz_scoring_13C" value="true"/> - <param name="use_smoothed_intensities" value="true"/> - <param name="report_convex_hulls" value="false"/> - <param name="remove_single_traces" value="false"/> - <param name="mz_scoring_by_elements" value="false"/> - <param name="elements" value="CHNOPS"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderMRM"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMRM_1_input.mzML"/> - <output name="out" file="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <param name="min_rt_distance" value="10.0"/> - <param name="min_num_peaks_per_feature" value="5"/> - <param name="min_signal_to_noise_ratio" value="2.0"/> - <param name="write_debug_files" value="false"/> - <param name="resample_traces" value="false"/> - <param name="write_debuginfo" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureFinderMultiplex"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta="5700" 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> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta="5700" 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> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta="5700" 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> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta="5700" 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> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta="5700" 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> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta="5700" 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> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta="5700" 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> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta="5700" 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> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta="5700" 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> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_multiplets" file="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta="5700" 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> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/> - <output name="out" file="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta="5700" 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> - </test> - </xml> - <xml name="autotest_FeatureFinderSuperHirn"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderSuperHirn_input_1.mzML"/> - <output name="out" file="FeatureFinderSuperHirn_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="centroiding"> - <param name="active" value="false"/> - <param name="window_width" value="5"/> - <param name="absolute_isotope_mass_precision" value="0.01"/> - <param name="relative_isotope_mass_precision" value="10.0"/> - <param name="minimal_peak_height" value="0.0"/> - <param name="min_ms_signal_intensity" value="50.0"/> - </section> - <section name="ms1"> - <param name="precursor_detection_scan_levels" value="1"/> - <param name="max_inter_scan_distance" value="0"/> - <param name="tr_resolution" value="0.01"/> - <param name="intensity_threshold" value="1000.0"/> - <param name="max_inter_scan_rt_distance" value="0.1"/> - <param name="min_nb_cluster_members" value="4"/> - <param name="detectable_isotope_factor" value="0.05"/> - <param name="intensity_cv" value="0.9"/> - <param name="retention_time_tolerance" value="0.5"/> - <param name="mz_tolerance" value="0.0"/> - </section> - <section name="ms1_feature_merger"> - <param name="active" value="true"/> - <param name="tr_resolution" value="0.01"/> - <param name="initial_apex_tr_tolerance" value="5.0"/> - <param name="feature_merging_tr_tolerance" value="1.0"/> - <param name="intensity_variation_percentage" value="25.0"/> - <param name="ppm_tolerance_for_mz_clustering" value="10.0"/> - </section> - <section name="ms1_feature_selection_options"> - <param name="start_elution_window" value="0.0"/> - <param name="end_elution_window" value="180.0"/> - <param name="mz_range_min" value="0.0"/> - <param name="mz_range_max" value="2000.0"/> - <param name="chrg_range_min" value="1"/> - <param name="chrg_range_max" value="5"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureFinderSuperHirn_input_2.mzML"/> - <output name="out" file="FeatureFinderSuperHirn_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="centroiding"> - <param name="active" value="true"/> - <param name="window_width" value="5"/> - <param name="absolute_isotope_mass_precision" value="0.01"/> - <param name="relative_isotope_mass_precision" value="10.0"/> - <param name="minimal_peak_height" value="0.0"/> - <param name="min_ms_signal_intensity" value="50.0"/> - </section> - <section name="ms1"> - <param name="precursor_detection_scan_levels" value="1"/> - <param name="max_inter_scan_distance" value="0"/> - <param name="tr_resolution" value="0.01"/> - <param name="intensity_threshold" value="1000.0"/> - <param name="max_inter_scan_rt_distance" value="0.1"/> - <param name="min_nb_cluster_members" value="4"/> - <param name="detectable_isotope_factor" value="0.05"/> - <param name="intensity_cv" value="0.9"/> - <param name="retention_time_tolerance" value="0.5"/> - <param name="mz_tolerance" value="0.0"/> - </section> - <section name="ms1_feature_merger"> - <param name="active" value="true"/> - <param name="tr_resolution" value="0.01"/> - <param name="initial_apex_tr_tolerance" value="5.0"/> - <param name="feature_merging_tr_tolerance" value="1.0"/> - <param name="intensity_variation_percentage" value="25.0"/> - <param name="ppm_tolerance_for_mz_clustering" value="10.0"/> - </section> - <section name="ms1_feature_selection_options"> - <param name="start_elution_window" value="0.0"/> - <param name="end_elution_window" value="180.0"/> - <param name="mz_range_min" value="0.0"/> - <param name="mz_range_max" value="2000.0"/> - <param name="chrg_range_min" value="1"/> - <param name="chrg_range_max" value="5"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureLinkerLabeled"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/> - <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="rt_estimate" value="false"/> - <param name="rt_pair_dist" value="-1.0"/> - <param name="rt_dev_low" value="0.4"/> - <param name="rt_dev_high" value="0.4"/> - <param name="mz_pair_dists" value="8.0"/> - <param name="mz_dev" value="0.1"/> - <param name="mrm" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/> - <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="rt_estimate" value="true"/> - <param name="rt_pair_dist" value="-121.0382"/> - <param name="rt_dev_low" value="123.3965"/> - <param name="rt_dev_high" value="123.3965"/> - <param name="mz_pair_dists" value="4.0"/> - <param name="mz_dev" value="0.1"/> - <param name="mrm" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureLinkerUnlabeledKD"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="Da"/> - <param name="nr_partitions" value="1"/> - <section name="warp"> - <param name="enabled" value="false"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="charge_merging" value="With_charge_zero"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_1_output.consensusXML,FeatureLinkerUnlabeledKD_1_output_2.consensusXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="true"/> - <section name="algorithm"> - <param name="mz_unit" value="Da"/> - <param name="nr_partitions" value="99999"/> - <section name="warp"> - <param name="enabled" value="false"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="charge_merging" value="With_charge_zero"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="Da"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="false"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="0.3"/> - <param name="charge_merging" value="With_charge_zero"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="ppm"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="true"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="5.0"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="30.0"/> - <param name="mz_tol" value="10.0"/> - <param name="charge_merging" value="Identical"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="ppm"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="true"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="5.0"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="30.0"/> - <param name="mz_tol" value="10.0"/> - <param name="charge_merging" value="With_charge_zero"/> - <param name="adduct_merging" value="Any"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="ppm"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="true"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="5.0"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="30.0"/> - <param name="mz_tol" value="10.0"/> - <param name="charge_merging" value="Any"/> - <param name="adduct_merging" value="With_unknown_adducts"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledKD_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="mz_unit" value="ppm"/> - <param name="nr_partitions" value="100"/> - <section name="warp"> - <param name="enabled" value="true"/> - <param name="rt_tol" value="100.0"/> - <param name="mz_tol" value="5.0"/> - <param name="max_pairwise_log_fc" value="0.5"/> - <param name="min_rel_cc_size" value="0.5"/> - <param name="max_nr_conflicts" value="0"/> - </section> - <section name="link"> - <param name="rt_tol" value="30.0"/> - <param name="mz_tol" value="10.0"/> - <param name="charge_merging" value="Any"/> - <param name="adduct_merging" value="Identical"/> - </section> - <section name="distance_RT"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - <param name="log_transform" value="enabled"/> - </section> - <section name="LOWESS"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureLinkerUnlabeledQT"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="false"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="true"/> - <section name="algorithm"> - <param name="use_identifications" value="false"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="false"/> - <param name="nr_partitions" value="99999"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="true"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="false"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="200.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="use_identifications" value="true"/> - <param name="nr_partitions" value="100"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="200.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FeatureLinkerUnlabeled"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="200.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.5"/> - <param name="unit" value="Da"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_2_input1.featureXML,FeatureLinkerUnlabeled_2_input2.featureXML,FeatureLinkerUnlabeled_2_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.5"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_3_input1.featureXML,FeatureLinkerUnlabeled_3_input2.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeled_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="second_nearest_gap" value="1.5"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="30.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/> - <output name="out" file="FeatureLinkerUnlabeled_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="keep_subelements" value="false"/> - <section name="algorithm"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="true"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="200.0"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.5"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FFEval"> -</xml> - <xml name="autotest_FidoAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="FidoAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="true"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="FidoAdapter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="true"/> - <param name="group_level" value="true"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_4_input.idXML"/> - <output name="out" file="FidoAdapter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_5_input.idXML"/> - <output name="out" file="FidoAdapter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="true"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.0"/> - <param name="peptide" value="0.0"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_zero_group" value="false"/> - <param name="accuracy" value=""/> - <param name="log2_states_precalc" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FidoAdapter_1_input.idXML"/> - <output name="out" file="FidoAdapter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="separate_runs" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="no_cleanup" value="false"/> - <param name="all_PSMs" value="false"/> - <param name="group_level" value="false"/> - <param name="log2_states" value="0"/> - <section name="prob"> - <param name="protein" value="0.9"/> - <param name="peptide" value="0.01"/> - <param name="spurious" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FileConverter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_1_input.mzData"/> - <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_2_input.someInputDTA2D"/> - <output name="out" file="FileConverter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_3_input.featureXML"/> - <output name="out" file="FileConverter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_4_input.mzXML"/> - <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_5_input.mzML"/> - <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> - <param name="out_type" value="mzXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_6_input.mzML"/> - <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> - <param name="out_type" value="mzXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_7_input.consensusXML"/> - <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_8_input.mzML"/> - <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta="5700" ftype="mzdata"/> - <param name="out_type" value="mzData"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_9_input.consensusXML"/> - <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_10_input.edta" ftype="edta"/> - <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_11_input.peplist"/> - <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/> - <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_13_input.peptides.kroenik"/> - <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_9_output.featureXML"/> - <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_10_input.edta" ftype="edta"/> - <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_16_input.edta" ftype="edta"/> - <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_17_input.consensusXML"/> - <output name="out" file="FileConverter_17.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="out_type" value="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_17_input.consensusXML"/> - <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="out_type" value="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_19_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_20_input.featureXML"/> - <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_4_input.mzXML"/> - <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_23_input.mzML"/> - <output name="out" file="FileConverter_23_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="true"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_24_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="true"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="true"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileConverter_26_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> - <param name="out_type" value="mzXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="true"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_26_output.mzXML"/> - <output name="out" file="FileConverter_26-2_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/> - <param name="out_type" value="mzXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="true"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_27_input.mzML"/> - <output name="out" file="FileConverter_27_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="true"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_28_input.mzML"/> - <output name="out" file="FileConverter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="true"/> - <param name="lossy_mass_accuracy" value="1e-05"/> - <param name="process_lowmemory" value="true"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> - <output name="out" file="FileConverter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_29_output.mzML"/> - <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta="5700"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="multiple"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_30_input.mzML"/> - <output name="out" file="FileConverter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="single"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_30_output.mzML"/> - <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileConverter_32_input.mzML"/> - <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="UID_postprocessing" value="ensure"/> - <param name="TIC_DTA2D" value="false"/> - <param name="MGF_compact" value="false"/> - <param name="force_MaxQuant_compatibility" value="false"/> - <param name="convert_to_chromatograms" value="false"/> - <param name="force_TPP_compatibility" value="false"/> - <param name="change_im_format" value="none"/> - <param name="write_scan_index" value="true"/> - <param name="lossy_compression" value="false"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="no_peak_picking" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ginkgotoxin-ms-switching.raw"/> - <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FileFilter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":30"/> - <param name="mz" value=":1000"/> - <param name="int" value=":20000"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value="30:"/> - <param name="mz" value="1000:"/> - <param name="int" value="100:"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="2"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_4_input.mzML"/> - <output name="out" file="FileFilter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="true"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_5_input.featureXML"/> - <output name="out" file="FileFilter_5_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="rt" value=":1000"/> - <param name="mz" value=":480"/> - <param name="int" value=":79000"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":0.6"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":3"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_5_input.featureXML"/> - <output name="out" file="FileFilter_6_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="rt" value="1000:"/> - <param name="mz" value="440:"/> - <param name="int" value="70000:"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value="0.51:"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value="3:"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_7_input.mzML"/> - <output name="out" file="FileFilter_7_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value="7000:"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_8_input.consensusXML"/> - <output name="out" file="FileFilter_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="rt" value="600:1400"/> - <param name="mz" value="700:2300"/> - <param name="int" value="1100:6000"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_9_input.mzML"/> - <output name="out" file="FileFilter_9_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value="SelectedIonMonitoring"/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_10_input.mzML"/> - <output name="out" file="FileFilter_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value="Collision-induced dissociation"/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_11_input.mzML"/> - <output name="out" file="FileFilter_11_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value="Plasma desorption"/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_12_input.mzML"/> - <output name="out" file="FileFilter_12_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="true"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_13_input.consensusXML"/> - <output name="out" file="FileFilter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featureXML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value="2"/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_14_input.consensusXML"/> - <output name="out" file="FileFilter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusXML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value="0 2"/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""Oxidation""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value="3000:4000"/> - <param name="mz" value="400:600"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""Oxidation""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_17_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value="3000:4000"/> - <param name="mz" value="400:600"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="true"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_18_input.consensusXML"/> - <output name="out" file="FileFilter_18_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""Oxidation""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_18_input.consensusXML"/> - <output name="out" file="FileFilter_19_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value="3000:4000"/> - <param name="mz" value="400:600"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="true"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""YDL217C""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_15_input.featureXML"/> - <output name="out" file="FileFilter_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="true"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="true"/> - <param name="remove_unassigned_ids" value="true"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_22_input.consensusXML"/> - <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""distinct_charges" "gt" "1,2""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_22_input.consensusXML"/> - <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""distinct_charges_size" "gt" "2""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_22_input.consensusXML"/> - <output name="out" file="FileFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="out_type" value="consensusxml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""DOESNOTEXIST" "lt" "whatever""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_25_input.mzML.gz"/> - <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="blacklist" value="FileFilter_25_input.idXML"/> - <param name="rt" value="1.0"/> - <param name="mz" value="0.05"/> - <param name="blacklist_imperfect" value="true"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_25_input.mzML.gz"/> - <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="blacklist" value="FileFilter_25_input.idXML"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="true"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_28_input.mzML.gz"/> - <output name="out" file="FileFilter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value="832:836"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="2"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_28_input.mzML.gz"/> - <output name="out" file="FileFilter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value="832:836"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_28_input.mzML.gz"/> - <output name="out" file="FileFilter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value="832:836"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_31_34_input.mzML"/> - <output name="out" file="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":2"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_31_34_input.mzML"/> - <output name="out" file="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":2"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_31_34_input.mzML"/> - <output name="out" file="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":35"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_31_34_input.mzML"/> - <output name="out" file="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":35"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_35_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_36_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="false"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_37_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="linear"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="intensity" value="slof"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output name="out" file="FileFilter_38_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="linear"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="intensity" value="pic"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_40_input.mzML"/> - <output name="out" file="FileFilter_40_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value="positive"/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_40_input.mzML"/> - <output name="out" file="FileFilter_41_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value="negative"/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_40_input.mzML"/> - <output name="out" file="FileFilter_42_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_43_input.mzML"/> - <output name="out" file="FileFilter_43.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_43.tmp.mzML"/> - <output name="out" file="FileFilter_43.dummy.tmp" compare="sim_size" delta="5700"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_44_input.mzML"/> - <output name="out" file="FileFilter_44_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_45_input.featureXML"/> - <output name="out" file="FileFilter_45_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""YSFS" "STLIPPPSK(Label:13C(6)15N(2))""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_46_input.featureXML"/> - <output name="out" file="FileFilter_46_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""YSFS" "STLIPPPSK(Label:13C(6)15N(2))""/> - <param name="sequence_comparison_method" value="exact"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_47_input.mzML"/> - <output name="out" file="FileFilter_47_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="file" value="FileFilter_47_input_select.mzML"/> - <param name="similarity_threshold" value="0.9"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_47_input.mzML"/> - <output name="out" file="FileFilter_48_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="false"/> - <section name="numpress"> - <param name="masstime" value="none"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="none"/> - <param name="float_da" value="none"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="file" value="FileFilter_47_input_select.mzML"/> - <param name="similarity_threshold" value="0.9"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="false"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_49_input.mzML"/> - <output name="out" file="FileFilter_49_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="int" value=":"/> - <param name="sort" value="false"/> - <section name="peak_options"> - <param name="sn" value="0.0"/> - <param name="rm_pc_charge" value=""/> - <param name="pc_mz_range" value=":"/> - <param name="pc_mz_list" value=""/> - <param name="level" value="1 2 3"/> - <param name="sort_peaks" value="false"/> - <param name="no_chromatograms" value="false"/> - <param name="remove_chromatograms" value="false"/> - <param name="remove_empty" value="false"/> - <param name="mz_precision" value="64"/> - <param name="int_precision" value="32"/> - <param name="indexed_file" value="true"/> - <param name="zlib_compression" value="true"/> - <section name="numpress"> - <param name="masstime" value="linear"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="intensity" value="pic"/> - <param name="float_da" value="slof"/> - </section> - </section> - <section name="spectra"> - <param name="remove_zoom" value="false"/> - <param name="remove_mode" value=""/> - <param name="remove_activation" value=""/> - <param name="remove_collision_energy" value=":"/> - <param name="remove_isolation_window_width" value=":"/> - <param name="select_zoom" value="false"/> - <param name="select_mode" value=""/> - <param name="select_activation" value=""/> - <param name="select_collision_energy" value=":"/> - <param name="select_isolation_window_width" value=":"/> - <param name="select_polarity" value=""/> - <section name="blackorwhitelist"> - <param name="similarity_threshold" value="-1.0"/> - <param name="rt" value="0.01"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - <param name="blacklist" value="true"/> - </section> - </section> - <section name="feature"> - <param name="q" value=":"/> - </section> - <section name="consensus"> - <param name="map" value=""/> - <param name="map_and" value="false"/> - <section name="blackorwhitelist"> - <param name="blacklist" value="true"/> - <param name="maps" value=""/> - <param name="rt" value="60.0"/> - <param name="mz" value="0.01"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - </section> - <section name="f_and_c"> - <param name="charge" value=":"/> - <param name="size" value=":"/> - <param name="remove_meta" value=""/> - </section> - <section name="id"> - <param name="remove_clashes" value="false"/> - <param name="keep_best_score_id" value="false"/> - <param name="sequences_whitelist" value=""/> - <param name="sequence_comparison_method" value="substring"/> - <param name="accessions_whitelist" value=""/> - <param name="remove_annotated_features" value="false"/> - <param name="remove_unannotated_features" value="false"/> - <param name="remove_unassigned_ids" value="false"/> - <param name="rt" value="0.1"/> - <param name="mz" value="0.001"/> - <param name="blacklist_imperfect" value="false"/> - </section> - <section name="algorithm"> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FileInfo"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_1_input.dta" ftype="dta"/> - <output name="out" file="FileInfo_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/> - <output name="out" file="FileInfo_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_3_input.featureXML"/> - <output name="out" file="FileInfo_3_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="true"/> - <param name="s" value="true"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_4_input.mzXML"/> - <output name="out" file="FileInfo_4_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_5_input.mzDat"/> - <output name="out" file="FileInfo_5_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="false"/> - <param name="s" value="true"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_6_input.mzData"/> - <output name="out" file="FileInfo_6_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="true"/> - <param name="d" value="true"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_7_input.consensusXML"/> - <output name="out" file="FileInfo_7_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="true"/> - <param name="s" value="true"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_9_input.mzML"/> - <output name="out" file="FileInfo_9_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="true"/> - <param name="p" value="true"/> - <param name="s" value="true"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_10_input.idXML"/> - <output name="out" file="FileInfo_10_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_12_input.mzML"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_13_input.consensusXML"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_14_input.mzid"/> - <output name="out" file="FileInfo_14_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="true"/> - <param name="i" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_15_input.mzid"/> - <output name="out" file="FileInfo_15_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="true"/> - <param name="i" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_16_input.trafoXML"/> - <output name="out" file="FileInfo_16_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_17_input.fasta"/> - <output name="out" file="FileInfo_17_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileInfo_18_input.fasta"/> - <output name="out" file="FileInfo_18_output.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="m" value="false"/> - <param name="p" value="false"/> - <param name="s" value="false"/> - <param name="d" value="false"/> - <param name="c" value="false"/> - <param name="v" value="false"/> - <param name="i" 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> - </xml> - <xml name="autotest_FileMerger"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_2_input1.dta,FileMerger_2_input2.dta" ftype="dta"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value="5.0 10.0"/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_3_input1.dta,FileMerger_3_input2.dta" ftype="dta"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="true"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_4_input1.dta2d,FileMerger_4_input2.dta2d" ftype="dta2d"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_5_input_rt1023.331.dta,FileMerger_5_input_rt2044.334.dta,FileMerger_5_input_rt889.32.dta" ftype="dta"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="true"/> - <param name="ms_level" value="2"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_6_input1.mzML,FileMerger_6_input2.mzML"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_6_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_7_input1.featureXML,FileMerger_7_input2.featureXML"/> - <param name="out_type" value="featureXML"/> - <output name="out" file="FileMerger_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/> - <param name="out_type" value="consensusXML"/> - <output name="out" file="FileMerger_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_9_input1.traML,FileMerger_9_input2.traML"/> - <param name="out_type" value="traML"/> - <output name="out" file="FileMerger_9_output.traML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_6_input2.mzML,FileMerger_6_input2_2.mzML"/> - <param name="out_type" value="mzML"/> - <output name="out" file="FileMerger_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_rows"/> - <section name="rt_concat"> - <param name="gap" value="10.0"/> - </section> - <output_collection name="rt_concat_trafo_out" count="2"/> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/> - <param name="out_type" value="consensusXML"/> - <output name="out" file="FileMerger_11_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="append_method" value="append_cols"/> - <section name="rt_concat"> - <param name="gap" value="0.0"/> - </section> - <section name="raw"> - <param name="rt_auto" value="false"/> - <param name="rt_custom" value=""/> - <param name="rt_filename" value="false"/> - <param name="ms_level" value="0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_FuzzyDiff"> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="whitelist" value=""<?xml-stylesheet""/> - <param name="matched_whitelist" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in1" value="FuzzyDiff_3_in1.featureXML"/> - <param name="in2" value="FuzzyDiff_3_in2.featureXML"/> - <param name="ratio" value="1.01"/> - <param name="absdiff" value="0.01"/> - <param name="verbose" value="1"/> - <param name="tab_width" value="8"/> - <param name="first_column" value="1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_GNPSExport"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="GNPSExport_single.consensusXML"/> - <param name="in_mzml" value="GNPSExport_mz1.mzML"/> - <output name="out" file="GNPSExport_1_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> - <param name="output_type" value="full_spectra"/> - <param name="precursor_mz_tolerance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <section name="merged_spectra"> - <param name="cos_similarity" value="0.95"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="GNPSExport_single.consensusXML"/> - <param name="in_mzml" value="GNPSExport_mz1.mzML"/> - <output name="out" file="GNPSExport_2_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> - <param name="output_type" value="merged_spectra"/> - <param name="precursor_mz_tolerance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <section name="merged_spectra"> - <param name="cos_similarity" value="0.95"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="GNPSExport_merged.consensusXML"/> - <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/> - <output name="out" file="GNPSExport_3_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> - <param name="output_type" value="full_spectra"/> - <param name="precursor_mz_tolerance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <section name="merged_spectra"> - <param name="cos_similarity" value="0.95"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="GNPSExport_merged.consensusXML"/> - <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/> - <output name="out" file="GNPSExport_4_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/> - <param name="output_type" value="full_spectra"/> - <param name="precursor_mz_tolerance" value="0.0001"/> - <param name="precursor_rt_tolerance" value="5.0"/> - <section name="merged_spectra"> - <param name="cos_similarity" value="0.95"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_HighResPrecursorMassCorrector"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_1035_1178_4_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.featureXML"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="4"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/> - <output name="out" file="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="feature"> - <param name="mz_tolerance" value="5.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - <param name="rt_tolerance" value="0.0"/> - <param name="max_trace" value="2"/> - <param name="believe_charge" value="false"/> - <param name="keep_original" value="false"/> - <param name="assign_all_matching" value="false"/> - </section> - <section name="nearest_peak"> - <param name="mz_tolerance" value="0.0"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <section name="highest_intensity_peak"> - <param name="mz_tolerance" value="0.2"/> - <param name="mz_tolerance_unit" value="ppm"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDConflictResolver"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDConflictResolver_1_input.featureXML"/> - <output name="out" file="IDConflictResolver_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="resolve_between_features" value="off"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDConflictResolver_2_input.consensusXML"/> - <output name="out" file="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="resolve_between_features" value="off"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDConflictResolver_3_input.consensusXML"/> - <output name="out" file="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="resolve_between_features" value="off"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDConflictResolver_4_input.featureXML"/> - <output name="out" file="IDConflictResolver_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="resolve_between_features" value="highest_intensity"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDExtractor"> -</xml> - <xml name="autotest_IDFileConverter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_1_input1.mascotXML"/> - <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PepXMLFile_test.pepxml"/> - <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="PepXMLFile_test.mzML"/> - <param name="mz_name" value="PepXMLFile_test"/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_3_input.protXML"/> - <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value="scan=(?<SCAN>\d+)"/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_1_input1.mascotXML"/> - <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_6_input1.pepXML"/> - <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="IDFileConverter_1_input2.mzML"/> - <param name="mz_name" value="F025589.dat.mzML"/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_7_input1.xml"/> - <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_8_input.mzid"/> - <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_9_input.idXML"/> - <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <param name="out_type" value="mzid"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_10_input.pepXML"/> - <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/> - <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_12_input.psms"/> - <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_12_input.psms"/> - <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="PEP"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_12_input.psms"/> - <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="score"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> - <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="spectra.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_16_input.pepXML"/> - <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_17_input.idXML"/> - <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_18_input.idXML"/> - <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_19_input.idXML"/> - <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_20_input.idXML"/> - <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_21_input.idXML"/> - <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="IDMapper_4_input.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.01"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSGFPlusAdapter_1_out.mzid"/> - <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_file" value="spectra.mzML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_23_input.mzid"/> - <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_24_input.pep.xml"/> - <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_25_input.idXML"/> - <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="out_type" value="pepXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_26_input.mzid"/> - <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_27_input.idXML"/> - <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="out_type" value="FASTA"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="-1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_27_input.idXML"/> - <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="out_type" value="FASTA"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="true"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_27_input.idXML"/> - <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="out_type" value="FASTA"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="true"/> - <param name="number_of_hits" value="2"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_27_input.idXML"/> - <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/> - <param name="out_type" value="FASTA"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_proteins_per_peptide" value="false"/> - <param name="scan_regex" value=""/> - <param name="no_spectra_data_override" value="false"/> - <param name="no_spectra_references_override" value="false"/> - <param name="add_ionmatch_annotation" value="0.0"/> - <param name="concatenate_peptides" value="false"/> - <param name="number_of_hits" value="1"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_31_input.mzid"/> - <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="mz_name" value=""/> - <param name="peptideprophet_analyzed" value="false"/> - <param name="score_type" value="qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDFilter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_1_input.idXML"/> - <output name="out" file="IDFilter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="proteins" value="IDFilter_1_input.fas"/> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_3_input.idXML"/> - <output name="out" file="IDFilter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="peptides" value="IDFilter_3_2_input.idXML"/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_4_input.idXML"/> - <output name="out" file="IDFilter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.08"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_5_input.idXML"/> - <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="32.0"/> - <param name="prot" value="25.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_5_input.idXML"/> - <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="32.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_5_input.idXML"/> - <output name="out" file="IDFilter_5b_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="25.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_5_input.idXML"/> - <output name="out" file="IDFilter_5c_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="true"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="25.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_6_input.idXML"/> - <output name="out" file="IDFilter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="2"/> - <param name="n_protein_hits" value="10"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="true"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_7_input.idXML"/> - <output name="out" file="IDFilter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_8_input.idXML"/> - <output name="out" file="IDFilter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value="200:350"/> - <param name="mz" value="999:1000"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_9_input.idXML"/> - <output name="out" file="IDFilter_9_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.05"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_10_input.idXML"/> - <output name="out" file="IDFilter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="true"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.3"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_11_input.idXML"/> - <output name="out" file="IDFilter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="true"/> - <param name="delete_unreferenced_peptide_hits" value="true"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_12_input.idXML"/> - <output name="out" file="IDFilter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_12_input.fasta"/> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_13_input.idXML"/> - <output name="out" file="IDFilter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_13_input.fasta"/> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_14_input.idXML"/> - <output name="out" file="IDFilter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_14_input.fasta"/> - <param name="enzyme" value="Trypsin/P"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_15_input.idXML"/> - <output name="out" file="IDFilter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_15_input.fasta"/> - <param name="enzyme" value="Trypsin/P"/> - <param name="specificity" value="semi"/> - <param name="missed_cleavages" value="1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_16_input.idXML"/> - <output name="out" file="IDFilter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="fasta" value="IDFilter_16_input.fasta"/> - <param name="enzyme" value="Trypsin/P"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="1"/> - <param name="methionine_cleavage" value="true"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> - <output name="out" file="IDFilter_17_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":2"/> - <param name="enzyme" value="Lys-N"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> - <output name="out" file="IDFilter_18_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value="2:"/> - <param name="enzyme" value="Lys-N"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> - <output name="out" file="IDFilter_19_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value="1:3"/> - <param name="enzyme" value="Lys-N"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> - <output name="out" file="IDFilter_20_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value="1:0"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""calcMZ" "gt" "750.0""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_16_input.idXML"/> - <output name="out" file="IDFilter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""end" "ne" "23""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFilter_16_input.idXML"/> - <output name="out" file="IDFilter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMapper_2_output.consensusXML"/> - <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.0"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""Q9HP81""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="remove_duplicate_psm" value="false"/> - <param name="remove_peptide_hits_by_metavalue" value=""/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Epifany_3_out.consensusXML"/> - <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="var_mods" value="false"/> - <param name="remove_shared_peptides" value="false"/> - <param name="keep_unreferenced_protein_hits" value="false"/> - <param name="remove_decoys" value="false"/> - <param name="delete_unreferenced_peptide_hits" value="false"/> - <section name="precursor"> - <param name="rt" value=":"/> - <param name="mz" value=":"/> - <param name="length" value=":"/> - <param name="charge" value=":"/> - </section> - <section name="score"> - <param name="pep" value="0.0"/> - <param name="prot" value="0.0"/> - <param name="protgroup" value="0.99"/> - </section> - <section name="whitelist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="blacklist"> - <param name="protein_accessions" value=""/> - <param name="ignore_modifications" value="false"/> - <param name="modifications" value=""/> - </section> - <section name="in_silico_digestion"> - <param name="enzyme" value="Trypsin"/> - <param name="specificity" value="full"/> - <param name="missed_cleavages" value="-1"/> - <param name="methionine_cleavage" value="false"/> - </section> - <section name="missed_cleavages"> - <param name="number_of_missed_cleavages" value=":"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="rt"> - <param name="p_value" value="0.0"/> - <param name="p_value_1st_dim" value="0.0"/> - </section> - <section name="mz"> - <param name="error" value="-1.0"/> - <param name="unit" value="ppm"/> - </section> - <section name="best"> - <param name="n_peptide_hits" value="0"/> - <param name="n_protein_hits" value="0"/> - <param name="strict" value="false"/> - <param name="n_to_m_peptide_hits" value=":"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDMapper"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_1_input.idXML"/> - <param name="in" value="IDMapper_1_input.featureXML"/> - <output name="out" file="IDMapper_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_tolerance" value="5.0"/> - <param name="mz_tolerance" value="1.0"/> - <param name="mz_measure" value="Da"/> - <param name="mz_reference" value="precursor"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="false"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_2_input.idXML"/> - <param name="in" value="IDMapper_2_input.consensusXML"/> - <output name="out" file="IDMapper_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="rt_tolerance" value="5.0"/> - <param name="mz_tolerance" value="1.0"/> - <param name="mz_measure" value="Da"/> - <param name="mz_reference" value="precursor"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="true"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_3_input.idXML"/> - <param name="in" value="IDMapper_3_input.featureXML"/> - <output name="out" file="IDMapper_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_tolerance" value="4.0"/> - <param name="mz_tolerance" value="3.0"/> - <param name="mz_measure" value="ppm"/> - <param name="mz_reference" value="precursor"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="true"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_4_input.idXML"/> - <param name="in" value="IDMapper_4_input.featureXML"/> - <output name="out" file="IDMapper_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_tolerance" value="10.0"/> - <param name="mz_tolerance" value="20.0"/> - <param name="mz_measure" value="ppm"/> - <param name="mz_reference" value="peptide"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="true"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"> - <param name="_in" value="IDMapper_4_input.mzML"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="ignore_charge" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="id" value="IDMapper_5_input.idXML"/> - <param name="in" value="IDMapper_5_input.featureXML"/> - <output name="out" file="IDMapper_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="rt_tolerance" value="20.0"/> - <param name="mz_tolerance" value="10.0"/> - <param name="mz_measure" value="ppm"/> - <param name="mz_reference" value="peptide"/> - <section name="feature"> - <param name="use_centroid_rt" value="false"/> - <param name="use_centroid_mz" value="false"/> - </section> - <section name="consensus"> - <param name="use_subelements" value="false"/> - <param name="annotate_ids_with_subelements" value="false"/> - </section> - <section name="spectra"> - <param name="_in" value="IDMapper_5_input.mzML"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDMassAccuracy"> - <test expect_num_outputs="5"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="number_of_bins" value="10"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <param name="id_in" value="MSGFPlusAdapter_1_out.idXML"/> - <output name="out_precursor" file="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="precursor_error_ppm" value="false"/> - <output name="out_fragment" file="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="fragment_error_ppm" value="false"/> - <param name="fragment_mass_tolerance" value="0.5"/> - <output name="out_precursor_fit" file="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <output name="out_fragment_fit" file="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_precursor_FLAG,out_fragment_FLAG,out_precursor_fit_FLAG,out_fragment_fit_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDMerger"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input2.idXML"/> - <output name="out" file="IDMerger_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="true"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMerger_2_input1.idXML,IDMerger_2_input2.idXML"/> - <output name="out" file="IDMerger_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="pepxml_protxml" value="true"/> - <param name="merge_proteins_add_PSMs" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input1_2.idXML"/> - <output name="out" file="IDMerger_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="degenerated_empty.idXML,degenerated_empty_2.idXML"/> - <output name="out" file="IDMerger_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="false"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMerger_2_input1.idXML"/> - <output name="out" file="IDMerger_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="add_to" value="IDMerger_5_input1.idXML"/> - <param name="annotate_file_origin" value="false"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_3_input1.idXML,IDRipper_3_input2.idXML"/> - <output name="out" file="IDRipper_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="annotate_file_origin" value="true"/> - <param name="pepxml_protxml" value="false"/> - <param name="merge_proteins_add_PSMs" 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> - </xml> - <xml name="autotest_IDPosteriorErrorProbability"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_Mascot_input.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_XTandem_input.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_OMSSA_input2.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="true"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_XTandem_input2.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="true"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_Mascot_input2.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="true"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_bad_data.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_bad_data_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="true"/> - <param name="prob_correct" value="false"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="fdr_for_targets_smaller" value="0.05"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/> - <output name="out" file="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="split_charge" value="false"/> - <param name="top_hits_only" value="false"/> - <param name="ignore_bad_data" value="false"/> - <param name="prob_correct" value="true"/> - <section name="fit_algorithm"> - <param name="number_of_bins" value="100"/> - <param name="incorrectly_assigned" value="Gumbel"/> - <param name="max_nr_iterations" value="1000"/> - <param name="neg_log_delta" value="6"/> - <param name="outlier_handling" value="ignore_iqr_outliers"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDRipper"/> - <xml name="autotest_IDRTCalibration"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRTCalibration_1_input.idXML"/> - <output name="out" file="IDRTCalibration_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="calibrant_1_reference" value="0.1"/> - <param name="calibrant_2_reference" value="0.9"/> - <param name="calibrant_1_input" value="10.0"/> - <param name="calibrant_2_input" value="90.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="degenerated_empty.idXML"/> - <output name="out" file="IDRTCalibration_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="calibrant_1_reference" value="0.1"/> - <param name="calibrant_2_reference" value="0.9"/> - <param name="calibrant_1_input" value="10.0"/> - <param name="calibrant_2_input" value="90.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDScoreSwitcher"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDFileConverter_12_output.idXML"/> - <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="proteins" value="false"/> - <param name="new_score" value="Percolator_PEP"/> - <param name="new_score_orientation" value="lower_better"/> - <param name="new_score_type" value="Posterior Error Probability"/> - <param name="old_score" value="Percolator_qvalue"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDScoreSwitcher_2_input.idXML"/> - <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="proteins" value="true"/> - <param name="new_score" value="Posterior Probability_score"/> - <param name="new_score_orientation" value="higher_better"/> - <param name="new_score_type" value="Posterior Probability"/> - <param name="old_score" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IDSplitter"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMapper_1_output.featureXML"/> - <output name="out" file="IDSplitter_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="id_out" file="IDSplitter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,id_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_InternalCalibration"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="InternalCalibration_1_BSA1.mzML"/> - <output name="out" file="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="ppm_match_tolerance" value="25.0"/> - <param name="ms_level" value="1"/> - <param name="RT_chunking" value="-1.0"/> - <section name="cal"> - <param name="id_in" value="InternalCalibration_1_BSA1_OMSSA.idXML"/> - <param name="lock_require_mono" value="false"/> - <param name="lock_require_iso" value="false"/> - <param name="model_type" value="linear"/> - </section> - <section name="RANSAC"> - <param name="enabled" value="true"/> - <param name="threshold" value="1.0"/> - <param name="pc_inliers" value="30"/> - <param name="iter" value="500"/> - </section> - <section name="goodness"> - <param name="median" value="4.0"/> - <param name="MAD" value="2.0"/> - </section> - <section name="quality_control"/> - <output name="quality_control_models" file="InternalCalibration_1_models.csv" compare="sim_size" delta="5700" ftype="csv"/> - <output name="quality_control_residuals" file="InternalCalibration_1_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/> - <output name="out" file="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="ppm_match_tolerance" value="25.0"/> - <param name="ms_level" value="1 2 3"/> - <param name="RT_chunking" value="60.0"/> - <section name="cal"> - <param name="lock_in" value="InternalCalibration_2_lock.csv" ftype="csv"/> - <param name="lock_require_mono" value="true"/> - <param name="lock_require_iso" value="false"/> - <param name="model_type" value="linear"/> - </section> - <section name="RANSAC"> - <param name="enabled" value="false"/> - <param name="threshold" value="10.0"/> - <param name="pc_inliers" value="30"/> - <param name="iter" value="70"/> - </section> - <section name="goodness"> - <param name="median" value="4.0"/> - <param name="MAD" value="2.0"/> - </section> - <section name="quality_control"/> - <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta="5700" ftype="csv"/> - <output name="quality_control_residuals" file="InternalCalibration_2_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_IsobaricAnalyzer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="type" value="itraq4plex"/> - <param name="in" value="IsobaricAnalyzer_input_1.mzML"/> - <output name="out" file="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="extraction"> - <param name="select_activation" value=""/> - <param name="reporter_mass_shift" value="0.1"/> - <param name="min_precursor_intensity" value="1.0"/> - <param name="keep_unannotated_precursor" value="true"/> - <param name="min_reporter_intensity" value="0.0"/> - <param name="discard_low_intensity_quantifications" value="false"/> - <param name="min_precursor_purity" value="0.0"/> - <param name="precursor_isotope_deviation" value="10.0"/> - <param name="purity_interpolation" value="true"/> - </section> - <section name="itraq4plex"> - <param name="channel_114_description" value="l1"/> - <param name="channel_115_description" value="l2"/> - <param name="channel_116_description" value="l3"/> - <param name="channel_117_description" value="lung"/> - <param name="reference_channel" value="114"/> - <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> - </section> - <section name="itraq8plex"> - <param name="channel_113_description" value=""/> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="channel_118_description" value=""/> - <param name="channel_119_description" value=""/> - <param name="channel_121_description" value=""/> - <param name="reference_channel" value="113"/> - <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> - </section> - <section name="quantification"> - <param name="isotope_correction" value="true"/> - <param name="normalization" value="false"/> - </section> - <section name="tmt10plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt11plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt16plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="channel_132N_description" value=""/> - <param name="channel_132C_description" value=""/> - <param name="channel_133N_description" value=""/> - <param name="channel_133C_description" value=""/> - <param name="channel_134N_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> - </section> - <section name="tmt6plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127_description" value=""/> - <param name="channel_128_description" value=""/> - <param name="channel_129_description" value=""/> - <param name="channel_130_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="type" value="itraq4plex"/> - <param name="in" value="TMTTenPlexMethod_test.mzML"/> - <output name="out" file="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="extraction"> - <param name="select_activation" value="High-energy collision-induced dissociation"/> - <param name="reporter_mass_shift" value="0.002"/> - <param name="min_precursor_intensity" value="1.0"/> - <param name="keep_unannotated_precursor" value="true"/> - <param name="min_reporter_intensity" value="0.0"/> - <param name="discard_low_intensity_quantifications" value="false"/> - <param name="min_precursor_purity" value="0.0"/> - <param name="precursor_isotope_deviation" value="10.0"/> - <param name="purity_interpolation" value="true"/> - </section> - <section name="itraq4plex"> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="reference_channel" value="114"/> - <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> - </section> - <section name="itraq8plex"> - <param name="channel_113_description" value=""/> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="channel_118_description" value=""/> - <param name="channel_119_description" value=""/> - <param name="channel_121_description" value=""/> - <param name="reference_channel" value="113"/> - <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> - </section> - <section name="quantification"> - <param name="isotope_correction" value="true"/> - <param name="normalization" value="false"/> - </section> - <section name="tmt10plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/5.0/0.0" "0.0/0.2/4.6/0.0" "0.0/0.2/4.6/0.3" "0.0/0.9/4.7/0.2" "0.0/0.5/3.2/0.0" "0.0/0.7/3.3/0.0" "0.0/1.3/2.5/0.0" "0.0/1.2/2.8/2.7" "0.0/1.5/2.0/0.0" "0.0/1.5/1.9/0.0""/> - </section> - <section name="tmt11plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt16plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="channel_132N_description" value=""/> - <param name="channel_132C_description" value=""/> - <param name="channel_133N_description" value=""/> - <param name="channel_133C_description" value=""/> - <param name="channel_134N_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> - </section> - <section name="tmt6plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127_description" value=""/> - <param name="channel_128_description" value=""/> - <param name="channel_129_description" value=""/> - <param name="channel_130_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="type" value="itraq4plex"/> - <param name="in" value="TMTTenPlexMethod_test.mzML"/> - <output name="out" file="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="extraction"> - <param name="select_activation" value="High-energy collision-induced dissociation"/> - <param name="reporter_mass_shift" value="0.002"/> - <param name="min_precursor_intensity" value="1.0"/> - <param name="keep_unannotated_precursor" value="true"/> - <param name="min_reporter_intensity" value="0.0"/> - <param name="discard_low_intensity_quantifications" value="false"/> - <param name="min_precursor_purity" value="0.0"/> - <param name="precursor_isotope_deviation" value="10.0"/> - <param name="purity_interpolation" value="true"/> - </section> - <section name="itraq4plex"> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="reference_channel" value="114"/> - <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> - </section> - <section name="itraq8plex"> - <param name="channel_113_description" value=""/> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="channel_118_description" value=""/> - <param name="channel_119_description" value=""/> - <param name="channel_121_description" value=""/> - <param name="reference_channel" value="113"/> - <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> - </section> - <section name="quantification"> - <param name="isotope_correction" value="true"/> - <param name="normalization" value="false"/> - </section> - <section name="tmt10plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt11plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt16plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="channel_132N_description" value=""/> - <param name="channel_132C_description" value=""/> - <param name="channel_133N_description" value=""/> - <param name="channel_133C_description" value=""/> - <param name="channel_134N_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> - </section> - <section name="tmt6plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127_description" value=""/> - <param name="channel_128_description" value=""/> - <param name="channel_129_description" value=""/> - <param name="channel_130_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="type" value="tmt10plex"/> - <param name="in" value="MS3_nonHierarchical.mzML"/> - <output name="out" file="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="extraction"> - <param name="select_activation" value="Collision-induced dissociation"/> - <param name="reporter_mass_shift" value="0.002"/> - <param name="min_precursor_intensity" value="1.0"/> - <param name="keep_unannotated_precursor" value="true"/> - <param name="min_reporter_intensity" value="0.0"/> - <param name="discard_low_intensity_quantifications" value="false"/> - <param name="min_precursor_purity" value="0.0"/> - <param name="precursor_isotope_deviation" value="10.0"/> - <param name="purity_interpolation" value="true"/> - </section> - <section name="itraq4plex"> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="reference_channel" value="114"/> - <param name="correction_matrix" value=""0.0/1.0/5.9/0.2" "0.0/2.0/5.6/0.1" "0.0/3.0/4.5/0.1" "0.1/4.0/3.5/0.1""/> - </section> - <section name="itraq8plex"> - <param name="channel_113_description" value=""/> - <param name="channel_114_description" value=""/> - <param name="channel_115_description" value=""/> - <param name="channel_116_description" value=""/> - <param name="channel_117_description" value=""/> - <param name="channel_118_description" value=""/> - <param name="channel_119_description" value=""/> - <param name="channel_121_description" value=""/> - <param name="reference_channel" value="113"/> - <param name="correction_matrix" value=""0.00/0.00/6.89/0.22" "0.00/0.94/5.90/0.16" "0.00/1.88/4.90/0.10" "0.00/2.82/3.90/0.07" "0.06/3.77/2.99/0.00" "0.09/4.71/1.88/0.00" "0.14/5.66/0.87/0.00" "0.27/7.44/0.18/0.00""/> - </section> - <section name="quantification"> - <param name="isotope_correction" value="true"/> - <param name="normalization" value="false"/> - </section> - <section name="tmt10plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/5.09/0.0" "0.0/0.25/5.27/0.0" "0.0/0.37/5.36/0.15" "0.0/0.65/4.17/0.1" "0.08/0.49/3.06/0.0" "0.01/0.71/3.07/0.0" "0.0/1.32/2.62/0.0" "0.02/1.28/2.75/2.53" "0.03/2.08/2.23/0.0" "0.08/1.99/1.65/0.0""/> - </section> - <section name="tmt11plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <section name="tmt16plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127N_description" value=""/> - <param name="channel_127C_description" value=""/> - <param name="channel_128N_description" value=""/> - <param name="channel_128C_description" value=""/> - <param name="channel_129N_description" value=""/> - <param name="channel_129C_description" value=""/> - <param name="channel_130N_description" value=""/> - <param name="channel_130C_description" value=""/> - <param name="channel_131N_description" value=""/> - <param name="channel_131C_description" value=""/> - <param name="channel_132N_description" value=""/> - <param name="channel_132C_description" value=""/> - <param name="channel_133N_description" value=""/> - <param name="channel_133C_description" value=""/> - <param name="channel_134N_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/8.02/0.0" "0.0/0.68/7.46/0.0" "0.0/0.71/6.94/0.0" "0.0/1.88/6.67/0.0" "0.0/1.34/5.59/0.0" "0.0/2.41/5.48/0.0" "0.0/2.34/5.19/0.0" "0.0/3.53/4.57/0.0" "0.0/2.67/4.16/0.0" "0.0/3.92/3.73/0.0" "0.0/3.69/3.14/0.0" "0.0/3.22/2.76/0.0" "0.0/4.11/2.0/0.0" "0.0/3.85/1.58/0.0" "0.0/4.63/1.18/0.0" "0.0/5.22/0.86/0.0""/> - </section> - <section name="tmt6plex"> - <param name="channel_126_description" value=""/> - <param name="channel_127_description" value=""/> - <param name="channel_128_description" value=""/> - <param name="channel_129_description" value=""/> - <param name="channel_130_description" value=""/> - <param name="channel_131_description" value=""/> - <param name="reference_channel" value="126"/> - <param name="correction_matrix" value=""0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0" "0.0/0.0/0.0/0.0""/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_LabeledEval"> -</xml> - <xml name="autotest_LuciphorAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="LuciphorAdapter_1_input.mzML"/> - <param name="id" value="LuciphorAdapter_1_input.idXML"/> - <output name="out" file="LuciphorAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="fragment_method" value="CID"/> - <param name="fragment_mass_tolerance" value="0.5"/> - <param name="fragment_error_units" value="Da"/> - <param name="min_mz" value="150.0"/> - <param name="target_modifications" value="Phospho (S),Phospho (T),Phospho (Y)"/> - <param name="neutral_losses" value=""sty -H3PO4 -97.97690""/> - <param name="decoy_mass" value="79.966331"/> - <param name="decoy_neutral_losses" value=""X -H3PO4 -97.97690""/> - <param name="max_charge_state" value="5"/> - <param name="max_peptide_length" value="40"/> - <param name="max_num_perm" value="16384"/> - <param name="modeling_score_threshold" value="0.95"/> - <param name="scoring_threshold" value="0.0"/> - <param name="min_num_psms_model" value="1"/> - <param name="run_mode" value="0"/> - <param name="rt_tolerance" value="0.01"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapAlignerIdentification"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/> - <output_collection name="out" count="1"/> - <section name="reference"> - <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input2.featureXML,MapAlignerIdentification_1_input1.featureXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="index" value="1"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="index" value="2"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_5_input1.consensusXML,MapAlignerIdentification_5_input2.consensusXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/> - <output_collection name="trafo_out" count="1"/> - <section name="reference"> - <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.0"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="true"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerIdentification_7_input1.idXML"/> - <output_collection name="out" count="1"/> - <output_collection name="trafo_out" count="1"/> - <section name="reference"> - <param name="file" value="MapAlignerIdentification_7_input2.idXML"/> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.5"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="false"/> - </section> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapAlignerPoseClustering"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/> - <output_collection name="out" count="3"/> - <output_collection name="trafo_out" count="3"/> - <section name="reference"> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="max_num_peaks_considered" value="400"/> - <section name="superimposer"> - <param name="mz_pair_max_distance" value="0.5"/> - <param name="rt_pair_distance_fraction" value="0.1"/> - <param name="num_used_points" value="2000"/> - <param name="scaling_bucket_size" value="0.005"/> - <param name="shift_bucket_size" value="3.0"/> - <param name="max_shift" value="1000.0"/> - <param name="max_scaling" value="2.0"/> - <param name="dump_buckets" value=""/> - <param name="dump_pairs" value=""/> - </section> - <section name="pairfinder"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="30.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerPoseClustering_2_input1.mzML,MapAlignerPoseClustering_2_input2.mzML,MapAlignerPoseClustering_2_input3.mzML"/> - <output_collection name="out" count="3"/> - <section name="reference"> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="max_num_peaks_considered" value="400"/> - <section name="superimposer"> - <param name="mz_pair_max_distance" value="0.5"/> - <param name="rt_pair_distance_fraction" value="0.1"/> - <param name="num_used_points" value="2000"/> - <param name="scaling_bucket_size" value="0.005"/> - <param name="shift_bucket_size" value="3.0"/> - <param name="max_shift" value="1000.0"/> - <param name="max_scaling" value="2.0"/> - <param name="dump_buckets" value=""/> - <param name="dump_pairs" value=""/> - </section> - <section name="pairfinder"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="false"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="100.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/> - <output_collection name="out" count="2"/> - <section name="reference"> - <param name="file" value="MapAlignerPoseClustering_1_input1.featureXML"/> - <param name="index" value="0"/> - </section> - <section name="algorithm"> - <param name="max_num_peaks_considered" value="400"/> - <section name="superimposer"> - <param name="mz_pair_max_distance" value="0.5"/> - <param name="rt_pair_distance_fraction" value="0.1"/> - <param name="num_used_points" value="2000"/> - <param name="scaling_bucket_size" value="0.005"/> - <param name="shift_bucket_size" value="3.0"/> - <param name="max_shift" value="1000.0"/> - <param name="max_scaling" value="2.0"/> - <param name="dump_buckets" value=""/> - <param name="dump_pairs" value=""/> - </section> - <section name="pairfinder"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="30.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML"/> - <output_collection name="trafo_out" count="2"/> - <section name="reference"> - <param name="index" value="2"/> - </section> - <section name="algorithm"> - <param name="max_num_peaks_considered" value="400"/> - <section name="superimposer"> - <param name="mz_pair_max_distance" value="0.5"/> - <param name="rt_pair_distance_fraction" value="0.1"/> - <param name="num_used_points" value="2000"/> - <param name="scaling_bucket_size" value="0.005"/> - <param name="shift_bucket_size" value="3.0"/> - <param name="max_shift" value="1000.0"/> - <param name="max_scaling" value="2.0"/> - <param name="dump_buckets" value=""/> - <param name="dump_pairs" value=""/> - </section> - <section name="pairfinder"> - <param name="second_nearest_gap" value="2.0"/> - <param name="use_identifications" value="false"/> - <param name="ignore_charge" value="true"/> - <param name="ignore_adduct" value="true"/> - <section name="distance_RT"> - <param name="max_difference" value="30.0"/> - <param name="exponent" value="1.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_MZ"> - <param name="max_difference" value="0.3"/> - <param name="unit" value="Da"/> - <param name="exponent" value="2.0"/> - <param name="weight" value="1.0"/> - </section> - <section name="distance_intensity"> - <param name="exponent" value="1.0"/> - <param name="weight" value="0.0"/> - <param name="log_transform" value="disabled"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapAlignerSpectrum"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerSpectrum_1_input1.mzML,MapAlignerSpectrum_1_input2.mzML,MapAlignerSpectrum_1_input3.mzML"/> - <output_collection name="out" count="3"/> - <section name="algorithm"> - <param name="gapcost" value="1.0"/> - <param name="affinegapcost" value="0.5"/> - <param name="cutoff_score" value="0.7"/> - <param name="bucketsize" value="100"/> - <param name="anchorpoints" value="100"/> - <param name="mismatchscore" value="-5.0"/> - <param name="scorefunction" value="SteinScottImproveScore"/> - </section> - <section name="model"> - <param name="type" value="interpolated"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </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> - </xml> - <xml name="autotest_MapAlignerTreeGuided"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/> - <output_collection name="out" count="3"/> - <section name="algorithm"> - <param name="model_type" value="b_spline"/> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <section name="align_algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.5"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="true"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/> - <output_collection name="trafo_out" count="3"/> - <section name="algorithm"> - <param name="model_type" value="b_spline"/> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <section name="align_algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.5"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/> - <output_collection name="out" count="3"/> - <section name="algorithm"> - <param name="model_type" value="b_spline"/> - <section name="model"> - <param name="type" value="b_spline"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <section name="align_algorithm"> - <param name="score_cutoff" value="false"/> - <param name="min_score" value="0.05"/> - <param name="min_run_occur" value="2"/> - <param name="max_rt_shift" value="0.5"/> - <param name="use_unassigned_peptides" value="true"/> - <param name="use_feature_rt" value="true"/> - </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> - </xml> - <xml name="autotest_MapNormalizer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_input.mzML"/> - <output name="out" file="MapNormalizer.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MapRTTransformer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_1_input.featureXML"/> - <output name="out" file="MapRTTransformer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_2_input.mzML"/> - <output name="out" file="MapRTTransformer_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="trafo_in" value="MapAlignerPoseClustering_1_trafo2.trafoXML"/> - <output name="trafo_out" file="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <param name="invert" value="true"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_4_input.chrom.mzML"/> - <output name="out" file="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_1_input.featureXML"/> - <output name="out" file="MapRTTransformer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_none.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="false"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapRTTransformer_1_input.featureXML"/> - <output name="out" file="MapRTTransformer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/> - <param name="invert" value="false"/> - <param name="store_original_rt" value="true"/> - <section name="model"> - <param name="type" value="none"/> - <section name="linear"> - <param name="symmetric_regression" value="false"/> - <param name="x_weight" value=""/> - <param name="y_weight" value=""/> - <param name="x_datum_min" value="1e-15"/> - <param name="x_datum_max" value="1000000000000000.0"/> - <param name="y_datum_min" value="1e-15"/> - <param name="y_datum_max" value="1000000000000000.0"/> - </section> - <section name="b_spline"> - <param name="wavelength" value="0.0"/> - <param name="num_nodes" value="5"/> - <param name="extrapolate" value="linear"/> - <param name="boundary_condition" value="2"/> - </section> - <section name="lowess"> - <param name="span" value="0.666666666666667"/> - <param name="num_iterations" value="3"/> - <param name="delta" value="-1.0"/> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="four-point-linear"/> - </section> - <section name="interpolated"> - <param name="interpolation_type" value="cspline"/> - <param name="extrapolation_type" value="two-point-linear"/> - </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> - </xml> - <xml name="autotest_MapStatistics"> -</xml> - <xml name="autotest_MaRaClusterAdapter"/> - <xml name="autotest_MascotAdapterOnline"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="keep_protein_links" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra_comet.mzML"/> - <output name="out" file="MascotAdapterOnline_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="Mascot_parameters"> - <param name="database" value="SwissProt"/> - <param name="search_type" value="MIS"/> - <param name="enzyme" value="Trypsin"/> - <param name="instrument" value="Default"/> - <param name="missed_cleavages" value="1"/> - <param name="precursor_mass_tolerance" value="3.0"/> - <param name="precursor_error_units" value="Da"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="fragment_error_units" value="Da"/> - <param name="charges" value="1,2,3"/> - <param name="taxonomy" value="All entries"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="special_modifications" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)"/> - <param name="mass_type" value="monoisotopic"/> - <param name="number_of_hits" value="0"/> - <param name="skip_spectrum_charges" value="false"/> - <param name="search_title" value="OpenMS_search"/> - <param name="username" value="OpenMS"/> - <param name="email" value="openmsjenkins@gmail.com"/> - </section> - <section name="Mascot_server"> - <param name="hostname" value="www.matrixscience.com"/> - <param name="host_port" value="80"/> - <param name="server_path" value=""/> - <param name="timeout" value="1500"/> - <param name="boundary" value="GZWgAaYKjHFeUaLOLEIOMq"/> - <param name="use_proxy" value="false"/> - <param name="proxy_host" value=""/> - <param name="proxy_port" value="0"/> - <param name="proxy_username" value=""/> - <param name="proxy_password" value=""/> - <param name="login" value="false"/> - <param name="username" value=""/> - <param name="password" value=""/> - <param name="use_ssl" value="false"/> - <param name="export_params" value="_ignoreionsscorebelow=0&_sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0"/> - <param name="skip_export" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MascotAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MascotAdapter_1_input.mzData"/> - <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta="5700"/> - <param name="out_type" value="mgf"/> - <param name="instrument" value="ESI-TRAP"/> - <param name="precursor_mass_tolerance" value="1.3"/> - <param name="peak_mass_tolerance" value="0.3"/> - <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/> - <param name="modifications" value=""Carboxymethyl (C)""/> - <param name="variable_modifications" value=""Variable_Modifications_TEST_1""/> - <param name="charges" value=""1+" "2+" "3+""/> - <param name="db" value="MSDB"/> - <param name="hits" value="AUTO"/> - <param name="cleavage" value="Trypsin"/> - <param name="missed_cleavages" value="1"/> - <param name="sig_threshold" value="0.05"/> - <param name="pep_homol" value="1.0"/> - <param name="pep_ident" value="1.0"/> - <param name="pep_rank" value="1"/> - <param name="prot_score" value="1.0"/> - <param name="pep_score" value="1.0"/> - <param name="pep_exp_z" value="1"/> - <param name="show_unassigned" value="1"/> - <param name="first_dim_rt" value="0.0"/> - <param name="boundary" value="ABCDEFGHIJKMNOPQRSTUVWXYZ"/> - <param name="mass_type" value="Monoisotopic"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MascotAdapter_2_input.mascotXML"/> - <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="instrument" value="Default"/> - <param name="precursor_mass_tolerance" value="2.0"/> - <param name="peak_mass_tolerance" value="1.0"/> - <param name="taxonomy" value="All entries"/> - <param name="modifications" value=""/> - <param name="variable_modifications" value=""/> - <param name="charges" value=""1+" "2+" "3+""/> - <param name="db" value="MSDB"/> - <param name="hits" value="AUTO"/> - <param name="cleavage" value="Trypsin"/> - <param name="missed_cleavages" value="0"/> - <param name="sig_threshold" value="0.05"/> - <param name="pep_homol" value="1.0"/> - <param name="pep_ident" value="1.0"/> - <param name="pep_rank" value="1"/> - <param name="prot_score" value="1.0"/> - <param name="pep_score" value="1.0"/> - <param name="pep_exp_z" value="1"/> - <param name="show_unassigned" value="1"/> - <param name="first_dim_rt" value="0.0"/> - <param name="boundary" value=""/> - <param name="mass_type" value="Monoisotopic"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MassCalculator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/> - <param name="in_seq" value=""/> - <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="charge" value="0 1"/> - <param name="format" value="table"/> - <param name="average_mass" value="false"/> - <param name="fragment_type" value="full"/> - <param name="separator" value=","/> - <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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_seq" value=""LDQWLC(Carbamidomethyl)EKL" "(Glu->pyro-Glu)EAM(Oxidation)APKHK" "RANVM(Oxidation)DYR" "FGVEQDVDMVFASFIR""/> - <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="charge" value="1 2 3"/> - <param name="format" value="list"/> - <param name="average_mass" value="false"/> - <param name="fragment_type" value="full"/> - <param name="separator" value=""/> - <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> - </xml> - <xml name="autotest_MassTraceExtractor"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MassTraceExtractor_1_input.mzML"/> - <output name="out" file="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="20.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="5.0"/> - <param name="max_trace_length" value="-1.0"/> - </section> - <section name="epd"> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - <param name="enabled" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MassTraceExtractor_1_input.mzML"/> - <output name="out" file="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="out_type" value="featurexml"/> - <section name="algorithm"> - <section name="common"> - <param name="noise_threshold_int" value="10.0"/> - <param name="chrom_peak_snr" value="3.0"/> - <param name="chrom_fwhm" value="5.0"/> - </section> - <section name="mtd"> - <param name="mass_error_ppm" value="20.0"/> - <param name="reestimate_mt_sd" value="true"/> - <param name="quant_method" value="area"/> - <param name="trace_termination_criterion" value="outlier"/> - <param name="trace_termination_outliers" value="5"/> - <param name="min_sample_rate" value="0.5"/> - <param name="min_trace_length" value="6.0"/> - <param name="max_trace_length" value="12.0"/> - </section> - <section name="epd"> - <param name="width_filtering" value="off"/> - <param name="min_fwhm" value="3.0"/> - <param name="max_fwhm" value="60.0"/> - <param name="masstrace_snr_filtering" value="false"/> - <param name="enabled" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MetaboliteAdductDecharger"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/> - <output name="out_fm" file="MetaboliteAdductDecharger_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <section name="MetaboliteFeatureDeconvolution"> - <param name="charge_min" value="1"/> - <param name="charge_max" value="3"/> - <param name="charge_span_max" value="3"/> - <param name="q_try" value="feature"/> - <param name="retention_max_diff" value="1.0"/> - <param name="retention_max_diff_local" value="1.0"/> - <param name="mass_max_diff" value="0.05"/> - <param name="unit" value="Da"/> - <param name="potential_adducts" value=""H:+:0.4" "Na:+:0.25" "NH4:+:0.25" "K:+:0.1" "H-2O-1:0:0.05""/> - <param name="max_neutrals" value="1"/> - <param name="use_minority_bound" value="true"/> - <param name="max_minority_bound" value="3"/> - <param name="min_rt_overlap" value="0.66"/> - <param name="intensity_filter" value="false"/> - <param name="negative_mode" value="false"/> - <param name="default_map_label" value="decharged features"/> - <param name="verbose_level" value="0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/> - <output name="out_cm" file="MetaboliteAdductDecharger_2_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="outpairs" file="MetaboliteAdductDecharger_2_output_2.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <section name="MetaboliteFeatureDeconvolution"> - <param name="charge_min" value="1"/> - <param name="charge_max" value="3"/> - <param name="charge_span_max" value="3"/> - <param name="q_try" value="feature"/> - <param name="retention_max_diff" value="1.0"/> - <param name="retention_max_diff_local" value="1.0"/> - <param name="mass_max_diff" value="0.05"/> - <param name="unit" value="Da"/> - <param name="potential_adducts" value=""H:+:0.4" "Na:+:0.25" "NH4:+:0.25" "K:+:0.1" "H-2O-1:0:0.05""/> - <param name="max_neutrals" value="1"/> - <param name="use_minority_bound" value="true"/> - <param name="max_minority_bound" value="3"/> - <param name="min_rt_overlap" value="0.66"/> - <param name="intensity_filter" value="false"/> - <param name="negative_mode" value="false"/> - <param name="default_map_label" value="decharged features"/> - <param name="verbose_level" value="0"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG,outpairs_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MetaboliteSpectralMatcher"> -</xml> - <xml name="autotest_MetaProSIP"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <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"/> - </conditional> - <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="5700" ftype="csv"/> - <output name="out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" delta="5700" 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> - </xml> - <xml name="autotest_MRMMapper"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MRMMapping_input.chrom.mzML"/> - <param name="tr" value="MRMMapping_input.TraML"/> - <output name="out" file="MRMMapping_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="precursor_tolerance" value="0.3"/> - <param name="product_tolerance" value="0.3"/> - <param name="map_multiple_assays" value="false"/> - <param name="error_on_unmapped" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MRMMapping_input.chrom.mzML"/> - <param name="tr" value="MRMMapping_input_2.TraML"/> - <output name="out" file="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="precursor_tolerance" value="0.01"/> - <param name="product_tolerance" value="0.01"/> - <param name="map_multiple_assays" value="false"/> - <param name="error_on_unmapped" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MRMPairFinder"> -</xml> - <xml name="autotest_MRMTransitionGroupPicker"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/> - <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/> - <output name="out" file="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/> - <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/> - <output name="out" file="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <section name="algorithm"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="true"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MSFraggerAdapter"/> - <xml name="autotest_MSGFPlusAdapter"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="add_decoys" value="false"/> - <param name="legacy_conversion" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <param name="database" value="proteins.fasta"/> - <param name="precursor_mass_tolerance" value="10.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="isotope_error_range" value="0,1"/> - <param name="fragment_method" value="from_spectrum"/> - <param name="instrument" value="high_res"/> - <param name="enzyme" value="Trypsin/P"/> - <param name="protocol" value="none"/> - <param name="tryptic" value="fully"/> - <param name="min_precursor_charge" value="1"/> - <param name="max_precursor_charge" value="3"/> - <param name="min_peptide_length" value="6"/> - <param name="max_peptide_length" value="40"/> - <param name="matches_per_spec" value="1"/> - <param name="add_features" value="false"/> - <param name="max_mods" value="2"/> - <param name="max_missed_cleavages" value="-1"/> - <param name="tasks" value="0"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MSSimulator"> -</xml> - <xml name="autotest_MSstatsConverter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="retention_time_summarization_method" value="max"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSstatsConverter_1_in.consensusXML"/> - <param name="in_design" value="MSstatsConverter_1_design.tsv" ftype="tabular"/> - <param name="method" value="LFQ"/> - <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> - <param name="msstats_condition" value="MSstats_Condition"/> - <param name="msstats_mixture" value="MSstats_Mixture"/> - <param name="labeled_reference_peptides" value="false"/> - <output name="out" file="MSstatsConverter_1_out.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="retention_time_summarization_method" value="manual"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSstatsConverter_2_in.consensusXML"/> - <param name="in_design" value="MSstatsConverter_2_design.tsv" ftype="tabular"/> - <param name="method" value="ISO"/> - <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> - <param name="msstats_condition" value="MSstats_Condition"/> - <param name="msstats_mixture" value="MSstats_Mixture"/> - <param name="labeled_reference_peptides" value="false"/> - <output name="out" file="MSstatsConverter_2_out.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="retention_time_summarization_method" value="manual"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MSstatsConverter_3_in.consensusXML"/> - <param name="in_design" value="MSstatsConverter_3_design.tsv" ftype="tabular"/> - <param name="method" value="ISO"/> - <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/> - <param name="msstats_condition" value="MSstats_Condition"/> - <param name="msstats_mixture" value="MSstats_Mixture"/> - <param name="labeled_reference_peptides" value="false"/> - <output name="out" file="MSstatsConverter_3_out.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MultiplexResolver"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MultiplexResolver_1_input.consensusXML"/> - <output name="out" file="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/> - <param name="missed_cleavages" value="1"/> - <param name="mass_tolerance" value="0.1"/> - <param name="mz_tolerance" value="10"/> - <param name="rt_tolerance" value="5"/> - </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_conflicts_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MultiplexResolver_2_input.consensusXML"/> - <output name="out" file="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/> - <param name="missed_cleavages" value="4"/> - <param name="mass_tolerance" value="0.1"/> - <param name="mz_tolerance" value="10"/> - <param name="rt_tolerance" value="5"/> - </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_conflicts_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MultiplexResolver_3_input.consensusXML"/> - <output name="out" file="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[][Leu3]"/> - <param name="missed_cleavages" value="2"/> - <param name="mass_tolerance" value="0.1"/> - <param name="mz_tolerance" value="10"/> - <param name="rt_tolerance" value="5"/> - </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_conflicts_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MultiplexResolver_4_input.consensusXML"/> - <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/> - <output name="out" file="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <output name="out_conflicts" file="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <section name="algorithm"> - <param name="labels" value="[Dimethyl0][Dimethyl6]"/> - <param name="missed_cleavages" value="3"/> - <param name="mass_tolerance" value="0.1"/> - <param name="mz_tolerance" value="10"/> - <param name="rt_tolerance" value="10"/> - </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_conflicts_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MyriMatchAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="MinPeptideMass" value="0.0"/> - <param name="MaxPeptideMass" value="10000.0"/> - <param name="MinPeptideLength" value="5"/> - <param name="MaxPeptideLength" value="75"/> - <param name="UseSmartPlusThreeModel" value="false"/> - <param name="NumIntensityClasses" value="3"/> - <param name="ClassSizeMultiplier" value="2.0"/> - <param name="MonoisotopeAdjustmentSet" value="[-1,2]"/> - <param name="SpectrumListFilters" value=""/> - <param name="ignoreConfigErrors" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="MyriMatchAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="precursor_mass_tolerance_unit" value="ppm"/> - <param name="precursor_mass_tolerance_avg" value="false"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="fragment_mass_tolerance_unit" value="Da"/> - <param name="database" value="proteins.fasta"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="NumChargeStates" value="3"/> - <param name="TicCutoffPercentage" value="0.98"/> - <param name="MaxDynamicMods" value="2"/> - <param name="MaxResultRank" value="5"/> - <param name="CleavageRules" value=""/> - <param name="MinTerminiCleavages" value="2"/> - <param name="MaxMissedCleavages" value="-1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_MzMLSplitter"/> - <xml name="autotest_MzTabExporter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_1_input.consensusXML"/> - <output name="out" file="MzTabExporter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_2_input.idXML"/> - <output name="out" file="MzTabExporter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_3_input.featureXML"/> - <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="Epifany_2_out.consensusXML"/> - <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_5_in.consensusXML"/> - <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_6_input.idXML"/> - <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="first_run_inference_only" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MzTabExporter_7_input.consensusXML"/> - <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="opt_columns" value="subfeatures"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_NoiseFilterGaussian"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterGaussian_1_input.mzML"/> - <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="gaussian_width" value="1.0"/> - <param name="ppm_tolerance" value="10.0"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/> - <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="gaussian_width" value="50.0"/> - <param name="ppm_tolerance" value="10.0"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterGaussian_1_input.mzML"/> - <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="gaussian_width" value="1.0"/> - <param name="ppm_tolerance" value="10.0"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/> - <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="gaussian_width" value="50.0"/> - <param name="ppm_tolerance" value="10.0"/> - <param name="use_ppm_tolerance" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_NoiseFilterSGolay"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> - <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="frame_length" value="9"/> - <param name="polynomial_order" value="4"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> - <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="frame_length" value="11"/> - <param name="polynomial_order" value="4"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterSGolay_1_input.mzML"/> - <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="frame_length" value="9"/> - <param name="polynomial_order" value="4"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/> - <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="frame_length" value="11"/> - <param name="polynomial_order" value="4"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_NovorAdapter"/> - <xml name="autotest_NucleicAcidSearchEngine"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="decharge_ms2" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NucleicAcidSearchEngine_1.mzML"/> - <param name="database" value="NucleicAcidSearchEngine_1.fasta"/> - <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="precursor"> - <param name="mass_tolerance" value="5.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="-2"/> - <param name="max_charge" value="-14"/> - <param name="include_unknown_charge" value="true"/> - <param name="use_avg_mass" value="false"/> - <param name="use_adducts" value="false"/> - <param name="potential_adducts" value=""K:+" "Na:+" "Na2:++" "K2:++" "NaK:++" "K3:+++" "Na3:+++" "NaK2:+++" "Na2K:+++""/> - <param name="isotopes" value="0 1 2"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="5.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="ions" value="a-B,c,w,y"/> - </section> - <section name="modifications"> - <param name="variable" value=""/> - <param name="variable_max_per_oligo" value="2"/> - <param name="resolve_ambiguities" value="false"/> - </section> - <section name="oligo"> - <param name="min_size" value="5"/> - <param name="max_size" value="0"/> - <param name="missed_cleavages" value="22"/> - <param name="enzyme" value="no cleavage"/> - </section> - <section name="report"> - <param name="top_hits" value="1"/> - </section> - <section name="fdr"> - <param name="decoy_pattern" value="DECOY_"/> - <param name="cutoff" value="0.05"/> - <param name="remove_decoys" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,id_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OMSSAAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="pc" value="1"/> - <param name="hs" value="4"/> - <param name="tez" value="1"/> - <param name="tom" value="0"/> - <param name="tem" value="0"/> - <param name="tex" value="1446.94"/> - <param name="zt" value="3"/> - <param name="z1" value="0.95"/> - <param name="zc" value="1"/> - <param name="zcc" value="2"/> - <param name="zoh" value="2"/> - <param name="no" value="4"/> - <param name="nox" value="40"/> - <param name="i" value="1,4"/> - <param name="sp" value="100"/> - <param name="sb1" value="1"/> - <param name="sct" value="0"/> - <param name="x" value="0"/> - <param name="hm" value="2"/> - <param name="ht" value="6"/> - <param name="mm" value="128"/> - <param name="mnm" value="false"/> - <param name="is" value="0.0"/> - <param name="ir" value="0.0"/> - <param name="ii" value="0.0"/> - <param name="chunk_size" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="OMSSAAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="database" value="proteins.fasta"/> - <param name="min_precursor_charge" value="1"/> - <param name="max_precursor_charge" value="3"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="v" value="1"/> - <param name="enzyme" value="Trypsin"/> - <param name="hl" value="30"/> - <param name="he" value="1.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenPepXLLF"> - <test expect_num_outputs="5"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenPepXLLF_input.mzML"/> - <param name="database" value="OpenPepXLLF_input.fasta"/> - <param name="decoy_string" value="decoy"/> - <param name="decoy_prefix" value="true"/> - <output name="out_idXML" file="OpenPepXLLF_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="OpenPepXLLF_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquestxml" file="OpenPepXLLF_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <output name="out_xquest_specxml" file="OpenPepXLLF_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="3"/> - <param name="max_charge" value="7"/> - <param name="corrections" value="2 1 0"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_xlinks" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="5"/> - <param name="missed_cleavages" value="2"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="cross_linker"> - <param name="residue1" value=""K" "N-term""/> - <param name="residue2" value=""K" "N-term""/> - <param name="mass" value="138.0680796"/> - <param name="mass_mono_link" value="156.07864431 155.094628715"/> - <param name="name" value="DSS"/> - </section> - <section name="algorithm"> - <param name="number_top_hits" value="5"/> - <param name="deisotope" value="auto"/> - <param name="use_sequence_tags" value="false"/> - <param name="sequence_tag_min_length" value="2"/> - </section> - <section name="ions"> - <param name="b_ions" value="true"/> - <param name="y_ions" value="true"/> - <param name="a_ions" value="false"/> - <param name="x_ions" value="false"/> - <param name="c_ions" value="false"/> - <param name="z_ions" value="false"/> - <param name="neutral_losses" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenPepXLLF_input2.mzML"/> - <param name="database" value="OpenPepXLLF_input2.fasta"/> - <param name="decoy_string" value="decoy_"/> - <param name="decoy_prefix" value="true"/> - <output name="out_idXML" file="OpenPepXLLF_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="3"/> - <param name="max_charge" value="7"/> - <param name="corrections" value="1 0"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="0.2"/> - <param name="mass_tolerance_xlinks" value="0.3"/> - <param name="mass_tolerance_unit" value="Da"/> - </section> - <section name="modifications"> - <param name="fixed" value="Carbamidomethyl (C)"/> - <param name="variable" value="Oxidation (M)"/> - <param name="variable_max_per_peptide" value="1"/> - </section> - <section name="peptide"> - <param name="min_size" value="5"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="cross_linker"> - <param name="residue1" value=""D" "E" "C-term""/> - <param name="residue2" value=""K" "S" "T" "Y" "N-term""/> - <param name="mass" value="-18.010595"/> - <param name="mass_mono_link" value=""/> - <param name="name" value="DMTMM"/> - </section> - <section name="algorithm"> - <param name="number_top_hits" value="1"/> - <param name="deisotope" value="auto"/> - <param name="use_sequence_tags" value="false"/> - <param name="sequence_tag_min_length" value="2"/> - </section> - <section name="ions"> - <param name="b_ions" value="true"/> - <param name="y_ions" value="true"/> - <param name="a_ions" value="false"/> - <param name="x_ions" value="false"/> - <param name="c_ions" value="false"/> - <param name="z_ions" value="false"/> - <param name="neutral_losses" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenPepXL"> - <test expect_num_outputs="5"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenPepXL_input.mzML"/> - <param name="consensus" value="OpenPepXL_input.consensusXML"/> - <param name="database" value="OpenPepXL_input.fasta"/> - <param name="decoy_string" value="decoy"/> - <param name="decoy_prefix" value="true"/> - <output name="out_idXML" file="OpenPepXL_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="OpenPepXL_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquestxml" file="OpenPepXL_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <output name="out_xquest_specxml" file="OpenPepXL_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="3"/> - <param name="max_charge" value="7"/> - <param name="corrections" value="2 1 0"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="0.2"/> - <param name="mass_tolerance_xlinks" value="0.3"/> - <param name="mass_tolerance_unit" value="Da"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="5"/> - <param name="missed_cleavages" value="2"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="cross_linker"> - <param name="residue1" value=""K" "N-term""/> - <param name="residue2" value=""K" "N-term""/> - <param name="mass_light" value="138.0680796"/> - <param name="mass_iso_shift" value="12.075321"/> - <param name="mass_mono_link" value="156.07864431 155.094628715"/> - <param name="name" value="DSS"/> - </section> - <section name="algorithm"> - <param name="number_top_hits" value="5"/> - <param name="deisotope" value="auto"/> - </section> - <section name="ions"> - <param name="b_ions" value="true"/> - <param name="y_ions" value="true"/> - <param name="a_ions" value="false"/> - <param name="x_ions" value="false"/> - <param name="c_ions" value="false"/> - <param name="z_ions" value="false"/> - <param name="neutral_losses" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathAnalyzer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <output name="out" file="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_mod_input.TraML"/> - <output name="out" file="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="true"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="8.0"/> - <param name="dia_byseries_ppm_diff" value="15.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <output name="out" file="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="true"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="8.0"/> - <param name="dia_byseries_ppm_diff" value="15.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <output name="out" file="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="original"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="true"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/> - <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/> - <output name="out" file="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="no_strict" value="false"/> - <param name="min_upper_edge_dist" value="0.0"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="40.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="legacy"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathAssayGenerator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="max_num_alternative_localizations" value="10000"/> - <param name="disable_identification_ms2_precursors" value="false"/> - <param name="disable_identification_specific_losses" value="false"/> - <param name="enable_identification_unspecific_losses" value="false"/> - <param name="enable_swath_specifity" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAssayGenerator_input.TraML"/> - <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="min_transitions" value="6"/> - <param name="max_transitions" value="6"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="2,3"/> - <param name="enable_detection_specific_losses" value="true"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="precursor_mz_threshold" value="0.025"/> - <param name="precursor_lower_mz_limit" value="400.0"/> - <param name="precursor_upper_mz_limit" value="1200.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="product_lower_mz_limit" value="350.0"/> - <param name="product_upper_mz_limit" value="2000.0"/> - <param name="enable_ipf" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="max_num_alternative_localizations" value="10000"/> - <param name="disable_identification_ms2_precursors" value="false"/> - <param name="disable_identification_specific_losses" value="false"/> - <param name="enable_identification_unspecific_losses" value="false"/> - <param name="enable_swath_specifity" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/> - <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="min_transitions" value="6"/> - <param name="max_transitions" value="6"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="precursor_mz_threshold" value="0.025"/> - <param name="precursor_lower_mz_limit" value="400.0"/> - <param name="precursor_upper_mz_limit" value="1200.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="product_lower_mz_limit" value="350.0"/> - <param name="product_upper_mz_limit" value="2000.0"/> - <param name="unimod_file" value="OpenSwathAssayGenerator_input_2_unimod.xml"/> - <param name="enable_ipf" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="max_num_alternative_localizations" value="10000"/> - <param name="disable_identification_ms2_precursors" value="false"/> - <param name="disable_identification_specific_losses" value="false"/> - <param name="enable_identification_unspecific_losses" value="false"/> - <param name="enable_swath_specifity" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/> - <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="min_transitions" value="6"/> - <param name="max_transitions" value="6"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="precursor_mz_threshold" value="0.025"/> - <param name="precursor_lower_mz_limit" value="400.0"/> - <param name="precursor_upper_mz_limit" value="1200.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="product_lower_mz_limit" value="350.0"/> - <param name="product_upper_mz_limit" value="2000.0"/> - <param name="unimod_file" value="OpenSwathAssayGenerator_input_3_unimod.xml"/> - <param name="enable_ipf" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathChromatogramExtractor"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> - <output name="out" file="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="-1.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="false"/> - <param name="extract_MS1" value="false"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> - <param name="rt_norm" value="OpenSwathChromatogramExtractor_input.trafoXML"/> - <output name="out" file="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="50.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="false"/> - <param name="extract_MS1" value="false"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/> - <output name="out" file="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="-1.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="false"/> - <param name="extract_MS1" value="true"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/> - <output name="out" file="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="-1.0"/> - <param name="ion_mobility_window" value="0.05"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="true"/> - <param name="extract_MS1" value="false"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="extraction_function" value="tophat"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/> - <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/> - <output name="out" file="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="rt_window" value="-1.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_window" value="0.05"/> - <param name="ppm" value="false"/> - <param name="is_swath" value="false"/> - <param name="extract_MS1" value="true"/> - <section name="model"> - <param name="type" value="linear"/> - <param name="symmetric_regression" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathConfidenceScoring"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/> - <output name="out" file="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/> - <param name="decoys" value="1"/> - <param name="transitions" value="2"/> - <section name="GLM"> - <param name="intercept" value="3.87333466"/> - <param name="delta_rt" value="-0.02898629"/> - <param name="dist_int" value="-7.75880768"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathDecoyGenerator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="min_decoy_fraction" value="0.8"/> - <param name="aim_decoy_fraction" value="1.0"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="shift_precursor_mz_shift" value="0.0"/> - <param name="shift_product_mz_shift" value="20.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="separate" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/> - <output name="out" file="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="method" value="pseudo-reverse"/> - <param name="decoy_tag" value="DECOY_"/> - <param name="switchKR" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="min_decoy_fraction" value="0.8"/> - <param name="aim_decoy_fraction" value="1.0"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="shift_precursor_mz_shift" value="0.0"/> - <param name="shift_product_mz_shift" value="20.0"/> - <param name="product_mz_threshold" value="0.8"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="separate" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/> - <output name="out" file="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="method" value="pseudo-reverse"/> - <param name="decoy_tag" value="DECOY_"/> - <param name="switchKR" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="min_decoy_fraction" value="0.8"/> - <param name="aim_decoy_fraction" value="1.0"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="shift_precursor_mz_shift" value="0.0"/> - <param name="shift_product_mz_shift" value="20.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="false"/> - <param name="enable_detection_unspecific_losses" value="false"/> - <param name="separate" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/> - <output name="out" file="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="method" value="pseudo-reverse"/> - <param name="decoy_tag" value="DECOY_"/> - <param name="switchKR" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="min_decoy_fraction" value="0.4"/> - <param name="aim_decoy_fraction" value="1.0"/> - <param name="shuffle_max_attempts" value="30"/> - <param name="shuffle_sequence_identity_threshold" value="0.5"/> - <param name="shift_precursor_mz_shift" value="0.0"/> - <param name="shift_product_mz_shift" value="20.0"/> - <param name="product_mz_threshold" value="0.025"/> - <param name="allowed_fragment_types" value="b,y"/> - <param name="allowed_fragment_charges" value="1,2,3,4"/> - <param name="enable_detection_specific_losses" value="true"/> - <param name="enable_detection_unspecific_losses" value="true"/> - <param name="separate" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/> - <output name="out" file="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <param name="method" value="pseudo-reverse"/> - <param name="decoy_tag" value="DECOY_"/> - <param name="switchKR" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathDIAPreScoring"> -</xml> - <xml name="autotest_OpenSwathFeatureXMLToTSV"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> - <output name="out" file="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="short_format" value="true"/> - <param name="best_scoring_peptide" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> - <output name="out" file="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="short_format" value="false"/> - <param name="best_scoring_peptide" value=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/> - <output name="out" file="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/> - <param name="short_format" value="true"/> - <param name="best_scoring_peptide" value="main_var_xx_lda_prelim_score"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathFileSplitter"/> - <xml name="autotest_OpenSwathMzMLFileCacher"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> - <param name="out_type" value="sqmass"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/> - <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> - <param name="out_type" value="sqmass"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/> - <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="true"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/> - <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <output name="out" file="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta="5700"/> - <param name="out_type" value="mzML"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="-1.0"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/> - <output name="out" file="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta="5700"/> - <param name="out_type" value="mzML"/> - <param name="lossy_compression" value="true"/> - <param name="full_meta" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="lossy_mass_accuracy" value="0.0001"/> - <param name="process_lowmemory" value="false"/> - <param name="lowmem_batchsize" value="500"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/> - <output name="out" file="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzml"/> - <param name="lossy_compression" value="false"/> - <param name="full_meta" 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> - </xml> - <xml name="autotest_OpenSwathRewriteToFeatureXML"> -</xml> - <xml name="autotest_OpenSwathRTNormalizer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> - <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> - <output name="out" file="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="estimateBestPeptides" value="false"/> - <section name="RTNormalization"> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <section name="peptideEstimation"> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> - <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> - <output name="out" file="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="estimateBestPeptides" value="true"/> - <section name="RTNormalization"> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <section name="peptideEstimation"> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="3"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="3"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/> - <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/> - <output name="out" file="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="estimateBestPeptides" value="false"/> - <section name="RTNormalization"> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - </section> - <section name="algorithm"> - <param name="stop_report_after_feature" value="-1"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="rt_normalization_factor" value="1.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="stop_after_intensity_ratio" value="0.0001"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="false"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="1.0"/> - <param name="minimal_quality" value="-10000.0"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="15"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="50.0"/> - <param name="use_gauss" value="true"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="1.0"/> - <param name="sn_win_len" value="1000.0"/> - <param name="sn_bin_count" value="30"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="false"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="interpolation_step" value="0.2"/> - <param name="tolerance_stdev_bounding_box" value="3.0"/> - <param name="max_iteration" value="500"/> - <section name="statistics"> - <param name="mean" value="1.0"/> - <param name="variance" value="1.0"/> - </section> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_elution_model_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <section name="peptideEstimation"> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_OpenSwathWorkflow"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="false"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta="5700" ftype="json"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,out_qc_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="false"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/> - <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> - <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="cache"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="cacheWorkingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/> - <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="true"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/> - <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="false"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="550.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_11_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/> - <param name="tr_type" value=""/> - <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/> - <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="true"/> - <param name="rt_extraction_window" value="-1.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.2"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="none"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="true"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/> - <param name="tr_type" value="pqp"/> - <output name="out_osw" file="OpenSwathWorkflow_13.osw" compare="sim_size" delta="5700" ftype="osw"/> - <output name="out_chrom" file="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="sqMass"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/> - <param name="tr_type" value="pqp"/> - <output name="out_osw" file="OpenSwathWorkflow_14.osw" compare="sim_size" delta="5700" ftype="osw"/> - <output name="out_chrom" file="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="2"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_15_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="true"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="workingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="2"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="false"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="workingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="0.05"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="true"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="false"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="cache"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="0.05"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="true"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="false"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="workingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_17_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/> - <param name="tr_type" value="pqp"/> - <output name="out_features" file="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="0.05"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="true"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="false"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="true"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="true"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="Th"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="false"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="normal"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_21_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> - <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/> - <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="0.05"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.6666666666666666"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="true"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="true"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="false"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,irt_trafo_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="sort_swath_maps" value="false"/> - <param name="enable_ms1" value="true"/> - <param name="enable_ipf" value="true"/> - <param name="out_chrom_type" value="mzML"/> - <param name="min_upper_edge_dist" value="0.0"/> - <param name="extra_rt_extraction_window" value="0.0"/> - <param name="mz_extraction_window_unit" value="ppm"/> - <param name="mz_extraction_window_ms1_unit" value="ppm"/> - <param name="use_ms1_ion_mobility" value="true"/> - <param name="matching_window_only" value="true"/> - <param name="irt_mz_extraction_window" value="50.0"/> - <param name="irt_mz_extraction_window_unit" value="ppm"/> - <param name="irt_im_extraction_window" value="-1.0"/> - <param name="min_rsq" value="0.95"/> - <param name="min_coverage" value="0.6"/> - <param name="split_file_input" value="false"/> - <param name="use_elution_model_score" value="false"/> - <param name="readOptions" value="workingInMemory"/> - <param name="mz_correction_function" value="none"/> - <param name="extraction_function" value="tophat"/> - <param name="batchSize" value="1000"/> - <param name="ms1_isotopes" value="3"/> - <param name="force" value="false"/> - <param name="test" value="false"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_22_input.mzML"/> - <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/> - <param name="tr_type" value=""/> - <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="sonar" value="false"/> - <param name="rt_extraction_window" value="600.0"/> - <param name="ion_mobility_window" value="-1.0"/> - <param name="mz_extraction_window" value="50.0"/> - <param name="mz_extraction_window_ms1" value="50.0"/> - <param name="im_extraction_window_ms1" value="-1.0"/> - <section name="Debugging"/> - <section name="Calibration"> - <param name="ms1_im_calibration" value="false"/> - <param name="im_correction_function" value="linear"/> - <param name="debug_im_file" value=""/> - <param name="debug_mz_file" value=""/> - </section> - <section name="Library"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <section name="RTNormalization"> - <param name="alignmentMethod" value="linear"/> - <param name="outlierMethod" value="iter_residual"/> - <param name="useIterativeChauvenet" value="false"/> - <param name="RANSACMaxIterations" value="1000"/> - <param name="RANSACMaxPercentRTThreshold" value="3"/> - <param name="RANSACSamplingSize" value="10"/> - <param name="estimateBestPeptides" value="false"/> - <param name="InitialQualityCutoff" value="0.5"/> - <param name="OverallQualityCutoff" value="5.5"/> - <param name="NrRTBins" value="10"/> - <param name="MinPeptidesPerBin" value="1"/> - <param name="MinBinsFilled" value="8"/> - <section name="lowess"> - <param name="span" value="0.05"/> - </section> - <section name="b_spline"> - <param name="num_nodes" value="5"/> - </section> - </section> - <section name="Scoring"> - <param name="stop_report_after_feature" value="5"/> - <param name="rt_normalization_factor" value="100.0"/> - <param name="quantification_cutoff" value="0.0"/> - <param name="write_convex_hull" value="false"/> - <param name="spectrum_addition_method" value="simple"/> - <param name="add_up_spectra" value="1"/> - <param name="spacing_for_spectra_resampling" value="0.005"/> - <param name="uis_threshold_sn" value="-1"/> - <param name="uis_threshold_peak_area" value="0"/> - <param name="scoring_model" value="default"/> - <param name="im_extra_drift" value="0.0"/> - <param name="strict" value="true"/> - <section name="TransitionGroupPicker"> - <param name="stop_after_feature" value="-1"/> - <param name="min_peak_width" value="-1.0"/> - <param name="peak_integration" value="original"/> - <param name="background_subtraction" value="none"/> - <param name="recalculate_peaks" value="true"/> - <param name="use_precursors" value="false"/> - <param name="use_consensus" value="true"/> - <param name="recalculate_peaks_max_z" value="0.75"/> - <param name="minimal_quality" value="-1.5"/> - <param name="resample_boundary" value="15.0"/> - <param name="compute_peak_quality" value="false"/> - <param name="compute_peak_shape_metrics" value="false"/> - <param name="compute_total_mi" value="false"/> - <param name="boundary_selection_method" value="largest"/> - <section name="PeakPickerMRM"> - <param name="sgolay_frame_length" value="11"/> - <param name="sgolay_polynomial_order" value="3"/> - <param name="gauss_width" value="30.0"/> - <param name="use_gauss" value="false"/> - <param name="peak_width" value="-1.0"/> - <param name="signal_to_noise" value="0.1"/> - <param name="write_sn_log_messages" value="false"/> - <param name="remove_overlapping_peaks" value="true"/> - <param name="method" value="corrected"/> - </section> - <section name="PeakIntegrator"> - <param name="integration_type" value="intensity_sum"/> - <param name="baseline_type" value="base_to_base"/> - <param name="fit_EMG" value="false"/> - </section> - </section> - <section name="DIAScoring"> - <param name="dia_extraction_window" value="0.05"/> - <param name="dia_extraction_unit" value="Th"/> - <param name="dia_centroided" value="false"/> - <param name="dia_byseries_intensity_min" value="300.0"/> - <param name="dia_byseries_ppm_diff" value="10.0"/> - <param name="dia_nr_isotopes" value="4"/> - <param name="dia_nr_charges" value="4"/> - <param name="peak_before_mono_max_ppm_diff" value="20.0"/> - </section> - <section name="EMGScoring"> - <param name="max_iteration" value="10"/> - </section> - <section name="Scores"> - <param name="use_shape_score" value="true"/> - <param name="use_coelution_score" value="true"/> - <param name="use_rt_score" value="true"/> - <param name="use_library_score" value="true"/> - <param name="use_intensity_score" value="true"/> - <param name="use_nr_peaks_score" value="true"/> - <param name="use_total_xic_score" value="true"/> - <param name="use_total_mi_score" value="false"/> - <param name="use_sn_score" value="true"/> - <param name="use_mi_score" value="true"/> - <param name="use_dia_scores" value="true"/> - <param name="use_ms1_correlation" value="false"/> - <param name="use_sonar_scores" value="false"/> - <param name="use_ion_mobility_scores" value="false"/> - <param name="use_ms1_fullscan" value="false"/> - <param name="use_ms1_mi" value="true"/> - <param name="use_uis_scores" value="false"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PeakPickerHiRes"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_input.mzML"/> - <output name="out" file="PeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="1.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value="1"/> - <param name="report_FWHM" value="true"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_2_input.mzML"/> - <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="1.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value="1"/> - <param name="report_FWHM" value="true"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_input.mzML"/> - <output name="out" file="PeakPickerHiRes_output_lowMem.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="1.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value="1"/> - <param name="report_FWHM" value="true"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="lowmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_2_input.mzML"/> - <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="1.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value="1"/> - <param name="report_FWHM" value="true"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="processOption" value="inmemory"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerHiRes_5_input.mzML"/> - <output name="out" file="PeakPickerHiRes_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="0.0"/> - <param name="spacing_difference_gap" value="4.0"/> - <param name="spacing_difference" value="1.5"/> - <param name="missing" value="1"/> - <param name="ms_levels" value=""/> - <param name="report_FWHM" value="false"/> - <param name="report_FWHM_unit" value="relative"/> - <section name="SignalToNoise"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - <param name="write_log_messages" value="true"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PeakPickerIterative"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerIterative_1_input.mzML"/> - <output name="out" file="PeakPickerIterative_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise_" value="1.0"/> - <param name="peak_width" value="0.04"/> - <param name="spacing_difference" value="1.5"/> - <param name="sn_bin_count_" value="30"/> - <param name="nr_iterations_" value="5"/> - <param name="sn_win_len_" value="20.0"/> - <param name="check_width_internally" value="false"/> - <param name="ms1_only" value="false"/> - <param name="clear_meta_data" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerIterative_2_input.mzML"/> - <output name="out" file="PeakPickerIterative_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise_" value="0.0"/> - <param name="peak_width" value="0.04"/> - <param name="spacing_difference" value="2.5"/> - <param name="sn_bin_count_" value="30"/> - <param name="nr_iterations_" value="5"/> - <param name="sn_win_len_" value="20.0"/> - <param name="check_width_internally" value="true"/> - <param name="ms1_only" value="false"/> - <param name="clear_meta_data" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PeakPickerWavelet"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="write_peak_meta_data" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerWavelet_input.mzML"/> - <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.2"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.5"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="100.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.5"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="write_peak_meta_data" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerWavelet_deconv_input.mzML"/> - <output name="out" file="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="2.0"/> - <param name="centroid_percentage" value="0.8"/> - <param name="peak_width" value="0.15"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="1.0"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="200.0"/> - <param name="peak_bound_ms2_level" value="50.0"/> - <param name="correlation" value="0.5"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="true"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.1"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="100"/> - <section name="penalties"> - <param name="position" value="1.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="write_peak_meta_data" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerWavelet_input.mzML"/> - <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.2"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.5"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="100.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.5"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="write_peak_meta_data" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeakPickerWavelet_input.mzML"/> - <output name="out" file="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.2"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.5"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="100.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.5"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PepNovoAdapter"> -</xml> - <xml name="autotest_PeptideIndexer"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_1_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_2_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="true"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_3_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="true"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_4_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="true"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="0"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_5_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_2.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_6_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="3"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_3.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_7_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="full"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_3.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_8_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="semi"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_3.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_9_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="remove"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_10_input.idXML"/> - <param name="fasta" value="PeptideIndexer_10_input.fasta"/> - <output name="out" file="PeptideIndexer_10_output.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="true"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="error"/> - <param name="aaa_max" value="3"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="true"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="auto"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_1.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_12_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="warn"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="empty.idXML"/> - <param name="fasta" value="PeptideIndexer_1.fasta"/> - <output name="out" file="PeptideIndexer_13_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="false"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="error"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="auto"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PeptideIndexer_14.idXML"/> - <param name="fasta" value="PeptideIndexer_2.fasta"/> - <output name="out" file="PeptideIndexer_14_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value=""/> - <param name="decoy_string_position" value="prefix"/> - <param name="missing_decoy_action" value="error"/> - <param name="write_protein_sequence" value="true"/> - <param name="write_protein_description" value="false"/> - <param name="keep_unreferenced_proteins" value="false"/> - <param name="unmatched_action" value="error"/> - <param name="aaa_max" value="4"/> - <param name="mismatches_max" value="0"/> - <param name="IL_equivalent" value="false"/> - <section name="enzyme"> - <param name="name" value="auto"/> - <param name="specificity" value="none"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PercolatorAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.5"/> - <param name="trainFDR" value="0.5"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PercolatorAdapter_1.idXML"/> - <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="out_type" value="idXML"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="ms2"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.01"/> - <param name="trainFDR" value="0.01"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_osw" value="PercolatorAdapter_2.osw"/> - <output name="out" file="PercolatorAdapter_2_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> - <param name="out_type" value="osw"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="ms1"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.01"/> - <param name="trainFDR" value="0.01"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_osw" value="PercolatorAdapter_2_out1.osw"/> - <output name="out" file="PercolatorAdapter_3_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> - <param name="out_type" value="osw"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="ms2"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.01"/> - <param name="trainFDR" value="0.01"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_osw" value="PercolatorAdapter_3_out1.osw"/> - <output name="out" file="PercolatorAdapter_4_out1.osw" compare="sim_size" delta="5700" ftype="osw"/> - <param name="out_type" value="osw"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="transition"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="generic_feature_set" value="false"/> - <param name="subset_max_train" value="0"/> - <param name="cpos" value="0.0"/> - <param name="cneg" value="0.0"/> - <param name="testFDR" value="0.5"/> - <param name="trainFDR" value="0.5"/> - <param name="maxiter" value="10"/> - <param name="nested_xval_bins" value="1"/> - <param name="quick_validation" value="false"/> - <param name="static" value="false"/> - <param name="default_direction" value=""/> - <param name="verbose" value="2"/> - <param name="unitnorm" value="false"/> - <param name="test_each_iteration" value="false"/> - <param name="override" value="false"/> - <param name="seed" value="1"/> - <param name="doc" value="0"/> - <param name="klammer" value="false"/> - <param name="decoy_pattern" value="random"/> - <param name="post_processing_tdc" value="false"/> - <param name="train_best_positive" value="false"/> - <param name="ipf_max_peakgroup_pep" value="0.7"/> - <param name="ipf_max_transition_isotope_overlap" value="0.5"/> - <param name="ipf_min_transition_sn" value="0.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PercolatorAdapter_1.idXML"/> - <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_pin" file="PercolatorAdapter_1_out1.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="idXML"/> - <param name="enzyme" value="trypsin"/> - <param name="peptide_level_fdrs" value="false"/> - <param name="protein_level_fdrs" value="false"/> - <param name="osw_level" value="ms2"/> - <param name="score_type" value="q-value"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_pin_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PhosphoScoring"> -</xml> - <xml name="autotest_PrecursorIonSelector"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="solver" value="GLPK"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <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="5700" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="solver" value="GLPK"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PrecursorIonSelector_features.featureXML"/> - <output name="out" file="PrecursorIonSelector_2_output.featureXML" compare="sim_size" delta="5700" 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> - </xml> - <xml name="autotest_PrecursorMassCorrector"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="max_charge" value="3"/> - <param name="intensity_threshold" value="-1.0"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PrecursorMassCorrector_1_input.mzML"/> - <output name="out" file="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="precursor_mass_tolerance" value="1.5"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ProteinInference"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinInference_1_input.idXML"/> - <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="merge_runs" value="all"/> - <param name="annotate_indist_groups" value="true"/> - <section name="Merging"> - <param name="annotate_origin" value="false"/> - <param name="allow_disagreeing_settings" value="false"/> - </section> - <section name="Algorithm"> - <param name="min_peptides_per_protein" value="1"/> - <param name="score_aggregation_method" value="maximum"/> - <param name="treat_charge_variants_separately" value="true"/> - <param name="treat_modification_variants_separately" value="true"/> - <param name="use_shared_peptides" value="false"/> - <param name="skip_count_annotation" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ProteinQuantifier"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.featureXML"/> - <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="median"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.featureXML"/> - <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="2"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="true"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_3_input.featureXML"/> - <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="2"/> - <param name="average" value="mean"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="0"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="0"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </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> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="true"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.consensusXML"/> - <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="3"/> - <param name="average" value="sum"/> - <param name="include_all" value="true"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="true"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="true"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </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> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ProteinQuantifier_input.idXML"/> - <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <param name="top" value="0"/> - <param name="average" value="sum"/> - <param name="include_all" value="false"/> - <param name="best_charge_and_fraction" value="false"/> - <param name="greedy_group_resolution" value="false"/> - <param name="ratios" value="false"/> - <param name="ratiosSILAC" value="false"/> - <section name="consensus"> - <param name="normalize" value="false"/> - <param name="fix_peptides" value="false"/> - </section> - <section name="format"> - <param name="separator" value=""/> - <param name="quoting" value="double"/> - <param name="replacement" value="_"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_ProteinResolver"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="fasta" value="ProteinResolver_1_input.fasta"/> - <param name="in" value="ProteinResolver_1_input.consensusXML"/> - <param name="in_path" value=""/> - <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/> - <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta="5700" ftype="csv"/> - <section name="resolver"> - <param name="missed_cleavages" value="2"/> - <param name="min_length" value="6"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="designer"> - <param name="experiment" value="ExperimentalSetting"/> - <param name="file" value="File"/> - <param name="separator" value="tab"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,protein_groups_FLAG,peptide_table_FLAG,protein_table_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_PSMFeatureExtractor"> -</xml> - <xml name="autotest_PTModel"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_positive" value="PTModel_1_input_positive.idXML"/> - <param name="in_negative" value="PTModel_1_input_negative.idXML"/> - <output name="out" file="PTModel_1_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> - <param name="c" value="0.5"/> - <param name="svm_type" value="C_SVC"/> - <param name="nu" value="0.5"/> - <param name="kernel_type" value="OLIGO"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="5.0"/> - <param name="max_positive_count" value="1000"/> - <param name="max_negative_count" value="1000"/> - <param name="redundant" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="true"/> - <param name="number_of_runs" value="10"/> - <param name="number_of_partitions" value="10"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="c_start" value="1.0"/> - <param name="c_step_size" value="100.0"/> - <param name="c_stop" value="1000.0"/> - <param name="nu_start" value="0.1"/> - <param name="nu_step_size" value="1.3"/> - <param name="nu_stop" value="0.9"/> - <param name="sigma_start" value="1.0"/> - <param name="sigma_step_size" value="1.3"/> - <param name="sigma_stop" value="15.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_QCCalculator"> -</xml> - <xml name="autotest_QCEmbedder"> -</xml> - <xml name="autotest_QCExporter"> -</xml> - <xml name="autotest_QCExtractor"> -</xml> - <xml name="autotest_QCImporter"> -</xml> - <xml name="autotest_QCMerger"> -</xml> - <xml name="autotest_QCShrinker"> -</xml> - <xml name="autotest_QualityControl"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_cm" value="QualityControl_1_in.consensusXML"/> - <param name="in_raw" value="QualityControl_1_in1.mzML.gz,QualityControl_1_in2.mzML.gz,QualityControl_1_in3.mzML.gz"/> - <param name="in_postFDR" value="QualityControl_1_in1.featureXML,QualityControl_1_in2.featureXML,QualityControl_1_in3.featureXML"/> - <output name="out" file="QualityControl_1_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="out_cm" file="QualityControl_1_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/> - <param name="in_contaminants" value="QualityControl_1.fasta"/> - <param name="in_trafo" value="QualityControl_1_in1.trafoXML,QualityControl_1_in2.trafoXML,QualityControl_1_in3.trafoXML"/> - <section name="FragmentMassError"> - <param name="unit" value="auto"/> - <param name="tolerance" value="20.0"/> - </section> - <section name="MS2_id_rate"> - <param name="assume_all_target" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_cm_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_RNADigestor"> -</xml> - <xml name="autotest_RNAMassCalculator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_seq" value=""AUCGGC""/> - <output name="out" file="RNAMassCalculator_1.txt" compare="sim_size" delta="5700" ftype="txt"/> - <param name="charge" value="-1 -2"/> - <param name="format" value="list"/> - <param name="average_mass" value="false"/> - <param name="fragment_type" value="full"/> - <param name="separator" value=""/> - <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> - </xml> - <xml name="autotest_RNPxlSearch"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RNPxlSearch_1_input.mzML"/> - <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="precursor"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value="Oxidation (M)"/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="6"/> - <param name="max_size" value="1000000"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="report"> - <param name="top_hits" value="1"/> - </section> - <section name="RNPxl"> - <param name="length" value="2"/> - <param name="sequence" value="GUA"/> - <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> - <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> - <param name="can_cross_link" value="U"/> - <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> - <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> - <param name="scoring" value="fast"/> - <param name="decoys" value="false"/> - <param name="CysteineAdduct" value="false"/> - <param name="filter_fractional_mass" value="false"/> - <param name="carbon_labeled_fragments" value="false"/> - <param name="only_xl" value="false"/> - <param name="filter_small_peptide_mass" value="600.0"/> - <param name="marker_ions_tolerance" value="0.05"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RNPxlSearch_1_input.mzML"/> - <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="precursor"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="20.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value="Oxidation (M)"/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="6"/> - <param name="max_size" value="1000000"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="report"> - <param name="top_hits" value="1"/> - </section> - <section name="RNPxl"> - <param name="length" value="2"/> - <param name="sequence" value="GUA"/> - <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> - <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> - <param name="can_cross_link" value="U"/> - <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> - <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> - <param name="scoring" value="fast"/> - <param name="decoys" value="true"/> - <param name="CysteineAdduct" value="false"/> - <param name="filter_fractional_mass" value="false"/> - <param name="carbon_labeled_fragments" value="false"/> - <param name="only_xl" value="false"/> - <param name="filter_small_peptide_mass" value="600.0"/> - <param name="marker_ions_tolerance" value="0.05"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RNPxlSearch_1_input.mzML"/> - <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_tsv" file="RNPxlSearch_3_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="6"/> - <param name="max_size" value="1000000"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="report"> - <param name="top_hits" value="3"/> - </section> - <section name="RNPxl"> - <param name="length" value="2"/> - <param name="sequence" value=""/> - <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> - <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> - <param name="can_cross_link" value="U"/> - <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> - <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> - <param name="scoring" value="fast"/> - <param name="decoys" value="false"/> - <param name="CysteineAdduct" value="false"/> - <param name="filter_fractional_mass" value="false"/> - <param name="carbon_labeled_fragments" value="false"/> - <param name="only_xl" value="false"/> - <param name="filter_small_peptide_mass" value="600.0"/> - <param name="marker_ions_tolerance" value="0.05"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RNPxlSearch_1_input.mzML"/> - <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_tsv" file="RNPxlSearch_4_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <section name="precursor"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="10.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="peptide"> - <param name="min_size" value="6"/> - <param name="max_size" value="1000000"/> - <param name="missed_cleavages" value="1"/> - <param name="enzyme" value="Trypsin"/> - </section> - <section name="report"> - <param name="top_hits" value="2"/> - </section> - <section name="RNPxl"> - <param name="length" value="2"/> - <param name="sequence" value=""/> - <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> - <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> - <param name="can_cross_link" value="U"/> - <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> - <param name="modifications" value=""U:" "U:-H2O" "U:-H2O-HPO3" "U:-HPO3""/> - <param name="scoring" value="fast"/> - <param name="decoys" value="true"/> - <param name="CysteineAdduct" value="false"/> - <param name="filter_fractional_mass" value="false"/> - <param name="carbon_labeled_fragments" value="false"/> - <param name="only_xl" value="false"/> - <param name="filter_small_peptide_mass" value="600.0"/> - <param name="marker_ions_tolerance" value="0.05"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_RNPxlXICFilter"> -</xml> - <xml name="autotest_RTEvaluation"> -</xml> - <xml name="autotest_RTModel"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RTModel_1_input.idXML"/> - <output name="out" file="RTModel_1_output.model" compare="sim_size" delta="5700" ftype="txt"/> - <param name="svm_type" value="NU_SVR"/> - <param name="nu" value="0.5"/> - <param name="p" value="0.1"/> - <param name="c" value="0.1"/> - <param name="kernel_type" value="POLY"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="max_std" value="10.0"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="5.0"/> - <param name="total_gradient_time" value="3000.0"/> - <param name="first_dim_rt" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="true"/> - <param name="number_of_runs" value="10"/> - <param name="number_of_partitions" value="10"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="p_start" value="1.0"/> - <param name="p_step_size" value="10.0"/> - <param name="p_stop" value="1000.0"/> - <param name="c_start" value="1.0"/> - <param name="c_step_size" value="10.0"/> - <param name="c_stop" value="1000.0"/> - <param name="nu_start" value="0.3"/> - <param name="nu_step_size" value="1.2"/> - <param name="nu_stop" value="0.7"/> - <param name="sigma_start" value="1.0"/> - <param name="sigma_step_size" value="1.3"/> - <param name="sigma_stop" value="15.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in_positive" value="RTModel_2_input_positive.idXML"/> - <param name="in_negative" value="RTModel_2_input_negative.idXML"/> - <output name="out" file="RTModel_2_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> - <param name="svm_type" value="NU_SVR"/> - <param name="nu" value="0.5"/> - <param name="p" value="0.1"/> - <param name="c" value="0.5"/> - <param name="kernel_type" value="OLIGO"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="max_std" value="10.0"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="5.0"/> - <param name="total_gradient_time" value="1.0"/> - <param name="first_dim_rt" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="true"/> - <param name="number_of_runs" value="10"/> - <param name="number_of_partitions" value="10"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="p_start" value="1.0"/> - <param name="p_step_size" value="10.0"/> - <param name="p_stop" value="1000.0"/> - <param name="c_start" value="1.0"/> - <param name="c_step_size" value="10.0"/> - <param name="c_stop" value="1000.0"/> - <param name="nu_start" value="0.3"/> - <param name="nu_step_size" value="1.2"/> - <param name="nu_stop" value="0.7"/> - <param name="sigma_start" value="1.0"/> - <param name="sigma_step_size" value="1.3"/> - <param name="sigma_stop" value="15.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RTModel_3_input.idXML"/> - <output name="out" file="RTModel_3_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> - <param name="svm_type" value="NU_SVR"/> - <param name="nu" value="0.5"/> - <param name="p" value="0.1"/> - <param name="c" value="0.001953125"/> - <param name="kernel_type" value="OLIGO"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="max_std" value="10.0"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="1.0"/> - <param name="total_gradient_time" value="1.0"/> - <param name="first_dim_rt" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="false"/> - <param name="number_of_runs" value="1"/> - <param name="number_of_partitions" value="5"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="p_start" value="1.0"/> - <param name="p_step_size" value="10.0"/> - <param name="p_stop" value="1000.0"/> - <param name="c_start" value="0.001953125"/> - <param name="c_step_size" value="2.0"/> - <param name="c_stop" value="0.001953125"/> - <param name="nu_start" value="0.4"/> - <param name="nu_step_size" value="1.2"/> - <param name="nu_stop" value="0.4"/> - <param name="sigma_start" value="5.0"/> - <param name="sigma_step_size" value="1.221055"/> - <param name="sigma_stop" value="5.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="RTModel_4_input.txt" ftype="txt"/> - <output name="out" file="RTModel_4_output.tmp" compare="sim_size" delta="5700" ftype="txt"/> - <param name="svm_type" value="NU_SVR"/> - <param name="nu" value="0.5"/> - <param name="p" value="0.1"/> - <param name="c" value="0.001953125"/> - <param name="kernel_type" value="OLIGO"/> - <param name="degree" value="1"/> - <param name="border_length" value="22"/> - <param name="max_std" value="10.0"/> - <param name="k_mer_length" value="1"/> - <param name="sigma" value="1.0"/> - <param name="total_gradient_time" value="1.0"/> - <param name="first_dim_rt" value="false"/> - <param name="additive_cv" value="false"/> - <section name="cv"> - <param name="skip_cv" value="false"/> - <param name="number_of_runs" value="1"/> - <param name="number_of_partitions" value="5"/> - <param name="degree_start" value="1"/> - <param name="degree_step_size" value="2"/> - <param name="degree_stop" value="4"/> - <param name="p_start" value="1.0"/> - <param name="p_step_size" value="10.0"/> - <param name="p_stop" value="1000.0"/> - <param name="c_start" value="0.001953125"/> - <param name="c_step_size" value="2.0"/> - <param name="c_stop" value="0.001953125"/> - <param name="nu_start" value="0.4"/> - <param name="nu_step_size" value="1.2"/> - <param name="nu_stop" value="0.4"/> - <param name="sigma_start" value="5.0"/> - <param name="sigma_step_size" value="1.221055"/> - <param name="sigma_stop" value="5.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SeedListGenerator"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="PepXMLFile_test.mzML"/> - <output name="out" file="SeedListGenerator_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="use_peptide_mass" 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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDMapper_1_output.featureXML"/> - <output name="out" file="SeedListGenerator_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/> - <param name="use_peptide_mass" 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> - </xml> - <xml name="autotest_SemanticValidator"> -</xml> - <xml name="autotest_SequenceCoverageCalculator"> -</xml> - <xml name="autotest_SimpleSearchEngine"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SimpleSearchEngine_1.mzML"/> - <param name="database" value="SimpleSearchEngine_1.fasta"/> - <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <section name="Search"> - <param name="enzyme" value="Trypsin"/> - <param name="decoys" value="false"/> - <section name="precursor"> - <param name="mass_tolerance" value="5.0"/> - <param name="mass_tolerance_unit" value="ppm"/> - <param name="min_charge" value="2"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="0.3"/> - <param name="mass_tolerance_unit" value="Da"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value="Oxidation (M)"/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <section name="annotate"> - <param name="PSM" value=""/> - </section> - <section name="peptide"> - <param name="min_size" value="7"/> - <param name="max_size" value="40"/> - <param name="missed_cleavages" value="1"/> - <param name="motif" value=""/> - </section> - <section name="report"> - <param name="top_hits" value="1"/> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SiriusAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_1_input.mzML"/> - <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="true"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_2_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> - <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="3"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="true"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_3_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> - <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="3"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="true"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_3_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/> - <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> - <param name="out_workspace_directory" value=""/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_4_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> - <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/> - <param name="out_workspace_directory" value=""/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_4_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/> - <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="true"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="all"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="false"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="converter_mode" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SiriusAdapter_2_input.mzML"/> - <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/> - <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/> - <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/> - <param name="out_workspace_directory" value=""/> - <section name="preprocessing"> - <param name="filter_by_num_masstraces" value="1"/> - <param name="precursor_mz_tolerance" value="0.005"/> - <param name="precursor_mz_tolerance_unit" value="Da"/> - <param name="precursor_rt_tolerance" value="5"/> - <param name="isotope_pattern_iterations" value="3"/> - <param name="feature_only" value="false"/> - <param name="no_masstrace_info_isotope_pattern" value="false"/> - </section> - <section name="sirius"> - <param name="profile" value="qtof"/> - <param name="candidates" value="5"/> - <param name="database" value="pubchem"/> - <param name="noise" value="0"/> - <param name="ppm_max" value="10"/> - <param name="isotope" value="both"/> - <param name="elements" value="CHNOP[5]S[8]Cl[1]"/> - <param name="compound_timeout" value="10"/> - <param name="tree_timeout" value="0"/> - <param name="top_n_hits" value="10"/> - <param name="auto_charge" value="true"/> - <param name="ion_tree" value="false"/> - <param name="no_recalibration" value="false"/> - <param name="most_intense_ms2" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG,out_fingerid_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SpecLibCreator"> -</xml> - <xml name="autotest_SpecLibSearcher"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SpecLibSearcher_1.mzML"/> - <param name="lib" value="SpecLibSearcher_1.MSP"/> - <output_collection name="out" count="1"/> - <param name="compare_function" value="ZhangSimilarityScore"/> - <section name="precursor"> - <param name="mass_tolerance" value="3.0"/> - <param name="mass_tolerance_unit" value="Da"/> - <param name="min_charge" value="1"/> - <param name="max_charge" value="5"/> - <param name="isotopes" value="0 1"/> - </section> - <section name="fragment"> - <param name="mass_tolerance" value="10.0"/> - </section> - <section name="report"> - <param name="top_hits" value="10"/> - </section> - <section name="filter"> - <param name="remove_peaks_below_threshold" value="2.01"/> - <param name="min_peaks" value="5"/> - <param name="max_peaks" value="150"/> - <param name="cut_peaks_below" value="1000"/> - </section> - <section name="modifications"> - <param name="fixed" value=""/> - <param name="variable" value=""/> - <param name="variable_max_per_peptide" value="2"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SpectraFilterBernNorm"> -</xml> - <xml name="autotest_SpectraFilterMarkerMower"> -</xml> - <xml name="autotest_SpectraFilterNLargest"> -</xml> - <xml name="autotest_SpectraFilterNormalizer"> -</xml> - <xml name="autotest_SpectraFilterParentPeakMower"> -</xml> - <xml name="autotest_SpectraFilterScaler"> -</xml> - <xml name="autotest_SpectraFilterSqrtMower"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" file="SpectraFilterSqrtMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SpectraFilterThresholdMower"> -</xml> - <xml name="autotest_SpectraFilterWindowMower"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SpectraFilterWindowMower_1_input.mzML"/> - <output name="out" file="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="windowsize" value="50.0"/> - <param name="peakcount" value="2"/> - <param name="movetype" value="slide"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="SpectraFilterWindowMower_2_input.mzML"/> - <output name="out" file="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <section name="algorithm"> - <param name="windowsize" value="20.0"/> - <param name="peakcount" value="4"/> - <param name="movetype" value="slide"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_SpectraMerger"> -</xml> - <xml name="autotest_SpectraSTSearchAdapter"/> - <xml name="autotest_StaticModification"> -</xml> - <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer"> -</xml> - <xml name="autotest_TargetedFileConverter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_1_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="minutes"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="seconds"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_4_input.mrm" ftype="mrm"/> - <output name="out" file="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/> - <output name="out" file="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_1_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="true"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_10_output.TraML.tmp"/> - <output name="out" file="TargetedFileConverter_10_output.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="tsv"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_11_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_11_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_8_output.TraML.tmp"/> - <output name="out" file="TargetedFileConverter_8_input.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="tsv"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="true"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_9_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_9_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="true"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_output.TraML"/> - <output name="out" file="ConvertTraMLToTSV_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="tsv"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_12_output.pqp.tmp"/> - <output name="out" file="TargetedFileConverter_12_input.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="true"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TargetedFileConverter_12_input.tsv" ftype="tabular"/> - <output name="out" file="TargetedFileConverter_13_output.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="TraML"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="ConvertTSVToTraML_5_output.TraML"/> - <output name="out" file="ConvertTraMLToTSV_output_2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="out_type" value="tsv"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="legacy_traml_id" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" ftype="tabular"/> - <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML" compare="sim_size" delta="5700" ftype="traml"/> - <param name="out_type" value="traml"/> - <section name="algorithm"> - <param name="retentionTimeInterpretation" value="iRT"/> - <param name="override_group_label_check" value="false"/> - <param name="force_invalid_mods" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_TextExporter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_1_input.featureXML"/> - <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="5"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_2_input.consensusXML"/> - <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="true"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="RT_then_MZ"/> - <param name="sort_by_maps" value="true"/> - <param name="sort_by_size" value="true"/> - </section> - <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/> - <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/> - <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_3_input.idXML"/> - <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_3_input.idXML"/> - <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="true"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_5_input.idXML"/> - <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="true"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="true"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_6_input.featureXML"/> - <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="true"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_7_input.consensusXML"/> - <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="RT_then_MZ"/> - <param name="sort_by_maps" value="true"/> - <param name="sort_by_size" value="true"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_1_input.featureXML"/> - <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="true"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="-1"/> - <param name="add_hit_metavalues" value="-1"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TextExporter_9_input.idXML"/> - <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="tabular"/> - <param name="separator" value=""/> - <param name="replacement" value="_"/> - <param name="quoting" value="none"/> - <param name="no_ids" value="false"/> - <section name="feature"> - <param name="minimal" value="false"/> - <param name="add_metavalues" value="-1"/> - </section> - <section name="id"> - <param name="proteins_only" value="false"/> - <param name="peptides_only" value="false"/> - <param name="protein_groups" value="false"/> - <param name="first_dim_rt" value="false"/> - <param name="add_metavalues" value="0"/> - <param name="add_hit_metavalues" value="0"/> - <param name="add_protein_hit_metavalues" value="-1"/> - </section> - <section name="consensus"> - <param name="sorting_method" value="none"/> - <param name="sort_by_maps" value="false"/> - <param name="sort_by_size" value="false"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_TICCalculator"> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="regular"/> - <param name="loadData" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="streaming"/> - <param name="loadData" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="streaming"/> - <param name="loadData" 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> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="indexed"/> - <param name="loadData" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MapNormalizer_output.mzML"/> - <param name="read_method" value="indexed_parallel"/> - <param name="loadData" value="true"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_TOFCalibration"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TOFCalibration_1_input.mzML"/> - <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/> - <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/> - <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/> - <param name="peak_data" value="false"/> - <section name="algorithm"> - <section name="PeakPicker"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.15"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.7"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="400.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.0"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="TOFCalibration_2_input.mzML"/> - <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/> - <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/> - <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/> - <param name="peak_data" value="true"/> - <section name="algorithm"> - <section name="PeakPicker"> - <param name="signal_to_noise" value="3.0"/> - <param name="centroid_percentage" value="0.6"/> - <param name="peak_width" value="0.15"/> - <param name="estimate_peak_width" value="false"/> - <param name="fwhm_lower_bound_factor" value="0.7"/> - <param name="fwhm_upper_bound_factor" value="20.0"/> - <section name="optimization"> - <param name="iterations" value="400"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="left_width" value="1.0"/> - <param name="right_width" value="1.0"/> - <param name="height" value="1.0"/> - </section> - <section name="2d"> - <param name="tolerance_mz" value="2.2"/> - <param name="max_peak_distance" value="1.2"/> - </section> - </section> - <section name="thresholds"> - <param name="peak_bound" value="400.0"/> - <param name="peak_bound_ms2_level" value="10.0"/> - <param name="correlation" value="0.0"/> - <param name="noise_level" value="0.1"/> - <param name="search_radius" value="3"/> - </section> - <section name="wavelet_transform"> - <param name="spacing" value="0.001"/> - </section> - <section name="deconvolution"> - <param name="deconvolution" value="false"/> - <param name="asym_threshold" value="0.3"/> - <param name="left_width" value="2.0"/> - <param name="right_width" value="2.0"/> - <param name="scaling" value="0.12"/> - <section name="fitting"> - <param name="fwhm_threshold" value="0.7"/> - <param name="eps_abs" value="9.999999747378752e-06"/> - <param name="eps_rel" value="9.999999747378752e-06"/> - <param name="max_iteration" value="10"/> - <section name="penalties"> - <param name="position" value="0.0"/> - <param name="height" value="1.0"/> - <param name="left_width" value="0.0"/> - <param name="right_width" value="0.0"/> - </section> - </section> - </section> - <section name="SignalToNoiseEstimationParameter"> - <param name="max_intensity" value="-1"/> - <param name="auto_max_stdev_factor" value="3.0"/> - <param name="auto_max_percentile" value="95"/> - <param name="auto_mode" value="0"/> - <param name="win_len" value="200.0"/> - <param name="bin_count" value="30"/> - <param name="stdev_mp" value="3.0"/> - <param name="min_required_elements" value="10"/> - <param name="noise_for_empty_window" value="1e+20"/> - </section> - </section> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_TransformationEvaluation"> -</xml> - <xml name="autotest_XFDR"> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in1.idXML"/> - <output name="out_idXML" file="XFDR_test_out1_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out1_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out1_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in1.idXML"/> - <output name="out_idXML" file="XFDR_test_out2_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out2_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out2_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="true"/> - <param name="no_qvalues" value="true"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in2.xquest.xml"/> - <output name="out_idXML" file="XFDR_test_out3_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out3_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out3_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="0.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in2.xquest.xml"/> - <output name="out_idXML" file="XFDR_test_out4_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out4_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out4_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-3.0"/> - <param name="maxborder" value="3.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in3.xquest.xml"/> - <output name="out_idXML" file="XFDR_test_out5_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out5_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out5_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-3.0"/> - <param name="maxborder" value="3.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in4.idXML"/> - <output name="out_idXML" file="XFDR_test_out6_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="false"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="-10.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - <test expect_num_outputs="4"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="XFDR_test_in2.xquest.xml"/> - <output name="out_idXML" file="XFDR_test_out7_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="out_mzIdentML" file="XFDR_test_out7_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/> - <output name="out_xquest" file="XFDR_test_out7_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/> - <param name="decoy_string" value="DECOY_"/> - <param name="minborder" value="-50.0"/> - <param name="maxborder" value="50.0"/> - <param name="mindeltas" value="0.0"/> - <param name="minionsmatched" value="0"/> - <param name="uniquexl" value="true"/> - <param name="no_qvalues" value="false"/> - <param name="minscore" value="0.0"/> - <param name="binsize" value="0.1"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> - </xml> - <xml name="autotest_XMLValidator"> -</xml> - <xml name="autotest_XTandemAdapter"> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="XTandemAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/> - <param name="ignore_adapter_param" value="false"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="precursor_error_units" value="ppm"/> - <param name="fragment_error_units" value="Da"/> - <param name="max_precursor_charge" value="0"/> - <param name="no_isotope_error" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="minimum_fragment_mz" value="150.0"/> - <param name="enzyme" value="Trypsin"/> - <param name="missed_cleavages" value="1"/> - <param name="semi_cleavage" value="false"/> - <param name="output_results" value="all"/> - <param name="max_valid_expect" value="0.1"/> - <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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="XTandemAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/> - <param name="ignore_adapter_param" value="false"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="precursor_error_units" value="ppm"/> - <param name="fragment_error_units" value="Da"/> - <param name="max_precursor_charge" value="0"/> - <param name="no_isotope_error" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="minimum_fragment_mz" value="150.0"/> - <param name="enzyme" value="Trypsin"/> - <param name="missed_cleavages" value="1"/> - <param name="semi_cleavage" value="false"/> - <param name="output_results" value="valid"/> - <param name="max_valid_expect" value="1e-14"/> - <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> - <test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="spectra.mzML"/> - <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteinslong.fasta"/> - <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/> - <param name="ignore_adapter_param" value="false"/> - <param name="precursor_mass_tolerance" value="5.0"/> - <param name="fragment_mass_tolerance" value="0.3"/> - <param name="precursor_error_units" value="ppm"/> - <param name="fragment_error_units" value="Da"/> - <param name="max_precursor_charge" value="0"/> - <param name="no_isotope_error" value="false"/> - <param name="fixed_modifications" value=""/> - <param name="variable_modifications" value="Oxidation (M)"/> - <param name="minimum_fragment_mz" value="150.0"/> - <param name="enzyme" value="Trypsin"/> - <param name="missed_cleavages" value="1"/> - <param name="semi_cleavage" value="false"/> - <param name="output_results" value="all"/> - <param name="max_valid_expect" value="0.1"/> - <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> - </xml> -<xml name="autotest_PTPredict"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_InspectAdapter"/></macros>
--- a/macros_discarded_auto.xml Fri Nov 06 19:42:25 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,378 +0,0 @@ - -<xml name="manutest_OpenSwathFileSplitter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <output_collection name="outputDirectory" count=""/> - <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_qc_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> -</test></xml> -<xml name="manutest_IDRipper"> -<test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_1_input.idXML"/> - <output_collection name="out_path" count=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test><test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_2_input.idXML"/> - <output_collection name="out_path" count=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test><test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_3_output.idXML"/> - <output_collection name="out_path" count=""/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml> -<xml name="manutest_MzMLSplitter"> -<test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output_collection name="out" count=""/> - <param name="parts" value="2"/> - <param name="size" value="0"/> - <param name="unit" value="MB"/> - <param name="no_chrom" value="false"/> - <param name="no_spec" 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><test expect_num_outputs="1"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <output_collection name="out" count=""/> - <param name="parts" value="1"/> - <param name="size" value="40"/> - <param name="unit" value="KB"/> - <param name="no_chrom" value="false"/> - <param name="no_spec" 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></xml> -<xml name="manutest_MSFraggerAdapter"> -<test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="java_heapmemory" value="2600"/> - <param name="in" value="spectra.mzML"/> - <output name="out" file="MSFraggerAdapter_7_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <output name="opt_out" file="MSFraggerAdapter_7_opt_out_tmp.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/> - <param name="database" value="proteins.fasta"/> - <section name="tolerance"> - <param name="precursor_mass_tolerance" value="20.0"/> - <param name="precursor_mass_unit" value="ppm"/> - <param name="precursor_true_tolerance" value="0.0"/> - <param name="precursor_true_unit" value="ppm"/> - <param name="fragment_mass_tolerance" value="20.0"/> - <param name="fragment_mass_unit" value="ppm"/> - <param name="isotope_error" value="0"/> - </section> - <section name="digest"> - <param name="search_enzyme_name" value="Trypsin"/> - <param name="search_enzyme_cutafter" value="KR"/> - <param name="search_enzyme_nocutbefore" value="P"/> - <param name="num_enzyme_termini" value="semi"/> - <param name="allowed_missed_cleavage" value="2"/> - <param name="min_length" value="7"/> - <param name="max_length" value="64"/> - <param name="mass_range_min" value="500.0"/> - <param name="mass_range_max" value="5000.0"/> - </section> - <section name="varmod"> - <param name="clip_nterm_m" value="false"/> - <param name="masses" value=""/> - <param name="syntaxes" value=""/> - <param name="enable_common" value="true"/> - <param name="not_allow_multiple_variable_mods_on_residue" value="false"/> - <param name="max_variable_mods_per_mod" value="2"/> - <param name="max_variable_mods_combinations" value="5000"/> - </section> - <section name="spectrum"> - <param name="minimum_peaks" value="10"/> - <param name="use_topn_peaks" value="50"/> - <param name="minimum_ratio" value="0.0"/> - <param name="clear_mz_range_min" value="0.0"/> - <param name="clear_mz_range_max" value="0.0"/> - <param name="max_fragment_charge" value="2"/> - <param name="override_charge" value="false"/> - <param name="precursor_charge_min" value="1"/> - <param name="precursor_charge_max" value="4"/> - </section> - <section name="search"> - <param name="track_zero_topn" value="0"/> - <param name="zero_bin_accept_expect" value="0.0"/> - <param name="zero_bin_mult_expect" value="1.0"/> - <param name="add_topn_complementary" value="0"/> - <param name="min_fragments_modeling" value="3"/> - <param name="min_matched_fragments" value="4"/> - <param name="output_report_topn" value="1"/> - <param name="output_max_expect" value="50.0"/> - </section> - <section name="statmod"> - <param name="add_cterm_peptide" value="0.0"/> - <param name="add_nterm_peptide" value="0.0"/> - <param name="add_cterm_protein" value="0.0"/> - <param name="add_nterm_protein" value="0.0"/> - <param name="add_G_glycine" value="0.0"/> - <param name="add_A_alanine" value="0.0"/> - <param name="add_S_serine" value="0.0"/> - <param name="add_P_proline" value="0.0"/> - <param name="add_V_valine" value="0.0"/> - <param name="add_T_threonine" value="0.0"/> - <param name="add_C_cysteine" value="57.021464"/> - <param name="add_L_leucine" value="0.0"/> - <param name="add_I_isoleucine" value="0.0"/> - <param name="add_N_asparagine" value="0.0"/> - <param name="add_D_aspartic_acid" value="0.0"/> - <param name="add_Q_glutamine" value="0.0"/> - <param name="add_K_lysine" value="0.0"/> - <param name="add_E_glutamic_acid" value="0.0"/> - <param name="add_M_methionine" value="0.0"/> - <param name="add_H_histidine" value="0.0"/> - <param name="add_F_phenylalanine" value="0.0"/> - <param name="add_R_arginine" value="0.0"/> - <param name="add_Y_tyrosine" value="0.0"/> - <param name="add_W_tryptophan" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,opt_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test><test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="java_heapmemory" value="2600"/> - <param name="in" value="spectra_comet.mzML"/> - <output name="out" file="MSFraggerAdapter_8_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="database" value="proteins.fasta"/> - <section name="tolerance"> - <param name="precursor_mass_tolerance" value="20.0"/> - <param name="precursor_mass_unit" value="ppm"/> - <param name="precursor_true_tolerance" value="0.0"/> - <param name="precursor_true_unit" value="ppm"/> - <param name="fragment_mass_tolerance" value="20.0"/> - <param name="fragment_mass_unit" value="ppm"/> - <param name="isotope_error" value="0"/> - </section> - <section name="digest"> - <param name="search_enzyme_name" value="Trypsin"/> - <param name="search_enzyme_cutafter" value="KR"/> - <param name="search_enzyme_nocutbefore" value="P"/> - <param name="num_enzyme_termini" value="semi"/> - <param name="allowed_missed_cleavage" value="2"/> - <param name="min_length" value="7"/> - <param name="max_length" value="64"/> - <param name="mass_range_min" value="500.0"/> - <param name="mass_range_max" value="5000.0"/> - </section> - <section name="varmod"> - <param name="clip_nterm_m" value="false"/> - <param name="masses" value=""/> - <param name="syntaxes" value=""/> - <param name="enable_common" value="true"/> - <param name="not_allow_multiple_variable_mods_on_residue" value="false"/> - <param name="max_variable_mods_per_mod" value="2"/> - <param name="max_variable_mods_combinations" value="5000"/> - </section> - <section name="spectrum"> - <param name="minimum_peaks" value="10"/> - <param name="use_topn_peaks" value="50"/> - <param name="minimum_ratio" value="0.0"/> - <param name="clear_mz_range_min" value="0.0"/> - <param name="clear_mz_range_max" value="0.0"/> - <param name="max_fragment_charge" value="2"/> - <param name="override_charge" value="false"/> - <param name="precursor_charge_min" value="1"/> - <param name="precursor_charge_max" value="4"/> - </section> - <section name="search"> - <param name="track_zero_topn" value="0"/> - <param name="zero_bin_accept_expect" value="0.0"/> - <param name="zero_bin_mult_expect" value="1.0"/> - <param name="add_topn_complementary" value="0"/> - <param name="min_fragments_modeling" value="3"/> - <param name="min_matched_fragments" value="4"/> - <param name="output_report_topn" value="1"/> - <param name="output_max_expect" value="50.0"/> - </section> - <section name="statmod"> - <param name="add_cterm_peptide" value="0.0"/> - <param name="add_nterm_peptide" value="0.0"/> - <param name="add_cterm_protein" value="0.0"/> - <param name="add_nterm_protein" value="0.0"/> - <param name="add_G_glycine" value="0.0"/> - <param name="add_A_alanine" value="0.0"/> - <param name="add_S_serine" value="0.0"/> - <param name="add_P_proline" value="0.0"/> - <param name="add_V_valine" value="0.0"/> - <param name="add_T_threonine" value="0.0"/> - <param name="add_C_cysteine" value="57.021464"/> - <param name="add_L_leucine" value="0.0"/> - <param name="add_I_isoleucine" value="0.0"/> - <param name="add_N_asparagine" value="0.0"/> - <param name="add_D_aspartic_acid" value="0.0"/> - <param name="add_Q_glutamine" value="0.0"/> - <param name="add_K_lysine" value="0.0"/> - <param name="add_E_glutamic_acid" value="0.0"/> - <param name="add_M_methionine" value="0.0"/> - <param name="add_H_histidine" value="0.0"/> - <param name="add_F_phenylalanine" value="0.0"/> - <param name="add_R_arginine" value="0.0"/> - <param name="add_Y_tyrosine" value="0.0"/> - <param name="add_W_tryptophan" value="0.0"/> - </section> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml> -<xml name="manutest_MaRaClusterAdapter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="verbose" value="2"/> - <param name="precursor_tolerance" value="20.0"/> - <param name="precursor_tolerance_units" value="ppm"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="MaRaClusterAdapter_1_in_1.mzML,MaRaClusterAdapter_1_in_2.mzML"/> - <param name="id_in" value="MaRaClusterAdapter_1_in_3.idXML"/> - <output name="out" file="MaRaClusterAdapter_2_out_1.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="pcut" value="-10.0"/> - <param name="min_cluster_size" value="1"/> - <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></xml> -<xml name="manutest_NovorAdapter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="NovorAdapter_in.mzML"/> - <output name="out" file="NovorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/> - <param name="enzyme" value="Trypsin"/> - <param name="fragmentation" value="CID"/> - <param name="massAnalyzer" value="Trap"/> - <param name="fragment_mass_tolerance" value="0.5"/> - <param name="precursor_mass_tolerance" value="15.0"/> - <param name="precursor_error_units" value="ppm"/> - <param name="variable_modifications" value="Acetyl (K)"/> - <param name="fixed_modifications" value="Carbamidomethyl (C)"/> - <param name="forbiddenResidues" value="I"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml> -<xml name="manutest_SpectraSTSearchAdapter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_isotopically_averaged_mass" value="false"/> - <param name="use_all_charge_states" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/> - <param name="output_files_type" value="pep.xml"/> - <output_collection name="output_files" count="1"/> - <param name="library_file" value="testLib.splib" ftype="splib"/> - <param name="sequence_database_type" value="AA"/> - <param name="precursor_mz_tolerance" value="3.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test><test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="use_isotopically_averaged_mass" value="false"/> - <param name="use_all_charge_states" value="false"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/> - <param name="output_files_type" value="tsv"/> - <output_collection name="output_files" count="1"/> - <param name="library_file" value="testLib.splib" ftype="splib"/> - <param name="sequence_database_type" value="AA"/> - <param name="precursor_mz_tolerance" value="3.0"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test></xml>
--- a/macros_test.xml Fri Nov 06 19:42:25 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,545 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<macros> - -<!-- a copy of a FileConverter test without the advanced options used - in order to check if this works (all other tests enable advanced) --> -<xml name="manutest_FileConverter"> -<test expect_num_outputs="1"> - <param name="in" value="FileConverter_1_input.mzData"/> - <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/> - <param name="out_type" value="mzML"/> -</test> -</xml> -<!-- tests contributed by the galaxyproteomics community --> -<xml name="manutest_ClusterMassTracesByPrecursor"> - <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> - <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> - <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/> - </test> -</xml> -<xml name="manutest_ClusterMassTraces"> - <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/> - <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/> - </test> -</xml> -<xml name="manutest_CVInspector"> - <!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml, see currently not working, see: https://github.com/OpenMS/OpenMS/pull/4425 --> - <test expect_num_outputs="1"> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/> - <param name="cv_names" value="XLMOD"/> - <param name="mapping_file" value="MAPPING/ms-mapping.xml"/> - <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/> - <output name="html" ftype="html" value="CVInspector.html"/> - </test> -</xml> -<xml name="manutest_DeMeanderize"> - <test expect_num_outputs="1"><!-- test with the output of a MSsimulator output generated by a test below --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="MSsimulator_MALDI.mzml"/> - <output name="out" ftype="mzml" value="DeMeanderize.mzml"/> - </test> -</xml> -<xml name="manutest_Digestor"> - <test expect_num_outputs="1"><!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="fasta" value="random.fa"/> - <output name="out" ftype="fasta" value="Digestor.fasta"/> - <param name="out_type" value="fasta"/> - </test> -</xml> -<xml name="manutest_EICExtractor"> - <test expect_num_outputs="1"><!-- just using some random test data --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="spectra.mzML"/> - <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/> - <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/> - </test> -</xml> -<xml name="manutest_ERPairFinder"> - <!-- TODO --> -</xml> -<xml name="manutest_FeatureFinderIsotopeWavelet"> - <test expect_num_outputs="1"><!--just use the input of another FeatureFinder --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="FeatureFinderCentroided_1_input.mzML"/> - <output name="out" value="FeatureFinderIsotopeWavelet.featureXML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_FFEval"> - <test expect_num_outputs="2"><!-- comparing an arbitarty FeatureFinder output with itself --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="FeatureFinderCentroided_1_output.featureXML"/> - <param name="truth" value="FeatureFinderCentroided_1_output.featureXML"/> - <param name="OPTIONAL_OUTPUTS" value="out_FLAG,out_roc_FLAG"/> - <output name="out" value="FFEval.featureXML" compare="sim_size"/> - <output name="out_roc" value="FFEval_roc.csv" ftype="csv"/> - </test> -</xml> -<xml name="manutest_IDExtractor"> - <test expect_num_outputs="1"><!-- --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/> - <param name="best_hits" value="true"/> - <param name="number_of_peptides" value="1"/> - <output name="out" value="IDExtractor.idXML" compare="sim_size"/> - </test> -</xml> -<!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> -<xml name="manutest_IDRipper"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_1_input.idXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output_collection name="out_path" count="2"> - <element name="IDRipper_1_output_1" file="IDRipper_1_output1.idXML" ftype="idxml" compare="sim_size" delta="5700"/> - <element name="IDRipper_1_output_2" file="IDRipper_1_output2.idXML" ftype="idxml" compare="sim_size" delta="5700"/> - </output_collection> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> -</test> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_2_input.idXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output_collection name="out_path" count="2"> - <element name="IDRipper_2_output1" file="IDRipper_2_output1.idXML" ftype="idxml"/> - <element name="IDRipper_2_output2" file="IDRipper_2_output2.idXML" ftype="idxml"/> - </output_collection> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> -</test> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="IDRipper_3_output.idXML"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output_collection name="out_path" count="2"> - <element name="IDRipper_3_input1" file="IDRipper_3_input1.idXML" ftype="idxml"/> - <element name="IDRipper_3_input2" file="IDRipper_3_input2.idXML" ftype="idxml"/> - </output_collection> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> -</test> -</xml> -<xml name="manutest_LabeledEval"> - <test expect_num_outputs="1"><!-- comparing an arbitarty featureXML that has a corresponding consensusXML --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/> - <param name="truth" value="FeatureLinkerLabeled_1_output.consensusXML"/> - <output name="stdout" value="LabeledEval.txt" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_MapStatistics"> - <test expect_num_outputs="1"><!-- test with a featureXML input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/> - <output name="out" ftype="txt" value="MapStatistics.txt"/> - </test> - <test expect_num_outputs="1"><!-- test with a consensusxml input --> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/> - <output name="out" ftype="txt" value="MapStatistics2.txt"/> - </test> -</xml> -<xml name="manutest_MetaboliteSpectralMatcher"> - <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML --> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="spectra.mzML"/> - <param name="database" value="MetaboliteSpectralDB.mzML"/> - <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/> - </test> -</xml> -<xml name="manutest_MRMPairFinder"> - <!-- TODO no idea about a useful input for pair_in --> -</xml> -<xml name="manutest_MSSimulator"> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/> - <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> - <output name="out" ftype="mzml" value="MSsimulator.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/> - <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/> - <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/> - </test> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter generate MALDI output for use in the test for DeMeanderize --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/> - <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> - <output name="out" ftype="mzml" value="MSsimulator_MALDI.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/> - <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/> - <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/> - <param name="algorithm|MSSim|Global|ionization_type" value="MALDI"/> - </test> -</xml> -<!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> -<xml name="manutest_MzMLSplitter"> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <param name="parts" value="2"/> - <param name="size" value="0"/> - <param name="unit" value="MB"/> - <param name="no_chrom" value="false"/> - <param name="no_spec" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - <output_collection name="out" type="list" count="2"> - <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/> - <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/> - </output_collection> -</test> -<test expect_num_outputs="2"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="FileFilter_1_input.mzML"/> - <param name="parts" value="1"/> - <param name="size" value="40"/> - <param name="unit" value="KB"/> - <param name="no_chrom" value="false"/> - <param name="no_spec" value="false"/> - <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - <output_collection name="out" type="list" count="2"> - <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/> - <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/> - </output_collection> -</test> -</xml> -<xml name="manutest_OpenSwathDIAPreScoring"> - <!-- data from a test that included all the needed test files --> - <test> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/> - <output_collection name="output_files" count="1"> - <element name="OpenSwathAnalyzer_2_swathfile_mzML.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> - </output_collection> - </test> - - <!-- test with two inputs (actually the same file .. symlinked) --> - <test> - <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/> - <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/> - <output_collection name="output_files" count="2"> - <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> - <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/> - </output_collection> - </test> -</xml> -<!-- adapted from macros_discarded_auto.xml (due to prefix-output)--> -<xml name="manutest_OpenSwathFileSplitter"> - <test expect_num_outputs="3"> - <conditional name="adv_opts_cond"> - <param name="adv_opts_selector" value="advanced"/> - <param name="force" value="false"/> - <param name="test" value="true"/> - </conditional> - <param name="in" value="OpenSwathWorkflow_1_input.mzML"/> - <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/> - <output_collection name="outputDirectory" count="6"> - <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/> - <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/> - </output_collection> - <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/> - <output name="ctd_out" ftype="xml"> - <assert_contents> - <is_valid_xml/> - </assert_contents> - </output> - </test> -</xml> -<xml name="manutest_OpenSwathRewriteToFeatureXML"> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> - <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/> - <param name="adv_opts_cond|test" value="true"/> - <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/> - </test> -</xml> -<xml name="manutest_PepNovoAdapter"> - <test expect_num_outputs="1"><!-- adapted from (dysfunctional) OMS 3rdParty tests (but model selection - unclear https://github.com/OpenMS/OpenMS/issues/4719)--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="PepNovo_1.mzML"/> - <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/> - <param name="model" value="LTQ_COMP"/> - </test> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="PepNovo_1.mzML"/> - <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/> - <param name="model" value="LTQ_COMP"/> - </test> -</xml> -<xml name="manutest_PhosphoScoring"> - <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="spectra.mzML"/> - <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/> - <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/> - </test> -</xml> -<xml name="manutest_PSMFeatureExtractor"> - <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/> - <param name="multiple_search_engines" value="true"/> - <param name="adv_opts_cond|adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|skip_db_check" value="true"/> - <param name="out_type" value="idxml"/> - <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/> - </test> - <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible --> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/> - <param name="multiple_search_engines" value="true"/> - <param name="adv_opts_cond|adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|skip_db_check" value="true"/> - <param name="out_type" value="mzid"/> - <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/> - </test> -</xml> -<xml name="manutest_QCCalculator"> - <test expect_num_outputs="1"><!-- took test data from another test w mzML input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/> - <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/> - </test> - <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,consensusXML input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/> - <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/> - <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/> - <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/> - </test> - <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,featureXML input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/> - <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/> - <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/> - <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/> - </test> -</xml> -<xml name="manutest_QCEmbedder"> - <!--TODO--> -</xml> -<xml name="manutest_QCExporter"> - <!--TODO--> -</xml> -<xml name="manutest_QCExtractor"> - <!--TODO--> -</xml> -<xml name="manutest_QCImporter"> - <!--TODO--> -</xml> -<xml name="manutest_QCMerger"> - <test expect_num_outputs="1"><!-- just using 2 outputs from QCCalculator as input (no2 did not work) --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/> - <output name="out" ftype="qcml" value="QCMerger.qcML"/> - </test> -</xml> -<xml name="manutest_QCShrinker"> - <test expect_num_outputs="1"><!-- just using an output of QCCalculator as input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="qcml" value="QCCalculator1.qcML"/> - <output name="out" ftype="qcml" value="QCShrinker.qcML"/> - </test> -</xml> -<xml name="manutest_RNADigestor"> - <test expect_num_outputs="1"><!--random RNAsequence input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="fasta" value="random_RNA.fa"/> - <output name="out" ftype="fasta" value="RNADigestor.fasta"/> - </test> -</xml> -<xml name="manutest_RNPxlXICFilter"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/> - <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/> - <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/> - </test> -</xml> -<xml name="manutest_RTEvaluation"> - <!-- just chosen an arbitrary input and autgenerated output--> - <test expect_num_outputs="1"> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/> - <output name="out" ftype="tabular" value="RTEvaluation.tsv"/> - </test> -</xml> -<xml name="manutest_SemanticValidator"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> - <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/> - <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4"> - <assert_contents><has_text text="Congratulations, the file is valid!"/></assert_contents> - </output> - </test> -</xml> -<xml name="manutest_SequenceCoverageCalculator"> - <test expect_num_outputs="1"><!-- took test data from another tool that also takes idXML and fasta as input --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/> - <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/> - <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpecLibCreator"> - <!--TODO could not find test data --> -</xml> -<xml name="manutest_SpectraFilterBernNorm"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterBernNorm.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterMarkerMower"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterMarkerMower.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterNLargest"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterNLargest.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterNormalizer"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterParentPeakMower"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterScaler"> - <test expect_num_outputs="1"> <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterScaler.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraFilterThresholdMower"> - <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> - <output name="out" value="SpectraFilterThresholdMower.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SpectraMerger"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/> - <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/> - </test> -</xml> -<xml name="manutest_SvmTheoreticalSpectrumGeneratorTrainer"> -<!-- -TODO model_output_file creates multiple files--> -</xml> -<xml name="manutest_TransformationEvaluation"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="trafoxml" value="FileInfo_16_input.trafoXML"/> - <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/> - <output name="out" ftype="trafoxml" value="TransformationEvaluation.trafoXML" compare="sim_size" delta="100000000"/> - </test> -</xml> -<xml name="manutest_XMLValidator"> - <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output--> - <param name="adv_opts_selector" value="advanced"/> - <param name="adv_opts_cond|test" value="true"/> - <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/> - <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4"> - <assert_contents><has_text text="Success: the file is valid!"/></assert_contents> - </output> - </test> -</xml> -<xml name="manutest_MetaboliteAdductDecharger"/><xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_FeatureFinderSuperHirn"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_SeedListGenerator"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_SequestAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/><xml name="manutest_DatabaseSuitability"/><xml name="manutest_StaticModification"/></macros>
--- a/prepare_test_data_manual.sh Fri Nov 06 19:42:25 2020 +0000 +++ b/prepare_test_data_manual.sh Thu Dec 01 18:59:52 2022 +0000 @@ -86,10 +86,13 @@ PhosphoScoring -in spectra.mzML -id MSGFPlusAdapter_1_out1.tmp -out PhosphoScoring.idxml > PhosphoScoring.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.idxml > PSMFeatureExtractor_1.stdout 2> stderr +# TODO PSMFeatureExtractor should have auto tests with 2.7 https://github.com/OpenMS/OpenMS/pull/5087 +PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out_type idXML -out PSMFeatureExtractor.idxml > PSMFeatureExtractor_1.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi -PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.mzid > PSMFeatureExtractor_2.stdout 2> stderr +PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out_type mzid -out PSMFeatureExtractor.mzid > PSMFeatureExtractor_2.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi +PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML -out_type idXML -out PSMFeatureExtractor_3.idXML > PSMFeatureExtractor_3.stdout 2> stderr +if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_3 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi QCCalculator -test -in OpenPepXL_input.mzML -out QCCalculator1.qcML > QCCalculator_1.stdout 2> stderr if [[ "$?" -ne "0" ]]; then >&2 echo 'QCCalculator_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/ /')"; fi
--- a/readme.md Fri Nov 06 19:42:25 2020 +0000 +++ b/readme.md Thu Dec 01 18:59:52 2022 +0000 @@ -22,11 +22,14 @@ Manual updates should only be done to -- the `@GALAXY_VERSION@"` token in `macros.xml` - and the manually contributed tests in `macros_test.xml` (The goal is that all tools that do not have an automatically generated test are covered here) - the `hardcoded_params.json` files +Wrapper versions are managed in `bump.json`. For tools listed in the file +the wrapper version will be set accordingly and otherwise `0` is used. +For a major update of the tool version the bump file should be reset (to `{}`). + In a few cases patches may be acceptable. Installation @@ -71,10 +74,15 @@ Preprocessing: -- For each input / output data set parameter a directory is crated (named by - the parameter) - For input data set parameters the links to the actual location of the data - sets are created + sets are created, the link names are `element_identifier`.`EXT`, where `EXT` + is an extension that is known by OpenMS +- In order to avoid name collisions for the created links each is placed in a + unique directory: `PARAM_NAME/DATASET_ID`, where `PARAM_NAME` is the name + of the parameter and `DATASET_ID` is the id of the Galaxy dataset +- the same happens for output parameters that are in 1:1 correspondence with + an input parameter + Main:
--- a/test-data.sh Fri Nov 06 19:42:25 2020 +0000 +++ b/test-data.sh Thu Dec 01 18:59:52 2022 +0000 @@ -1,22 +1,25 @@ #!/usr/bin/env bash -VERSION=2.6 -FILETYPES="filetypes.txt" -CONDAPKG="https://anaconda.org/bioconda/openms/2.6.0/download/linux-64/openms-2.6.0-h4afb90d_0.tar.bz2" +VERSION=2.8 +FILETYPES="aux/filetypes.txt" +CONDAPKG="https://anaconda.org/bioconda/openms/2.8.0/download/linux-64/openms-2.8.0-h7ca0330_0.tar.bz2" # import the magic . ./generate-foo.sh # install conda if [ -z "$tmp" ]; then - tmp=$(mktemp -d) - created="yes" + tmp=$(mktemp -d) + created="yes" fi export OPENMSGIT="$tmp/OpenMS$VERSION.0-git" export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/" -export OPENMSENV="$tmp/OpenMS$VERSION-env" -export CTDCONVERTER="$tmp/CTDConverter" +export OPENMSENV="OpenMS$VERSION-env" + +if [ -z "$CTDCONVERTER" ]; then + export CTDCONVERTER="$tmp/CTDConverter" +fi if [[ -z "$1" ]]; then autotests="/dev/null" @@ -25,11 +28,11 @@ fi if type conda > /dev/null; then - true + true else - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh - bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda" - source "$tmp/miniconda/bin/activate" + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh + bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda" + source "$tmp/miniconda/bin/activate" fi eval "$(conda shell.bash hook)" @@ -42,24 +45,27 @@ echo "Clone OpenMS $VERSION sources" if [[ ! -d $OPENMSGIT ]]; then - git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT - cd $OPENMSGIT - git submodule init - git submodule update - cd - + # TODO >2.8 reenable original release branch .. also in else branch + # the plus branch contains commits from https://github.com/OpenMS/OpenMS/pull/5920 and https://github.com/OpenMS/OpenMS/pull/5917 + # git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT + git clone -b release/$VERSION.0-plus https://github.com/bernt-matthias/OpenMS.git $OPENMSGIT + cd $OPENMSGIT + git submodule init + git submodule update + cd - else - cd $OPENMSGIT - git pull origin release/$VERSION.0 - cd - + cd $OPENMSGIT + git pull origin release/$VERSION.0-plus + cd - fi echo "Create OpenMS $VERSION conda env" # TODO currently add lxml (needed by CTDConverter) # TODO for some reason a to recent openjdk is used if conda env list | grep "$OPENMSENV"; then - true + true else - conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -p $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.4 lxml + conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION omssa=2.1.9 ctdopts=1.5 lxml # chmod -R u-w $OPENMSENV fi ############################################################################### @@ -69,10 +75,10 @@ echo "Download OpenMS $VERSION package $CONDAPKG" if [[ ! -d $OPENMSPKG ]]; then - mkdir $OPENMSPKG - wget -q -P $OPENMSPKG/ "$CONDAPKG" - tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/ - rm $OPENMSPKG/"$(basename $CONDAPKG)" + mkdir $OPENMSPKG + wget -q -P $OPENMSPKG/ "$CONDAPKG" + tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/ + rm $OPENMSPKG/"$(basename $CONDAPKG)" fi ############################################################################### @@ -81,40 +87,46 @@ ############################################################################### echo "Clone CTDConverter" if [[ ! -d $CTDCONVERTER ]]; then - #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter - git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER + #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter + git clone -b topic/fix-selects2 https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER else - cd $CTDCONVERTER - git pull origin topic/cdata - cd - + cd $CTDCONVERTER + git pull origin topic/fix-selects2 + cd - fi +conda activate $OPENMSENV +cd $CTDCONVERTER +python -m pip install . --no-deps +cd - +conda deactivate -############################################################################### -## copy all the test data files to test-data -## most of it (outputs) will be overwritten later, but its needed for -## prepare_test_data -############################################################################### + +# ############################################################################### +# ## copy all the test data files to test-data +# ## most of it (outputs) will be overwritten later, but its needed for +# ## prepare_test_data +# ############################################################################### echo "Get test data" -find test-data -type f,l,d ! -name "*fa" ! -name "*loc" -delete +find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" -delete cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/ cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/ cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/ cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/ -if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then - wget -nc https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML - mv MetaboliteSpectralDB.mzML test-data/ +if [ ! -f test-data/MetaboliteSpectralDB.mzML ]; then + wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML + mv MetaboliteSpectralDB.mzML test-data/ fi ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv if [ ! -d test-data/pepnovo_models/ ]; then - mkdir -p /tmp/pepnovo - wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip - unzip PepNovo.20120423.zip -d /tmp/pepnovo/ - mv /tmp/pepnovo/Models test-data/pepnovo_models/ - rm PepNovo.20120423.zip - rm -rf /tmp/pepnovo + mkdir -p /tmp/pepnovo + wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip + unzip PepNovo.20120423.zip -d /tmp/pepnovo/ + mv /tmp/pepnovo/Models test-data/pepnovo_models/ + rm PepNovo.20120423.zip + rm -rf /tmp/pepnovo fi ############################################################################### ## generate ctd files using the binaries in the conda package @@ -124,17 +136,13 @@ rm -rf ctd mkdir -p ctd -# TODO because of https://github.com/OpenMS/OpenMS/issues/4641 -# this needs to be done from within test-data -cd test-data for i in $OPENMSPKG/bin/* do - b=$(basename $i) - echo $b - $b -write_ctd ../ctd/ - sed -i -e 's/²/^2/' ../ctd/$b.ctd + b=$(basename $i) + echo $b + $b -write_ctd ctd/ + sed -i -e 's/²/^2/' ctd/$b.ctd done -cd - ############################################################################### ## fix ini files: OpenMS test data contains ini files with outdated ini files. ## e.g. variables might be in different nodes, outdated variables present, new @@ -146,17 +154,17 @@ echo "Update test INI files" for ini in test-data/*ini do - tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/') - bin=$(which $tool) - if [[ -z $bin ]]; then + tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/') + bin=$(which $tool) + if [[ -z $bin ]]; then >&2 echo "missing binary to convert $ini" - continue - fi - cp $ini $ini.backup - $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr - if [[ "$?" -ne "0" ]]; then - >&2 echo "could not convert $ini" - fi + continue + fi + cp $ini $ini.backup + $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr + if [[ "$?" -ne "0" ]]; then + >&2 echo "could not convert $ini" + fi done ############################################################################### @@ -185,17 +193,17 @@ prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh -# prepare_test_data > tmp_test_data.sh -# # remove calls not needed for the tools listed in any .list file -# echo LIST $LIST -# if [ ! -z "$LIST" ]; then -# REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//') -# else -# REX=".*" -# fi -# echo REX $REX -# cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh -# rm tmp_test_data.sh +## prepare_test_data > tmp_test_data.sh +## # remove calls not needed for the tools listed in any .list file +## echo LIST $LIST +## if [ ! -z "$LIST" ]; then +## REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//') +## else +## REX=".*" +## fi +## echo REX $REX +## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh +## rm tmp_test_data.sh echo "Execute test shell script" chmod u+x prepare_test_data.sh @@ -204,14 +212,13 @@ cd - || exit -############################################################################### -## create/update test data for the manually generated tests -## - run convert once with the manual tests only and -## - update test-data (needs to run 2x) -############################################################################### +# ############################################################################### +# ## create/update test data for the manually generated tests +# ## - run convert once with the manual tests only and +# ## - update test-data (needs to run 2x) +# ############################################################################### echo "Execute test shell script for manually curated tests" chmod u+x prepare_test_data_manual.sh - cd ./test-data || exit ../prepare_test_data_manual.sh cd - || exit @@ -220,22 +227,28 @@ ############################################################################### ## auto generate tests ############################################################################### + echo "Write test macros to $autotests" echo "<macros>" > "$autotests" -for i in $(ls *xml |grep -v macros) + +for i in $(ls ctd/*ctd) do - b=$(basename "$i" .xml) - get_tests2 "$b" >> "$autotests" + b=$(basename "$i" .ctd) + get_tests2 "$b" >> "$autotests" done echo "</macros>" >> "$autotests" -echo "Create test data links" -link_tmp_files +# echo "Create test data links" +# Breaks DecoyDatabase +# link_tmp_files # tests for tools using output_prefix parameters can not be auto generated # hence we output the tests for manual curation in macros_test.xml # and remove them from the autotests -# -> OpenSwathFileSplitter IDRipper MzMLSplitter +# -> OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator +# TODO reevaluate in >2.8 +# - https://github.com/OpenMS/OpenMS/pull/5873 +# - https://github.com/OpenMS/OpenMS/pull/5912 # # Furthermore we remove tests for tools without binaries in conda # -> MSFragger MaRaClusterAdapter NovorAdapter @@ -243,23 +256,23 @@ # not able to specify composite test data # -> SpectraSTSearchAdapter if [[ ! -z "$1" ]]; then - echo "" > macros_discarded_auto.xml - for i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter - do - echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml - xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml - echo "</xml>" >> macros_discarded_auto.xml - xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp - mv tmp macros_autotest.xml - done - >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml" + echo "" > macros_discarded_auto.xml + for i in OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter + do + echo "<xml name=\"manutest_$i\">" >> macros_discarded_auto.xml + xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >> macros_discarded_auto.xml + echo "</xml>" >> macros_discarded_auto.xml + xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp + mv tmp macros_autotest.xml + done + >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml" fi conda deactivate ## remove broken symlinks in test-data find test-data/ -xtype l -delete -# if [ ! -z "$created" ]; then -# echo "Removing temporary directory" -# rm -rf "$tmp" -# fi +if [ ! -z "$created" ]; then + echo "Removing temporary directory" + rm -rf "$tmp" +fi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pepnovo_models.loc Thu Dec 01 18:59:52 2022 +0000 @@ -0,0 +1,13 @@ +#name value path +default_models CID_IT_TRYP ${__HERE__}/pepnovo_models/ +default_models LTQ_COMP ${__HERE__}/pepnovo_models/ +default_models DBC4_PEAK ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_TAG5 ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_TAG6 ${__HERE__}/pepnovo_models/ +default_models ITDNV_PEAK ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_SCORE ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_TAG3 ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_DNVPART ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_TAG4 ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_DB ${__HERE__}/pepnovo_models/ +default_models CID_IT_TRYP_CSP ${__HERE__}/pepnovo_models/
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random.fa Thu Dec 01 18:59:52 2022 +0000 @@ -0,0 +1,18 @@ +>RND24402 Randomly generated sequence, created by ExPASy tool RandSeq, using average amino acid composition +LALLTDKYSVTKSIKGYAGQQQKCTDDEGLAEDSAAMSLVPIRAAWTISVSVDLFYLGIV +TNVTKDSVEHLVGIPLVTHEFMASRCEMRGQVVSATFGSWQKAESKAYRIPLKATPLDEF +VESAVYLFGGSSNEYECVLIGNSHPVLIFLDIDAVPGARKPRTGFFMAEGFHSKGETRAL +VGKSPPLGEYRKGAFHFTFPIKEAIRLGPPKKRIMGYRDALEGGLNHYVQTQVLVLLPMI +QVARRWENGLGLLVGKFLKLPTHPLDLNQVTLCWSEAVTEDNKRFLLTIKTSAQGKSAPT +SHINYVPQHNSMELMAINGSPFAAQHKSNDEIESMRDLSKLYADAETLESHGERGVRHQA +TETKISKVTNLRRKLPQLLDLNVVDNACNWESVGAHVLEYVLVNLYLKELQEPKVELQPR +LNETTMKAGASSLGVESGASAHSFYKGGVSEAKLRFRHVATPAAARIWWCVVMFRINRRY +DGITYNSVGEQLSGVHEYVRAAQLFGLTTGKNLRSTGIVIIKLSTAIDLECLVQAKPKEA +YVLANDYIGAKPHPARLETGPALVLFIVETINNDTLNAAILITALGGKFLNVRPDLLFGV +QALFGCVRMFRHADCTIGREKFVQTEISHKAKFLYEINEFFLERILQFEEAKSPVGAPAY +DIPIGRGLVMDSSTDLWNIYVVELISGQEKRTGIDPDTPMGTSHNLYMTDARLDERDQRS +FLNSEFVKPSKLANGSEWADPYVEPDKTEVIAFFPATLIVIMADGSALNGQVCIQPAKDN +SKMADDLATVHIGQDRPCDWGISASHEYDEVNRPARINGVMMQQLMAEDNQGPGASPRDQ +MGDADDLKEIKWNKYVIDNEIIGRERGISAERVKIFLGDTLTARGLLDSPPGQTKVFDLR +PRQSDKNQSGMFKRDQNAMYFPLEYDRIGAQTDTGSLYSTLITKFASISIDLVKLSMPRE +KQIDEERLHSEFIENQKRSALPAVQKNLACISCVEACRGT
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/random_RNA.fa Thu Dec 01 18:59:52 2022 +0000 @@ -0,0 +1,2 @@ +> random RNA +GUGUUACUGCCACGAAACAAAAUGUUCAAGACACCGGGCGCCAUCUGUAUAUUACUCGCCAAUCAGACGGUCUGCAACGCUACAGACAUGGAGCUCAGCGCUGACGAUGUCGCCGGACCAAGUACGAUCACUUUGCUCGUGCAAAUGUUCGUCCGCAUUGGGCACUAUAACUCGAAUUGUCGAAUCCGGGUGGCGAGCCGCCACUUAUAGGAUAAAUAUUCAAACUAACAUUAUGGCGCCAAAUCUGCAAUCUCUACUUUAGACAUUAUAUACCCACAUUUACAAUUAGAGUUAUUAUUAGUUAACGUGUGCCAGAGCAGGGAUGGCUCUUGUCAGCCAUAGUUGUGUGAACGGGCUGUAUUUCCUUCCUAAUUAUAGAGCGGCACCGGAAAGCAAUGCACGAUCCACGAGGGCACUUCACAUGGUCACAAACAGUCAUUCUGGUACCCUGAUUCGUUCCCGAAAGGGAAGUAUAUACACGGCCCCCGUGUAUAUCGCCAGUCACACGGCAGGAGCGAGAGUUCGUUUGUAUACAUGCCCAGGAGCCUUCUCUAACUUUUGAAGCUGUGCAACUUUGUUGGCGCGUCACCACUAAGUCAGCUUAAUAGACAGCAGAUGGGAGAAUUUACCAUUUCAUUUUGUCCGAGCUGAUACCGGUAGGUCAUCUCUAAUCACCCGUUAUCCUCUCGUAAUAUAAUCGCUACUAAGGUAUGAAGGUGUCUGCGAAAGGUAACGUAAAUCAUUCUCGGCUCCUUGCAAAGUACGACUAGGAUCCAUCGUACACAUCCGGACGAAGAUGUAAAAUUGACGCCCCUGUAGGCCGUGAGACAGACGUGAGCCAAACCAUCUGCUCUACUUCUGGAGGCCUUGAAUAGUGGCGCGUUGUGUAAUCUUAAGAGAGAUUUUACUUGGAAUUACAGCCUACUUUGACCAGUAGCGCAUUGUGAACAAAUAUUCCCGUACGCGUCCAAUUGCAGCAAAACGUGGGCCUGUGUCCAGU
--- a/tools_blacklist.txt Fri Nov 06 19:42:25 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -# seems not possible for 2.5 https://github.com/OpenMS/OpenMS/issues/4426 -# DigestorMotif - -# deprecated https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_IDDecoyProbability.html -# https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/a16242.html -IDDecoyProbability - -# personal communication with author V. Bafna: -# "InsPect is no longer maintained as there are many better tools including MS-GF+" -InspectAdapter - -# licence? see https://github.com/bioconda/bioconda-recipes/issues/18953 -#MSFraggerAdapter - -# https://github.com/OpenMS/OpenMS/issues/4550#issuecomment-594065727 -ProteomicsLFQ - -# https://github.com/OpenMS/OpenMS/issues/4401 -InclusionExclusionListCreator -RTPredict -PTPredict