Mercurial > repos > galaxyp > openms_idfilter
changeset 15:a5d785af0ad8 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:21:56 +0000 |
| parents | ca799a7246e7 |
| children | 093a52644633 |
| files | 404-urls.patch IDFilter.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, 2140 insertions(+), 28871 deletions(-) [+] |
line wrap: on
line diff
--- a/404-urls.patch Fri Nov 06 19:40:55 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/IDFilter.xml Fri Nov 06 19:40:55 2020 +0000 +++ b/IDFilter.xml Thu Dec 01 19:21:56 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: [ID Processing]--> -<tool id="IDFilter" name="IDFilter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="IDFilter" name="IDFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Filters results from protein or peptide identification engines based on different criteria.</description> <macros> <token name="@EXECUTABLE@">IDFilter</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -81,24 +79,24 @@ <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="consensusxml,idxml" optional="false" label="input file" help=" select consensusxml,idxml data sets(s)"/> - <param name="var_mods" argument="-var_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep only peptide hits with variable modifications (as defined in the 'SearchParameters' section of the input file)" help=""/> - <param name="remove_shared_peptides" argument="-remove_shared_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only peptides matching exactly one protein are kept" help="Remember that isoforms count as different proteins!"/> - <param name="keep_unreferenced_protein_hits" argument="-keep_unreferenced_protein_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Proteins not referenced by a peptide are retained in the IDs" help=""/> - <param name="remove_decoys" argument="-remove_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove proteins according to the information in the user parameters" help="Usually used in combination with 'delete_unreferenced_peptide_hits'"/> - <param name="delete_unreferenced_peptide_hits" argument="-delete_unreferenced_peptide_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Peptides not referenced by any protein are deleted in the IDs" help="Usually used in combination with 'score:prot' or 'thresh:prot'"/> + <param argument="-in" type="data" format="consensusxml,idxml" optional="false" label="input file" help=" select consensusxml,idxml data sets(s)"/> + <param argument="-var_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep only peptide hits with variable modifications (as defined in the 'SearchParameters' section of the input file)" help=""/> + <param argument="-remove_shared_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only peptides matching exactly one protein are kept" help="Remember that isoforms count as different proteins!"/> + <param argument="-keep_unreferenced_protein_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Proteins not referenced by a peptide are retained in the IDs" help=""/> + <param argument="-remove_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove proteins according to the information in the user parameters" help="Usually used in combination with 'delete_unreferenced_peptide_hits'"/> + <param argument="-delete_unreferenced_peptide_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Peptides not referenced by any protein are deleted in the IDs" help="Usually used in combination with 'score:prot' or 'thresh:prot'"/> <section name="precursor" title="Filtering by precursor attributes (RT, m/z, charge, length)" help="" expanded="false"> <param name="rt" argument="-precursor:rt" type="text" optional="true" value=":" label="Retention time range to extract" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="rt"/> </param> <param name="mz" argument="-precursor:mz" type="text" optional="true" value=":" label="Mass-to-charge range to extract" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="mz"/> </param> <param name="length" argument="-precursor:length" type="text" optional="true" value=":" label="Keep only peptide hits with a sequence length in this range" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="length"/> </param> <param name="charge" argument="-precursor:charge" type="text" optional="true" value=":" label="Keep only peptide hits with charge states in this range" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="charge"/> </param> </section> <section name="score" title="Filtering by peptide/protein score" help="" expanded="false"> @@ -109,13 +107,12 @@ <section name="whitelist" title="Filtering by whitelisting (only peptides/proteins from a given set can pass)" help="" expanded="false"> <param name="proteins" argument="-whitelist:proteins" type="data" format="fasta" optional="true" label="Filename of a FASTA file containing protein sequences" help="All peptides that are not referencing a protein in this file are removed.. All proteins whose accessions are not present in this file are removed select fasta data sets(s)"/> <param name="protein_accessions" argument="-whitelist:protein_accessions" type="text" optional="true" value="" label="All peptides that do not reference at least one of the provided protein accession are removed" help="Only proteins of the provided list are retained (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_string_val"/> - <expand macro="list_string_san"/> + <expand macro="list_string_val" name="protein_accessions"/> + <expand macro="list_string_san" name="protein_accessions"/> </param> <param name="peptides" argument="-whitelist:peptides" type="data" format="idxml" optional="true" label="Only peptides with the same sequence and modification assignment as any peptide in this file are kept" help="Use with 'whitelist:ignore_modifications' to only compare by sequence.. select idxml data sets(s)"/> <param name="ignore_modifications" argument="-whitelist:ignore_modifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compare whitelisted peptides by sequence only" help=""/> <param name="modifications" argument="-whitelist:modifications" multiple="true" type="select" optional="true" label="Keep only peptides with sequences that contain (any of) the selected modification(s)" help=""> - <option value="">default (nothing chosen)</option> <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> @@ -1485,7 +1482,6 @@ <option value="Glu->Pro (E)">Glu->Pro (E)</option> <option value="Glu->pyro-Glu (N-term E)">Glu->pyro-Glu (N-term E)</option> <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> - <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> <option value="Glu->Ser (E)">Glu->Ser (E)</option> @@ -3044,19 +3040,18 @@ <option value="ZGB (K)">ZGB (K)</option> <option value="ZGB (N-term)">ZGB (N-term)</option> <option value="ZQG (K)">ZQG (K)</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="modifications"/> </param> </section> <section name="blacklist" title="Filtering by blacklisting (only peptides/proteins NOT present in a given set can pass)" help="" expanded="false"> <param name="proteins" argument="-blacklist:proteins" type="data" format="fasta" optional="true" label="Filename of a FASTA file containing protein sequences" help="All peptides that are referencing a protein in this file are removed.. All proteins whose accessions are present in this file are removed select fasta data sets(s)"/> <param name="protein_accessions" argument="-blacklist:protein_accessions" type="text" optional="true" value="" label="All peptides that reference at least one of the provided protein accession are removed" help="Only proteins not in the provided list are retained (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_string_val"/> - <expand macro="list_string_san"/> + <expand macro="list_string_val" name="protein_accessions"/> + <expand macro="list_string_san" name="protein_accessions"/> </param> <param name="peptides" argument="-blacklist:peptides" type="data" format="idxml" optional="true" label="Peptides with the same sequence and modification assignment as any peptide in this file are filtered out" help="Use with 'blacklist:ignore_modifications' to only compare by sequence.. select idxml data sets(s)"/> <param name="ignore_modifications" argument="-blacklist:ignore_modifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compare blacklisted peptides by sequence only" help=""/> <param name="modifications" argument="-blacklist:modifications" multiple="true" type="select" optional="true" label="Remove all peptides with sequences that contain (any of) the selected modification(s)" help=""> - <option value="">default (nothing chosen)</option> <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> @@ -4426,7 +4421,6 @@ <option value="Glu->Pro (E)">Glu->Pro (E)</option> <option value="Glu->pyro-Glu (N-term E)">Glu->pyro-Glu (N-term E)</option> <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> - <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> <option value="Glu->Ser (E)">Glu->Ser (E)</option> @@ -5985,95 +5979,98 @@ <option value="ZGB (K)">ZGB (K)</option> <option value="ZGB (N-term)">ZGB (N-term)</option> <option value="ZQG (K)">ZQG (K)</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="modifications"/> + </param> + <param name="RegEx" argument="-blacklist:RegEx" type="text" optional="true" value="" label="Remove all peptides with (unmodified) sequences matched by the RegEx" help="e.g. [BJXZ] removes ambiguous peptides"> + <expand macro="list_string_san" name="RegEx"/> </param> </section> <section name="in_silico_digestion" title="This filter option removes peptide hits which are not in the list of in silico peptides generated by the rules specified below" help="" expanded="false"> <param name="fasta" argument="-in_silico_digestion:fasta" type="data" format="fasta" optional="true" label="fasta protein sequence database" help=" select fasta data sets(s)"/> - <param name="enzyme" argument="-in_silico_digestion:enzyme" type="select" optional="false" label="enzyme used for the digestion of the sample" help=""> + <param name="enzyme" argument="-in_silico_digestion:enzyme" type="select" optional="true" label="enzyme used for the digestion of the sample" help=""> <option value="Trypsin" selected="true">Trypsin</option> + <option value="cyanogen-bromide">cyanogen-bromide</option> + <option value="Clostripain/P">Clostripain/P</option> + <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> + <option value="no cleavage">no cleavage</option> + <option value="unspecific cleavage">unspecific cleavage</option> + <option value="Arg-C/P">Arg-C/P</option> + <option value="Formic_acid">Formic_acid</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-N">Lys-N</option> + <option value="leukocyte elastase">leukocyte elastase</option> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="Alpha-lytic protease">Alpha-lytic protease</option> + <option value="Lys-C/P">Lys-C/P</option> + <option value="PepsinA">PepsinA</option> + <option value="TrypChymo">TrypChymo</option> <option value="Trypsin/P">Trypsin/P</option> <option value="V8-DE">V8-DE</option> <option value="V8-E">V8-E</option> - <option value="leukocyte elastase">leukocyte elastase</option> - <option value="Lys-C">Lys-C</option> - <option value="Lys-N">Lys-N</option> - <option value="Asp-N">Asp-N</option> - <option value="Asp-N/B">Asp-N/B</option> - <option value="Lys-C/P">Lys-C/P</option> - <option value="PepsinA">PepsinA</option> - <option value="TrypChymo">TrypChymo</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="2-iodobenzoate">2-iodobenzoate</option> + <option value="iodosobenzoate">iodosobenzoate</option> <option value="staphylococcal protease/D">staphylococcal protease/D</option> <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> <option value="Glu-C+P">Glu-C+P</option> <option value="PepsinA + P">PepsinA + P</option> - <option value="cyanogen-bromide">cyanogen-bromide</option> - <option value="Clostripain/P">Clostripain/P</option> - <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> - <option value="Arg-C/P">Arg-C/P</option> - <option value="Asp-N_ambic">Asp-N_ambic</option> - <option value="Chymotrypsin">Chymotrypsin</option> - <option value="no cleavage">no cleavage</option> - <option value="unspecific cleavage">unspecific cleavage</option> + <option value="Arg-C">Arg-C</option> <option value="Chymotrypsin/P">Chymotrypsin/P</option> <option value="CNBr">CNBr</option> - <option value="Formic_acid">Formic_acid</option> - <option value="Arg-C">Arg-C</option> - <option value="proline endopeptidase">proline endopeptidase</option> - <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> - <option value="Alpha-lytic protease">Alpha-lytic protease</option> - <option value="2-iodobenzoate">2-iodobenzoate</option> - <option value="iodosobenzoate">iodosobenzoate</option> - <expand macro="list_string_san"/> + <option value="Asp-N">Asp-N</option> + <option value="Asp-N/B">Asp-N/B</option> + <expand macro="list_string_san" name="enzyme"/> </param> - <param name="specificity" argument="-in_silico_digestion:specificity" display="radio" type="select" optional="false" label="Specificity of the filte" help=""> + <param name="specificity" argument="-in_silico_digestion:specificity" type="select" optional="true" label="Specificity of the filte" help=""> <option value="none">none</option> <option value="semi">semi</option> <option value="full" selected="true">full</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="specificity"/> </param> <param name="missed_cleavages" argument="-in_silico_digestion:missed_cleavages" type="integer" optional="true" min="-1" value="-1" label="range of allowed missed cleavages in the peptide sequences" help="By default missed cleavages are ignored"/> <param name="methionine_cleavage" argument="-in_silico_digestion:methionine_cleavage" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow methionine cleavage at the N-terminus of the protein" help=""/> </section> <section name="missed_cleavages" title="This filter option removes peptide hits which do not confirm with the allowed missed cleavages specified below" help="" expanded="false"> <param name="number_of_missed_cleavages" argument="-missed_cleavages:number_of_missed_cleavages" type="text" optional="true" value=":" label="range of allowed missed cleavages in the peptide sequences" help="For example: 0:1 -> peptides with two or more missed cleavages will be removed,. 0:0 -> peptides with any missed cleavages will be removed"> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="number_of_missed_cleavages"/> </param> - <param name="enzyme" argument="-missed_cleavages:enzyme" type="select" optional="false" label="enzyme used for the digestion of the sample" help=""> + <param name="enzyme" argument="-missed_cleavages:enzyme" type="select" optional="true" label="enzyme used for the digestion of the sample" help=""> <option value="Trypsin" selected="true">Trypsin</option> + <option value="cyanogen-bromide">cyanogen-bromide</option> + <option value="Clostripain/P">Clostripain/P</option> + <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> + <option value="no cleavage">no cleavage</option> + <option value="unspecific cleavage">unspecific cleavage</option> + <option value="Arg-C/P">Arg-C/P</option> + <option value="Formic_acid">Formic_acid</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-N">Lys-N</option> + <option value="leukocyte elastase">leukocyte elastase</option> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="Alpha-lytic protease">Alpha-lytic protease</option> + <option value="Lys-C/P">Lys-C/P</option> + <option value="PepsinA">PepsinA</option> + <option value="TrypChymo">TrypChymo</option> <option value="Trypsin/P">Trypsin/P</option> <option value="V8-DE">V8-DE</option> <option value="V8-E">V8-E</option> - <option value="leukocyte elastase">leukocyte elastase</option> - <option value="Lys-C">Lys-C</option> - <option value="Lys-N">Lys-N</option> - <option value="Asp-N">Asp-N</option> - <option value="Asp-N/B">Asp-N/B</option> - <option value="Lys-C/P">Lys-C/P</option> - <option value="PepsinA">PepsinA</option> - <option value="TrypChymo">TrypChymo</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="2-iodobenzoate">2-iodobenzoate</option> + <option value="iodosobenzoate">iodosobenzoate</option> <option value="staphylococcal protease/D">staphylococcal protease/D</option> <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> <option value="Glu-C+P">Glu-C+P</option> <option value="PepsinA + P">PepsinA + P</option> - <option value="cyanogen-bromide">cyanogen-bromide</option> - <option value="Clostripain/P">Clostripain/P</option> - <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> - <option value="Arg-C/P">Arg-C/P</option> - <option value="Asp-N_ambic">Asp-N_ambic</option> - <option value="Chymotrypsin">Chymotrypsin</option> - <option value="no cleavage">no cleavage</option> - <option value="unspecific cleavage">unspecific cleavage</option> + <option value="Arg-C">Arg-C</option> <option value="Chymotrypsin/P">Chymotrypsin/P</option> <option value="CNBr">CNBr</option> - <option value="Formic_acid">Formic_acid</option> - <option value="Arg-C">Arg-C</option> - <option value="proline endopeptidase">proline endopeptidase</option> - <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> - <option value="Alpha-lytic protease">Alpha-lytic protease</option> - <option value="2-iodobenzoate">2-iodobenzoate</option> - <option value="iodosobenzoate">iodosobenzoate</option> - <expand macro="list_string_san"/> + <option value="Asp-N">Asp-N</option> + <option value="Asp-N/B">Asp-N/B</option> + <expand macro="list_string_san" name="enzyme"/> </param> </section> <section name="rt" title="Filtering by RT predicted by 'RTPredict'" help="" expanded="false"> @@ -6082,29 +6079,30 @@ </section> <section name="mz" title="Filtering by mass erro" help="" expanded="false"> <param name="error" argument="-mz:error" type="float" optional="true" value="-1.0" label="Filtering by deviation to theoretical mass (disabled for negative values)" help=""/> - <param name="unit" argument="-mz:unit" display="radio" type="select" optional="false" label="Absolute or relative erro" help=""> + <param name="unit" argument="-mz:unit" type="select" optional="true" label="Absolute or relative erro" help=""> <option value="Da">Da</option> <option value="ppm" selected="true">ppm</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="unit"/> </param> </section> <section name="best" title="Filtering best hits per spectrum (for peptides) or from proteins" help="" expanded="false"> + <param name="n_spectra" argument="-best:n_spectra" type="integer" optional="true" min="0" value="0" label="Keep only the 'n' best spectra" help="(i.e., PeptideIdentifications) (for n > 0). A spectrum is considered better if it has a higher scoring peptide hit than the other spectrum"/> <param name="n_peptide_hits" argument="-best:n_peptide_hits" type="integer" optional="true" min="0" value="0" label="Keep only the 'n' highest scoring peptide hits per spectrum (for n > 0)" help=""/> <param name="n_protein_hits" argument="-best:n_protein_hits" type="integer" optional="true" min="0" value="0" label="Keep only the 'n' highest scoring protein hits (for n > 0)" help=""/> <param name="strict" argument="-best:strict" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep only the highest scoring peptide hit" help="Similar to n_peptide_hits=1, but if there are ties between two or more highest scoring hits, none are kept"/> <param name="n_to_m_peptide_hits" argument="-best:n_to_m_peptide_hits" type="text" optional="true" value=":" label="Peptide hit rank range to extracts" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="n_to_m_peptide_hits"/> </param> </section> <expand macro="adv_opts_macro"> - <param name="remove_duplicate_psm" argument="-remove_duplicate_psm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Removes duplicated PSMs per spectrum and retains the one with the higher score" help=""/> - <param name="remove_peptide_hits_by_metavalue" argument="-remove_peptide_hits_by_metavalue" type="text" optional="true" value="" label="Expects a 3-tuple (=3 entries in the list)" help="i.e. <name> 'lt|eq|gt|ne' <value>; the first is the name of meta value, followed by the comparison operator (equal, less, greater, not equal) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)! (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_string_val"/> - <expand macro="list_string_san"/> + <param argument="-remove_duplicate_psm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Removes duplicated PSMs per spectrum and retains the one with the higher score" help=""/> + <param argument="-remove_peptide_hits_by_metavalue" type="text" optional="true" value="" label="Expects a 3-tuple (=3 entries in the list)" help="i.e. <name> 'lt|eq|gt|ne' <value>; the first is the name of meta value, followed by the comparison operator (equal, less, greater, not equal) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)! (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val" name="remove_peptide_hits_by_metavalue"/> + <expand macro="list_string_san" name="remove_peptide_hits_by_metavalue"/> </param> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> + <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> @@ -6117,13 +6115,1811 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_IDFilter"/> - <expand macro="manutest_IDFilter"/> + <tests><!-- TOPP_IDFilter_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_1_input.idXML"/> + <output name="out" file="IDFilter_1_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_3 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_3_input.idXML"/> + <output name="out" file="IDFilter_3_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </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"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_4 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_4_input.idXML"/> + <output name="out" file="IDFilter_4_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_5 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_5_input.idXML"/> + <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_5a --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_5_input.idXML"/> + <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_5b --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_5_input.idXML"/> + <output name="out" file="IDFilter_5b_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_5c --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_5_input.idXML"/> + <output name="out" file="IDFilter_5c_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_6 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_6_input.idXML"/> + <output name="out" file="IDFilter_6_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_7 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_7_input.idXML"/> + <output name="out" file="IDFilter_7_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_8 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_8_input.idXML"/> + <output name="out" file="IDFilter_8_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_9 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_9_input.idXML"/> + <output name="out" file="IDFilter_9_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_10 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_10_input.idXML"/> + <output name="out" file="IDFilter_10_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_11 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_11_input.idXML"/> + <output name="out" file="IDFilter_11_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_12 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_12_input.idXML"/> + <output name="out" file="IDFilter_12_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_13 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_13_input.idXML"/> + <output name="out" file="IDFilter_13_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_14 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_14_input.idXML"/> + <output name="out" file="IDFilter_14_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_15 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_15_input.idXML"/> + <output name="out" file="IDFilter_15_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_16 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_16_input.idXML"/> + <output name="out" file="IDFilter_16_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_17 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> + <output name="out" file="IDFilter_17_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_18 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> + <output name="out" file="IDFilter_18_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_19 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> + <output name="out" file="IDFilter_19_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_20 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_missed_cleavages_input.idXML"/> + <output name="out" file="IDFilter_20_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_21 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_16_input.idXML"/> + <output name="out" file="IDFilter_21_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_22 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDFilter_16_input.idXML"/> + <output name="out" file="IDFilter_22_output.idXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_23 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="IDMapper_2_output.consensusXML"/> + <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> + <!-- TOPP_IDFilter_24 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <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"/> + </section> + <param name="in" value="Epifany_3_out.consensusXML"/> + <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta_frac="0.7" 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"/> + </section> + <section name="blacklist"> + <param name="protein_accessions" value=""/> + <param name="ignore_modifications" value="false"/> + <param name="modifications"/> + <param name="RegEx" 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_spectra" value="0"/> + <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> </tests> <help><![CDATA[Filters results from protein or peptide identification engines based on different criteria. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IDFilter.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDFilter.html]]></help> <expand macro="references"/> </tool>
--- a/OMSSAAdapter.patch Fri Nov 06 19:40:55 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 19:40:55 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 19:40:55 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 19:40:55 2020 +0000 +++ b/fill_ctd.py Thu Dec 01 19:21:56 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 19:40:55 2020 +0000 +++ b/fill_ctd_clargs.py Thu Dec 01 19:21:56 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 19:40:55 2020 +0000 +++ b/generate-foo.sh Thu Dec 01 19:21:56 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 19:40:55 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 $i.json & -# done
--- a/hardcoded_params.json Fri Nov 06 19:40:55 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,236 +0,0 @@ -{ - "#": "blacklist parameters", - - "version": [{"value": "@"}], - "debug": [{"value": "@"}], - "algorithm:debug": [{"value": "@"}], - "java_memory": [{"value": "@"}], - "java_permgen": [{"value": "@"}], - "#": "type of input is always determined from the file extension ", - "in_type": [{"value": "@"}], - - "#": "tool specific blacklist parameters", - - "convert_back": [{"value": "@", "tools": ["OpenSwathMzMLFileCacher"]}], - "NET_executable": [{ - "value": "@", - "tools": ["FileConverter"] - }], - - - "params_file": [{"value": "@", "tools": ["SpectraSTSearchAdapter"]}], - - "#": "TODO not usable in 2.5 https://github.com/OpenMS/OpenMS/issues/4456, corresponding test currently disabled", - "consensus_out": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], - "#": "TODO would need treatment as prefix-output", - "output_directory": [{"value": "@", "tools": ["MaRaClusterAdapter"]}], - - "#": "hardcode parameter values", - - "comet_version": [{ - "value":"2016.01 rev. 3" - }], - "comet_executable": [{ - "value":"comet" - }], - "crux_executable": [{ - "value": "crux" - }], - "fido_executable": [{ - "value":"Fido" - }], - "fidocp_executable": [{ - "value":"FidoChooseParameters" - }], - "maracluster_executable": [{ - "value":"/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster" - }], - "mascot_directory": [{ - "value":"TODO" - }], - "myrimatch_executable": [{ - "value":"myrimatch" - }], - "omssa_executable": [{ - "value":"$(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 19:40:55 2020 +0000 +++ b/macros.xml Thu Dec 01 19:21:56 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 19:40:55 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 19:40:55 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 19:40:55 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 19:40:55 2020 +0000 +++ b/prepare_test_data_manual.sh Thu Dec 01 19:21:56 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$(cat stderr | sed 's/^/ /')"; fi
--- a/readme.md Fri Nov 06 19:40:55 2020 +0000 +++ b/readme.md Thu Dec 01 19:21:56 2022 +0000 @@ -22,11 +22,14 @@ Manual updates should only be done to -- the `@GALAXY_VERSION@"` token in `macros.xml` - and the manually contributed tests in `macros_test.xml` (The goal is that all tools that do not have an automatically generated test are covered here) - the `hardcoded_params.json` files +Wrapper versions are managed in `bump.json`. For tools listed in the file +the wrapper version will be set accordingly and otherwise `0` is used. +For a major update of the tool version the bump file should be reset (to `{}`). + In a few cases patches may be acceptable. Installation @@ -71,10 +74,15 @@ Preprocessing: -- For each input / output data set parameter a directory is crated (named by - the parameter) - For input data set parameters the links to the actual location of the data - sets are created + sets are created, the link names are `element_identifier`.`EXT`, where `EXT` + is an extension that is known by OpenMS +- In order to avoid name collisions for the created links each is placed in a + unique directory: `PARAM_NAME/DATASET_ID`, where `PARAM_NAME` is the name + of the parameter and `DATASET_ID` is the id of the Galaxy dataset +- the same happens for output parameters that are in 1:1 correspondence with + an input parameter + Main:
--- a/test-data.sh Fri Nov 06 19:40:55 2020 +0000 +++ b/test-data.sh Thu Dec 01 19:21:56 2022 +0000 @@ -1,22 +1,25 @@ #!/usr/bin/env bash -VERSION=2.6 -FILETYPES="filetypes.txt" -CONDAPKG="https://anaconda.org/bioconda/openms/2.6.0/download/linux-64/openms-2.6.0-h4afb90d_0.tar.bz2" +VERSION=2.8 +FILETYPES="aux/filetypes.txt" +CONDAPKG="https://anaconda.org/bioconda/openms/2.8.0/download/linux-64/openms-2.8.0-h7ca0330_0.tar.bz2" # import the magic . ./generate-foo.sh # install conda if [ -z "$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 19:21:56 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 19:21:56 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 19:21:56 2022 +0000 @@ -0,0 +1,2 @@ +> random RNA +GUGUUACUGCCACGAAACAAAAUGUUCAAGACACCGGGCGCCAUCUGUAUAUUACUCGCCAAUCAGACGGUCUGCAACGCUACAGACAUGGAGCUCAGCGCUGACGAUGUCGCCGGACCAAGUACGAUCACUUUGCUCGUGCAAAUGUUCGUCCGCAUUGGGCACUAUAACUCGAAUUGUCGAAUCCGGGUGGCGAGCCGCCACUUAUAGGAUAAAUAUUCAAACUAACAUUAUGGCGCCAAAUCUGCAAUCUCUACUUUAGACAUUAUAUACCCACAUUUACAAUUAGAGUUAUUAUUAGUUAACGUGUGCCAGAGCAGGGAUGGCUCUUGUCAGCCAUAGUUGUGUGAACGGGCUGUAUUUCCUUCCUAAUUAUAGAGCGGCACCGGAAAGCAAUGCACGAUCCACGAGGGCACUUCACAUGGUCACAAACAGUCAUUCUGGUACCCUGAUUCGUUCCCGAAAGGGAAGUAUAUACACGGCCCCCGUGUAUAUCGCCAGUCACACGGCAGGAGCGAGAGUUCGUUUGUAUACAUGCCCAGGAGCCUUCUCUAACUUUUGAAGCUGUGCAACUUUGUUGGCGCGUCACCACUAAGUCAGCUUAAUAGACAGCAGAUGGGAGAAUUUACCAUUUCAUUUUGUCCGAGCUGAUACCGGUAGGUCAUCUCUAAUCACCCGUUAUCCUCUCGUAAUAUAAUCGCUACUAAGGUAUGAAGGUGUCUGCGAAAGGUAACGUAAAUCAUUCUCGGCUCCUUGCAAAGUACGACUAGGAUCCAUCGUACACAUCCGGACGAAGAUGUAAAAUUGACGCCCCUGUAGGCCGUGAGACAGACGUGAGCCAAACCAUCUGCUCUACUUCUGGAGGCCUUGAAUAGUGGCGCGUUGUGUAAUCUUAAGAGAGAUUUUACUUGGAAUUACAGCCUACUUUGACCAGUAGCGCAUUGUGAACAAAUAUUCCCGUACGCGUCCAAUUGCAGCAAAACGUGGGCCUGUGUCCAGU
--- a/tools_blacklist.txt Fri Nov 06 19:40:55 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