Mercurial > repos > galaxyp > openms_cometadapter

comparison CometAdapter.xml @ 8:e75929491905 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:11:13 +0000
parents a4ada39679ae
children df0c77da6c87
comparison
equal deleted inserted replaced
7:59da0b9a95c8 8:e75929491905
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Identification]--> 3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="CometAdapter" name="CometAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="CometAdapter" name="CometAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Annotates MS/MS spectra using Comet.</description> 5 <description>Annotates MS/MS spectra using Comet.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">CometAdapter</token> 7 <token name="@EXECUTABLE@">CometAdapter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
64 <configfiles> 62 <configfiles>
65 <inputs name="args_json" data_style="paths"/> 63 <inputs name="args_json" data_style="paths"/>
66 <configfile name="hardcoded_json"><![CDATA[{"comet_executable": "comet", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 64 <configfile name="hardcoded_json"><![CDATA[{"comet_executable": "comet", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
67 </configfiles> 65 </configfiles>
68 <inputs> 66 <inputs>
69 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/> 67 <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
70 <param name="database" argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/> 68 <param argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/>
71 <param name="default_params_file" argument="-default_params_file" type="data" format="txt" optional="true" label="Default Comet params file" help="All parameters of this take precedence. A template file can be generated using 'comet.exe -p' select txt data sets(s)"/> 69 <param argument="-default_params_file" type="data" format="txt" optional="true" label="Default Comet params file" help="All parameters of this take precedence. A template file can be generated using 'comet.exe -p' select txt data sets(s)"/>
72 <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance)" help="See also precursor_error_units to set the unit"/> 70 <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (Comet parameter: peptide_mass_tolerance)" help="See also precursor_error_units to set the unit"/>
73 <param name="precursor_error_units" argument="-precursor_error_units" display="radio" type="select" optional="false" label="Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)" help=""> 71 <param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor monoisotopic mass tolerance for parameter precursor_mass_tolerance (Comet parameter: peptide_mass_units)" help="">
74 <option value="amu">amu</option> 72 <option value="amu">amu</option>
75 <option value="ppm" selected="true">ppm</option> 73 <option value="ppm" selected="true">ppm</option>
76 <option value="Da">Da</option> 74 <option value="Da">Da</option>
77 <expand macro="list_string_san"/> 75 <expand macro="list_string_san" name="precursor_error_units"/>
78 </param> 76 </param>
79 <param name="isotope_error" argument="-isotope_error" type="select" optional="false" label="This parameter controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement" help="Use -8/-4/0/4/8 only for SILAC"> 77 <param argument="-isotope_error" type="select" optional="true" label="This parameter controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement" help="Use -8/-4/0/4/8 only for SILAC">
80 <option value="off" selected="true">off</option> 78 <option value="off" selected="true">off</option>
81 <option value="0/1">0/1</option> 79 <option value="0/1">0/1</option>
82 <option value="0/1/2">0/1/2</option> 80 <option value="0/1/2">0/1/2</option>
83 <option value="0/1/2/3">0/1/2/3</option> 81 <option value="0/1/2/3">0/1/2/3</option>
84 <option value="-8/-4/0/4/8">-8/-4/0/4/8</option> 82 <option value="-8/-4/0/4/8">-8/-4/0/4/8</option>
85 <expand macro="list_string_san"/> 83 <option value="-1/0/1/2/3">-1/0/1/2/3</option>
84 <expand macro="list_string_san" name="isotope_error"/>
86 </param> 85 </param>
87 <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0001" value="0.01" label="This is half the bin size, which is used to segment the MS/MS spectrum" help="Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size"/> 86 <param argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0001" value="0.01" label="This is half the bin size, which is used to segment the MS/MS spectrum" help="Thus, the value should be a bit higher than for other search engines, since the bin might not be centered around the peak apex (see 'fragment_bin_offset').CAUTION: Low tolerances have heavy impact on RAM usage (since Comet uses a lot of bins in this case). Consider using use_sparse_matrix and/or spectrum_batch_size"/>
88 <param name="fragment_error_units" argument="-fragment_error_units" display="radio" type="select" optional="false" label="Fragment monoisotopic mass error units" help=""> 87 <param argument="-fragment_error_units" type="select" optional="true" label="Fragment monoisotopic mass error units" help="">
89 <option value="Da" selected="true">Da</option> 88 <option value="Da" selected="true">Da</option>
90 <expand macro="list_string_san"/> 89 <expand macro="list_string_san" name="fragment_error_units"/>
91 </param> 90 </param>
92 <param name="fragment_bin_offset" argument="-fragment_bin_offset" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Offset of fragment bins" help="Recommended by Comet: low-res: 0.4, high-res: 0.0"/> 91 <param argument="-fragment_bin_offset" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Offset of fragment bins" help="Recommended by Comet: low-res: 0.4, high-res: 0.0"/>
93 <param name="instrument" argument="-instrument" display="radio" type="select" optional="false" label="Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only" help=""> 92 <param argument="-instrument" type="select" optional="true" label="Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only" help="">
94 <option value="low_res">low_res</option> 93 <option value="low_res">low_res</option>
95 <option value="high_res" selected="true">high_res</option> 94 <option value="high_res" selected="true">high_res</option>
96 <expand macro="list_string_san"/> 95 <expand macro="list_string_san" name="instrument"/>
97 </param> 96 </param>
98 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help=""> 97 <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
99 <option value="Arg-C">Arg-C</option>
100 <option value="Asp-N">Asp-N</option>
101 <option value="Trypsin" selected="true">Trypsin</option>
102 <option value="unspecific cleavage">unspecific cleavage</option>
103 <option value="Chymotrypsin">Chymotrypsin</option>
104 <option value="CNBr">CNBr</option> 98 <option value="CNBr">CNBr</option>
105 <option value="Lys-C">Lys-C</option> 99 <option value="Lys-C">Lys-C</option>
100 <option value="Trypsin" selected="true">Trypsin</option>
101 <option value="Arg-C">Arg-C</option>
102 <option value="Chymotrypsin">Chymotrypsin</option>
103 <option value="Asp-N">Asp-N</option>
104 <option value="unspecific cleavage">unspecific cleavage</option>
106 <option value="Lys-N">Lys-N</option> 105 <option value="Lys-N">Lys-N</option>
107 <option value="PepsinA">PepsinA</option> 106 <option value="PepsinA">PepsinA</option>
108 <option value="Trypsin/P">Trypsin/P</option> 107 <option value="Trypsin/P">Trypsin/P</option>
109 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> 108 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
110 <expand macro="list_string_san"/> 109 <expand macro="list_string_san" name="enzyme"/>
111 </param> 110 </param>
112 <param name="num_enzyme_termini" argument="-num_enzyme_termini" display="radio" type="select" optional="false" label="Specify the termini where the cleavage rule has to match" help=""> 111 <param argument="-num_enzyme_termini" type="select" optional="true" label="Specify the termini where the cleavage rule has to match" help="">
113 <option value="semi">semi</option> 112 <option value="semi">semi</option>
114 <option value="fully" selected="true">fully</option> 113 <option value="fully" selected="true">fully</option>
115 <option value="C-term unspecific">C-term unspecific</option> 114 <option value="C-term unspecific">C-term unspecific</option>
116 <option value="N-term unspecific">N-term unspecific</option> 115 <option value="N-term unspecific">N-term unspecific</option>
117 <expand macro="list_string_san"/> 116 <expand macro="list_string_san" name="num_enzyme_termini"/>
118 </param> 117 </param>
119 <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" max="5" value="1" label="Number of possible cleavage sites missed by the enzyme" help="It has no effect if enzyme is unspecific cleavage"/> 118 <param argument="-missed_cleavages" type="integer" optional="true" min="0" max="5" value="1" label="Number of possible cleavage sites missed by the enzyme" help="It has no effect if enzyme is unspecific cleavage"/>
120 <param name="min_peptide_length" argument="-min_peptide_length" type="integer" optional="true" min="5" max="63" value="5" label="Minimum peptide length to conside" help=""/> 119 <param argument="-min_peptide_length" type="integer" optional="true" min="5" max="63" value="5" label="Minimum peptide length to conside" help=""/>
121 <param name="max_peptide_length" argument="-max_peptide_length" type="integer" optional="true" min="5" max="63" value="63" label="Maximum peptide length to conside" help=""/> 120 <param argument="-max_peptide_length" type="integer" optional="true" min="5" max="63" value="63" label="Maximum peptide length to conside" help=""/>
122 <param name="num_hits" argument="-num_hits" type="integer" optional="true" value="1" label="Number of peptide hits in output file" help=""/> 121 <param argument="-num_hits" type="integer" optional="true" value="1" label="Number of peptide hits in output file" help=""/>
123 <param name="precursor_charge" argument="-precursor_charge" type="text" optional="true" value="0:0" label="Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3" help=""> 122 <param argument="-precursor_charge" type="text" optional="true" value="0:0" label="Precursor charge range to search (if spectrum is not annotated with a charge or if override_charge!=keep any known): 0:[num] == search all charges, 2:6 == from +2 to +6, 3:3 == +3" help="">
124 <expand macro="list_string_san"/> 123 <expand macro="list_string_san" name="precursor_charge"/>
125 </param> 124 </param>
126 <param name="override_charge" argument="-override_charge" display="radio" type="select" optional="false" label="_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state" help="For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range"> 125 <param argument="-override_charge" type="select" optional="true" label="_keep any known_: keep any precursor charge state (from input), _ignore known_: ignore known precursor charge state and use precursor_charge parameter, _ignore outside range_: ignore precursor charges outside precursor_charge range, _keep known search unknown_: keep any known precursor charge state" help="For unknown charge states, search as singly charged if there is no signal above the precursor m/z or use the precursor_charge range">
127 <option value="keep any known">keep any known</option> 126 <option value="keep any known">keep any known</option>
128 <option value="ignore known">ignore known</option> 127 <option value="ignore known">ignore known</option>
129 <option value="ignore outside range">ignore outside range</option> 128 <option value="ignore outside range">ignore outside range</option>
130 <option value="keep known search unknown" selected="true">keep known search unknown</option> 129 <option value="keep known search unknown" selected="true">keep known search unknown</option>
131 <expand macro="list_string_san"/> 130 <expand macro="list_string_san" name="override_charge"/>
132 </param> 131 </param>
133 <param name="ms_level" argument="-ms_level" type="integer" optional="true" min="2" max="3" value="2" label="MS level to analyze, valid are levels 2 (default) or 3" help=""/> 132 <param argument="-ms_level" type="integer" optional="true" min="2" max="3" value="2" label="MS level to analyze, valid are levels 2 (default) or 3" help=""/>
134 <param name="activation_method" argument="-activation_method" type="select" optional="false" label="If not ALL, only searches spectra of the given method" help=""> 133 <param argument="-activation_method" type="select" optional="true" label="If not ALL, only searches spectra of the given method" help="">
135 <option value="ALL" selected="true">ALL</option> 134 <option value="ALL" selected="true">ALL</option>
136 <option value="CID">CID</option> 135 <option value="CID">CID</option>
137 <option value="ECD">ECD</option> 136 <option value="ECD">ECD</option>
138 <option value="ETD">ETD</option> 137 <option value="ETD">ETD</option>
139 <option value="PQD">PQD</option> 138 <option value="PQD">PQD</option>
140 <option value="HCD">HCD</option> 139 <option value="HCD">HCD</option>
141 <option value="IRMPD">IRMPD</option> 140 <option value="IRMPD">IRMPD</option>
142 <expand macro="list_string_san"/> 141 <expand macro="list_string_san" name="activation_method"/>
143 </param> 142 </param>
144 <param name="max_fragment_charge" argument="-max_fragment_charge" type="integer" optional="true" min="1" max="5" value="3" label="Set maximum fragment charge state to analyze as long as still lower than precursor charge - 1" help="(Allowed max 5)"/> 143 <param argument="-max_fragment_charge" type="integer" optional="true" min="1" max="5" value="3" label="Set maximum fragment charge state to analyze as long as still lower than precursor charge - 1" help="(Allowed max 5)"/>
145 <param name="clip_nterm_methionine" argument="-clip_nterm_methionine" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, also considers the peptide sequence w/o N-term methionine separately and applies appropriate N-term mods to it" help=""/> 144 <param argument="-clip_nterm_methionine" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set to true, also considers the peptide sequence w/o N-term methionine separately and applies appropriate N-term mods to it" help=""/>
146 <param name="fixed_modifications" argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> 145 <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
147 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 146 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
148 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 147 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
149 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 148 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
150 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 149 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
151 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 150 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
1510 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 1509 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
1511 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1510 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1512 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1511 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1513 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1512 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1514 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1513 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1515 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1516 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1514 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1517 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option> 1515 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
1518 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> 1516 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
1519 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1517 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1520 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1518 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
3070 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 3068 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
3071 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 3069 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
3072 <option value="ZGB (K)">ZGB (K)</option> 3070 <option value="ZGB (K)">ZGB (K)</option>
3073 <option value="ZGB (N-term)">ZGB (N-term)</option> 3071 <option value="ZGB (N-term)">ZGB (N-term)</option>
3074 <option value="ZQG (K)">ZQG (K)</option> 3072 <option value="ZQG (K)">ZQG (K)</option>
3075 <expand macro="list_string_san"/> 3073 <expand macro="list_string_san" name="fixed_modifications"/>
3076 </param> 3074 </param>
3077 <param name="variable_modifications" argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> 3075 <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
3078 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 3076 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
3079 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 3077 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
3080 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 3078 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
3081 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 3079 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
3082 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 3080 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
4441 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 4439 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
4442 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 4440 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
4443 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 4441 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
4444 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 4442 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
4445 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 4443 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
4446 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4447 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 4444 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4448 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option> 4445 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
4449 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> 4446 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
4450 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 4447 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
4451 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 4448 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
6001 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 5998 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
6002 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 5999 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
6003 <option value="ZGB (K)">ZGB (K)</option> 6000 <option value="ZGB (K)">ZGB (K)</option>
6004 <option value="ZGB (N-term)">ZGB (N-term)</option> 6001 <option value="ZGB (N-term)">ZGB (N-term)</option>
6005 <option value="ZQG (K)">ZQG (K)</option> 6002 <option value="ZQG (K)">ZQG (K)</option>
6006 <expand macro="list_string_san"/> 6003 <expand macro="list_string_san" name="variable_modifications"/>
6007 </param> 6004 </param>
6008 <param name="binary_modifications" argument="-binary_modifications" type="text" optional="true" value="" label="List of modification group indices" help="Indices correspond to the binary modification index used by comet to group individually searched lists of variable modifications.. Note: if set, both variable_modifications and binary_modifications need to have the same number of entries as the N-th entry corresponds to the N-th variable_modification.. if left empty (default), all entries are internally set to 0 generating all permutations of modified and unmodified residues.. For a detailed explanation please see the parameter description in the Comet help (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6005 <param argument="-binary_modifications" type="text" optional="true" value="" label="List of modification group indices" help="Indices correspond to the binary modification index used by comet to group individually searched lists of variable modifications.. Note: if set, both variable_modifications and binary_modifications need to have the same number of entries as the N-th entry corresponds to the N-th variable_modification.. if left empty (default), all entries are internally set to 0 generating all permutations of modified and unmodified residues.. For a detailed explanation please see the parameter description in the Comet help (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6009 <expand macro="list_integer_valsan"/> 6006 <expand macro="list_integer_valsan" name="binary_modifications"/>
6010 </param> 6007 </param>
6008 <param argument="-reindex" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Recalculate peptide to protein association using OpenMS" help="Annotates target-decoy information"/>
6009 <section name="PeptideIndexing" title="" help="" expanded="false">
6010 <param name="decoy_string" argument="-PeptideIndexing:decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
6011 <expand macro="list_string_san" name="decoy_string"/>
6012 </param>
6013 <param name="decoy_string_position" argument="-PeptideIndexing:decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
6014 <option value="prefix" selected="true">prefix</option>
6015 <option value="suffix">suffix</option>
6016 <expand macro="list_string_san" name="decoy_string_position"/>
6017 </param>
6018 <param name="missing_decoy_action" argument="-PeptideIndexing:missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
6019 <option value="error">error</option>
6020 <option value="warn" selected="true">warn</option>
6021 <option value="silent">silent</option>
6022 <expand macro="list_string_san" name="missing_decoy_action"/>
6023 </param>
6024 <param name="write_protein_sequence" argument="-PeptideIndexing:write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
6025 <param name="write_protein_description" argument="-PeptideIndexing:write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
6026 <param name="keep_unreferenced_proteins" argument="-PeptideIndexing:keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
6027 <param name="unmatched_action" argument="-PeptideIndexing:unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
6028 <option value="error" selected="true">error</option>
6029 <option value="warn">warn</option>
6030 <option value="remove">remove</option>
6031 <expand macro="list_string_san" name="unmatched_action"/>
6032 </param>
6033 <param name="aaa_max" argument="-PeptideIndexing:aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
6034 <param name="mismatches_max" argument="-PeptideIndexing:mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
6035 <param name="IL_equivalent" argument="-PeptideIndexing:IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/>
6036 <section name="enzyme" title="" help="" expanded="false">
6037 <param name="name" argument="-PeptideIndexing:enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
6038 <option value="auto" selected="true">auto</option>
6039 <option value="Trypsin">Trypsin</option>
6040 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
6041 <option value="Glu-C+P">Glu-C+P</option>
6042 <option value="PepsinA + P">PepsinA + P</option>
6043 <option value="cyanogen-bromide">cyanogen-bromide</option>
6044 <option value="Clostripain/P">Clostripain/P</option>
6045 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
6046 <option value="no cleavage">no cleavage</option>
6047 <option value="proline endopeptidase">proline endopeptidase</option>
6048 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
6049 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
6050 <option value="2-iodobenzoate">2-iodobenzoate</option>
6051 <option value="iodosobenzoate">iodosobenzoate</option>
6052 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
6053 <option value="Trypsin/P">Trypsin/P</option>
6054 <option value="V8-DE">V8-DE</option>
6055 <option value="V8-E">V8-E</option>
6056 <option value="leukocyte elastase">leukocyte elastase</option>
6057 <option value="PepsinA">PepsinA</option>
6058 <option value="TrypChymo">TrypChymo</option>
6059 <option value="Asp-N">Asp-N</option>
6060 <option value="unspecific cleavage">unspecific cleavage</option>
6061 <option value="Asp-N/B">Asp-N/B</option>
6062 <option value="Asp-N_ambic">Asp-N_ambic</option>
6063 <option value="Chymotrypsin">Chymotrypsin</option>
6064 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
6065 <option value="CNBr">CNBr</option>
6066 <option value="Arg-C/P">Arg-C/P</option>
6067 <option value="Lys-N">Lys-N</option>
6068 <option value="Lys-C/P">Lys-C/P</option>
6069 <option value="Formic_acid">Formic_acid</option>
6070 <option value="Lys-C">Lys-C</option>
6071 <option value="Arg-C">Arg-C</option>
6072 <expand macro="list_string_san" name="name"/>
6073 </param>
6074 <param name="specificity" argument="-PeptideIndexing:enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input.. 'full': both internal cleavage sites must match.. 'semi': one of two internal cleavage sites must match.. 'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
6075 <option value="auto" selected="true">auto</option>
6076 <option value="full">full</option>
6077 <option value="semi">semi</option>
6078 <option value="none">none</option>
6079 <expand macro="list_string_san" name="specificity"/>
6080 </param>
6081 </section>
6082 </section>
6011 <expand macro="adv_opts_macro"> 6083 <expand macro="adv_opts_macro">
6012 <param name="use_A_ions" argument="-use_A_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use A ions for PSM" help=""/> 6084 <param argument="-use_A_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use A ions for PSM" help=""/>
6013 <param name="use_B_ions" argument="-use_B_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="use B ions for PSM" help=""/> 6085 <param argument="-use_B_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="use B ions for PSM" help=""/>
6014 <param name="use_C_ions" argument="-use_C_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use C ions for PSM" help=""/> 6086 <param argument="-use_C_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use C ions for PSM" help=""/>
6015 <param name="use_X_ions" argument="-use_X_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use X ions for PSM" help=""/> 6087 <param argument="-use_X_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use X ions for PSM" help=""/>
6016 <param name="use_Y_ions" argument="-use_Y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="use Y ions for PSM" help=""/> 6088 <param argument="-use_Y_ions" type="boolean" truevalue="true" falsevalue="false" checked="true" label="use Y ions for PSM" help=""/>
6017 <param name="use_Z_ions" argument="-use_Z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use Z ions for PSM" help=""/> 6089 <param argument="-use_Z_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use Z ions for PSM" help=""/>
6018 <param name="use_NL_ions" argument="-use_NL_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use neutral loss (NH3, H2O) ions from b/y for PSM" help=""/> 6090 <param argument="-use_NL_ions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use neutral loss (NH3, H2O) ions from b/y for PSM" help=""/>
6019 <param name="second_enzyme" argument="-second_enzyme" type="select" optional="true" label="Additional enzyme used for peptide digestion" help=""> 6091 <param argument="-second_enzyme" type="select" optional="true" label="Additional enzyme used for peptide digestion" help="">
6020 <option value="">default (nothing chosen)</option>
6021 <option value="Arg-C">Arg-C</option>
6022 <option value="Asp-N">Asp-N</option>
6023 <option value="Trypsin">Trypsin</option>
6024 <option value="unspecific cleavage">unspecific cleavage</option>
6025 <option value="Chymotrypsin">Chymotrypsin</option>
6026 <option value="CNBr">CNBr</option> 6092 <option value="CNBr">CNBr</option>
6027 <option value="Lys-C">Lys-C</option> 6093 <option value="Lys-C">Lys-C</option>
6094 <option value="Trypsin">Trypsin</option>
6095 <option value="Arg-C">Arg-C</option>
6096 <option value="Chymotrypsin">Chymotrypsin</option>
6097 <option value="Asp-N">Asp-N</option>
6098 <option value="unspecific cleavage">unspecific cleavage</option>
6028 <option value="Lys-N">Lys-N</option> 6099 <option value="Lys-N">Lys-N</option>
6029 <option value="PepsinA">PepsinA</option> 6100 <option value="PepsinA">PepsinA</option>
6030 <option value="Trypsin/P">Trypsin/P</option> 6101 <option value="Trypsin/P">Trypsin/P</option>
6031 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> 6102 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
6032 <expand macro="list_string_san"/> 6103 <expand macro="list_string_san" name="second_enzyme"/>
6033 </param> 6104 </param>
6034 <param name="digest_mass_range" argument="-digest_mass_range" type="text" optional="true" value="600:5000" label="MH+ peptide mass range to analyze" help=""> 6105 <param argument="-digest_mass_range" type="text" optional="true" value="600:5000" label="MH+ peptide mass range to analyze" help="">
6035 <expand macro="list_string_san"/> 6106 <expand macro="list_string_san" name="digest_mass_range"/>
6036 </param> 6107 </param>
6037 <param name="max_precursor_charge" argument="-max_precursor_charge" type="integer" optional="true" min="1" max="9" value="5" label="set maximum precursor charge state to analyze (allowed max 9)" help=""/> 6108 <param argument="-max_precursor_charge" type="integer" optional="true" min="1" max="9" value="5" label="set maximum precursor charge state to analyze (allowed max 9)" help=""/>
6038 <param name="spectrum_batch_size" argument="-spectrum_batch_size" type="integer" optional="true" min="0" value="20000" label="max" help="number of spectra to search at a time; use 0 to search the entire scan range in one batch"/> 6109 <param argument="-spectrum_batch_size" type="integer" optional="true" min="0" value="20000" label="max" help="number of spectra to search at a time; use 0 to search the entire scan range in one batch"/>
6039 <param name="mass_offsets" argument="-mass_offsets" type="text" optional="true" value="0.0" label="One or more mass offsets to search (values subtracted from deconvoluted precursor mass)" help="Has to include 0.0 if you want the default mass to be searched (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 6110 <param argument="-mass_offsets" type="text" optional="true" value="0.0" label="One or more mass offsets to search (values subtracted from deconvoluted precursor mass)" help="Has to include 0.0 if you want the default mass to be searched (space separated list, in order to allow for spaces in list items surround them by single quotes)">
6040 <expand macro="list_float_valsan"/> 6111 <expand macro="list_float_valsan" name="mass_offsets"/>
6041 </param> 6112 </param>
6042 <param name="minimum_peaks" argument="-minimum_peaks" type="integer" optional="true" value="10" label="Required minimum number of peaks in spectrum to search (default 10)" help=""/> 6113 <param argument="-minimum_peaks" type="integer" optional="true" value="10" label="Required minimum number of peaks in spectrum to search (default 10)" help=""/>
6043 <param name="minimum_intensity" argument="-minimum_intensity" type="float" optional="true" min="0.0" value="0.0" label="Minimum intensity value to read in" help=""/> 6114 <param argument="-minimum_intensity" type="float" optional="true" min="0.0" value="0.0" label="Minimum intensity value to read in" help=""/>
6044 <param name="remove_precursor_peak" argument="-remove_precursor_peak" display="radio" type="select" optional="false" label="no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD)" help="phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance"> 6115 <param argument="-remove_precursor_peak" type="select" optional="true" label="no = no removal, yes = remove all peaks around precursor m/z, charge_reduced = remove all charge reduced precursor peaks (for ETD/ECD)" help="phosphate_loss = remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. See also remove_precursor_tolerance">
6045 <option value="no" selected="true">no</option> 6116 <option value="no" selected="true">no</option>
6046 <option value="yes">yes</option> 6117 <option value="yes">yes</option>
6047 <option value="charge_reduced">charge_reduced</option> 6118 <option value="charge_reduced">charge_reduced</option>
6048 <option value="phosphate_loss">phosphate_loss</option> 6119 <option value="phosphate_loss">phosphate_loss</option>
6049 <expand macro="list_string_san"/> 6120 <expand macro="list_string_san" name="remove_precursor_peak"/>
6050 </param> 6121 </param>
6051 <param name="remove_precursor_tolerance" argument="-remove_precursor_tolerance" type="float" optional="true" value="1.5" label="one-sided tolerance for precursor removal in Thompson" help=""/> 6122 <param argument="-remove_precursor_tolerance" type="float" optional="true" value="1.5" label="one-sided tolerance for precursor removal in Thompson" help=""/>
6052 <param name="clear_mz_range" argument="-clear_mz_range" type="text" optional="true" value="0:0" label="for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range, if not 0:0" help=""> 6123 <param argument="-clear_mz_range" type="text" optional="true" value="0:0" label="for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range, if not 0:0" help="">
6053 <expand macro="list_string_san"/> 6124 <expand macro="list_string_san" name="clear_mz_range"/>
6054 </param> 6125 </param>
6055 <param name="max_variable_mods_in_peptide" argument="-max_variable_mods_in_peptide" type="integer" optional="true" value="5" label="Set a maximum number of variable modifications per peptide" help=""/> 6126 <param argument="-max_variable_mods_in_peptide" type="integer" optional="true" value="5" label="Set a maximum number of variable modifications per peptide" help=""/>
6056 <param name="require_variable_mod" argument="-require_variable_mod" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, requires at least one variable modification per peptide" help=""/> 6127 <param argument="-require_variable_mod" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If true, requires at least one variable modification per peptide" help=""/>
6057 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 6128 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
6058 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 6129 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
6059 <expand macro="list_string_san"/> 6130 <expand macro="list_string_san" name="test"/>
6060 </param> 6131 </param>
6061 </expand> 6132 </expand>
6062 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 6133 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
6063 <option value="pin_out_FLAG">pin_out (Output file - for Percolator input)</option> 6134 <option value="pin_out_FLAG">pin_out (Output file - for Percolator input)</option>
6064 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 6135 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
6071 </data> 6142 </data>
6072 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 6143 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
6073 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 6144 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
6074 </data> 6145 </data>
6075 </outputs> 6146 </outputs>
6076 <tests> 6147 <tests><!-- TOPP_CometAdapter_1 -->
6077 <expand macro="autotest_CometAdapter"/> 6148 <test expect_num_outputs="3">
6078 <expand macro="manutest_CometAdapter"/> 6149 <section name="adv_opts">
6150 <param name="use_A_ions" value="false"/>
6151 <param name="use_B_ions" value="true"/>
6152 <param name="use_C_ions" value="false"/>
6153 <param name="use_X_ions" value="false"/>
6154 <param name="use_Y_ions" value="true"/>
6155 <param name="use_Z_ions" value="false"/>
6156 <param name="use_NL_ions" value="false"/>
6157 <param name="second_enzyme"/>
6158 <param name="digest_mass_range" value="600:5000"/>
6159 <param name="max_precursor_charge" value="5"/>
6160 <param name="spectrum_batch_size" value="1000"/>
6161 <param name="mass_offsets" value="0.0"/>
6162 <param name="minimum_peaks" value="10"/>
6163 <param name="minimum_intensity" value="0.0"/>
6164 <param name="remove_precursor_peak" value="no"/>
6165 <param name="remove_precursor_tolerance" value="1.5"/>
6166 <param name="clear_mz_range" value="0:0"/>
6167 <param name="max_variable_mods_in_peptide" value="5"/>
6168 <param name="require_variable_mod" value="false"/>
6169 <param name="force" value="true"/>
6170 <param name="test" value="true"/>
6171 </section>
6172 <param name="in" value="spectra_comet.mzML"/>
6173 <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6174 <param name="database" value="proteins.fasta"/>
6175 <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
6176 <param name="precursor_mass_tolerance" value="3.0"/>
6177 <param name="precursor_error_units" value="ppm"/>
6178 <param name="isotope_error" value="off"/>
6179 <param name="fragment_mass_tolerance" value="0.50025"/>
6180 <param name="fragment_error_units" value="Da"/>
6181 <param name="fragment_bin_offset" value="0.25"/>
6182 <param name="instrument" value="high_res"/>
6183 <param name="enzyme" value="Trypsin"/>
6184 <param name="num_enzyme_termini" value="fully"/>
6185 <param name="missed_cleavages" value="1"/>
6186 <param name="min_peptide_length" value="5"/>
6187 <param name="max_peptide_length" value="63"/>
6188 <param name="num_hits" value="5"/>
6189 <param name="precursor_charge" value="0:0"/>
6190 <param name="override_charge" value="keep any known"/>
6191 <param name="ms_level" value="2"/>
6192 <param name="activation_method" value="ALL"/>
6193 <param name="max_fragment_charge" value="3"/>
6194 <param name="clip_nterm_methionine" value="false"/>
6195 <param name="fixed_modifications"/>
6196 <param name="variable_modifications"/>
6197 <param name="binary_modifications" value=""/>
6198 <param name="reindex" value="true"/>
6199 <section name="PeptideIndexing">
6200 <param name="decoy_string" value=""/>
6201 <param name="decoy_string_position" value="prefix"/>
6202 <param name="missing_decoy_action" value="warn"/>
6203 <param name="write_protein_sequence" value="false"/>
6204 <param name="write_protein_description" value="false"/>
6205 <param name="keep_unreferenced_proteins" value="false"/>
6206 <param name="unmatched_action" value="error"/>
6207 <param name="aaa_max" value="3"/>
6208 <param name="mismatches_max" value="0"/>
6209 <param name="IL_equivalent" value="false"/>
6210 <section name="enzyme">
6211 <param name="name" value="auto"/>
6212 <param name="specificity" value="auto"/>
6213 </section>
6214 </section>
6215 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
6216 <output name="ctd_out" ftype="xml">
6217 <assert_contents>
6218 <is_valid_xml/>
6219 </assert_contents>
6220 </output>
6221 </test>
6222 <!-- TOPP_CometAdapter_2 -->
6223 <test expect_num_outputs="3">
6224 <section name="adv_opts">
6225 <param name="use_A_ions" value="false"/>
6226 <param name="use_B_ions" value="true"/>
6227 <param name="use_C_ions" value="false"/>
6228 <param name="use_X_ions" value="false"/>
6229 <param name="use_Y_ions" value="true"/>
6230 <param name="use_Z_ions" value="false"/>
6231 <param name="use_NL_ions" value="false"/>
6232 <param name="second_enzyme"/>
6233 <param name="digest_mass_range" value="600:5000"/>
6234 <param name="max_precursor_charge" value="5"/>
6235 <param name="spectrum_batch_size" value="1000"/>
6236 <param name="mass_offsets" value="0.0"/>
6237 <param name="minimum_peaks" value="10"/>
6238 <param name="minimum_intensity" value="0.0"/>
6239 <param name="remove_precursor_peak" value="no"/>
6240 <param name="remove_precursor_tolerance" value="1.5"/>
6241 <param name="clear_mz_range" value="0:0"/>
6242 <param name="max_variable_mods_in_peptide" value="5"/>
6243 <param name="require_variable_mod" value="false"/>
6244 <param name="force" value="true"/>
6245 <param name="test" value="true"/>
6246 </section>
6247 <param name="in" value="CometAdapter_2_prepared.mzML"/>
6248 <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6249 <param name="database" value="CometAdapter_2_in.fasta"/>
6250 <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
6251 <param name="precursor_mass_tolerance" value="3.0"/>
6252 <param name="precursor_error_units" value="Da"/>
6253 <param name="isotope_error" value="off"/>
6254 <param name="fragment_mass_tolerance" value="0.50025"/>
6255 <param name="fragment_error_units" value="Da"/>
6256 <param name="fragment_bin_offset" value="0.25"/>
6257 <param name="instrument" value="high_res"/>
6258 <param name="enzyme" value="Trypsin"/>
6259 <param name="num_enzyme_termini" value="fully"/>
6260 <param name="missed_cleavages" value="1"/>
6261 <param name="min_peptide_length" value="5"/>
6262 <param name="max_peptide_length" value="63"/>
6263 <param name="num_hits" value="5"/>
6264 <param name="precursor_charge" value="0:0"/>
6265 <param name="override_charge" value="keep any known"/>
6266 <param name="ms_level" value="2"/>
6267 <param name="activation_method" value="ALL"/>
6268 <param name="max_fragment_charge" value="3"/>
6269 <param name="clip_nterm_methionine" value="false"/>
6270 <param name="fixed_modifications"/>
6271 <param name="variable_modifications"/>
6272 <param name="binary_modifications" value=""/>
6273 <param name="reindex" value="true"/>
6274 <section name="PeptideIndexing">
6275 <param name="decoy_string" value=""/>
6276 <param name="decoy_string_position" value="prefix"/>
6277 <param name="missing_decoy_action" value="warn"/>
6278 <param name="write_protein_sequence" value="false"/>
6279 <param name="write_protein_description" value="false"/>
6280 <param name="keep_unreferenced_proteins" value="false"/>
6281 <param name="unmatched_action" value="error"/>
6282 <param name="aaa_max" value="3"/>
6283 <param name="mismatches_max" value="0"/>
6284 <param name="IL_equivalent" value="false"/>
6285 <section name="enzyme">
6286 <param name="name" value="auto"/>
6287 <param name="specificity" value="auto"/>
6288 </section>
6289 </section>
6290 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
6291 <output name="ctd_out" ftype="xml">
6292 <assert_contents>
6293 <is_valid_xml/>
6294 </assert_contents>
6295 </output>
6296 </test>
6297 <!-- TOPP_CometAdapter_3 -->
6298 <test expect_num_outputs="3">
6299 <section name="adv_opts">
6300 <param name="use_A_ions" value="false"/>
6301 <param name="use_B_ions" value="true"/>
6302 <param name="use_C_ions" value="false"/>
6303 <param name="use_X_ions" value="false"/>
6304 <param name="use_Y_ions" value="true"/>
6305 <param name="use_Z_ions" value="false"/>
6306 <param name="use_NL_ions" value="false"/>
6307 <param name="second_enzyme"/>
6308 <param name="digest_mass_range" value="600:5000"/>
6309 <param name="max_precursor_charge" value="5"/>
6310 <param name="spectrum_batch_size" value="20000"/>
6311 <param name="mass_offsets" value="0.0"/>
6312 <param name="minimum_peaks" value="10"/>
6313 <param name="minimum_intensity" value="0.0"/>
6314 <param name="remove_precursor_peak" value="no"/>
6315 <param name="remove_precursor_tolerance" value="1.5"/>
6316 <param name="clear_mz_range" value="0:0"/>
6317 <param name="max_variable_mods_in_peptide" value="3"/>
6318 <param name="require_variable_mod" value="false"/>
6319 <param name="force" value="false"/>
6320 <param name="test" value="true"/>
6321 </section>
6322 <param name="in" value="CometAdapter_3.mzML"/>
6323 <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6324 <param name="database" value="CometAdapter_3.fasta"/>
6325 <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
6326 <param name="precursor_mass_tolerance" value="5.0"/>
6327 <param name="precursor_error_units" value="ppm"/>
6328 <param name="isotope_error" value="off"/>
6329 <param name="fragment_mass_tolerance" value="0.01"/>
6330 <param name="fragment_error_units" value="Da"/>
6331 <param name="fragment_bin_offset" value="0.0"/>
6332 <param name="instrument" value="high_res"/>
6333 <param name="enzyme" value="Trypsin"/>
6334 <param name="num_enzyme_termini" value="fully"/>
6335 <param name="missed_cleavages" value="3"/>
6336 <param name="min_peptide_length" value="5"/>
6337 <param name="max_peptide_length" value="63"/>
6338 <param name="num_hits" value="5"/>
6339 <param name="precursor_charge" value="0:0"/>
6340 <param name="override_charge" value="keep known search unknown"/>
6341 <param name="ms_level" value="2"/>
6342 <param name="activation_method" value="ALL"/>
6343 <param name="max_fragment_charge" value="3"/>
6344 <param name="clip_nterm_methionine" value="false"/>
6345 <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
6346 <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term),Phospho (S),Phospho (T),Phospho (Y)"/>
6347 <param name="binary_modifications" value=""/>
6348 <param name="reindex" value="true"/>
6349 <section name="PeptideIndexing">
6350 <param name="decoy_string" value=""/>
6351 <param name="decoy_string_position" value="prefix"/>
6352 <param name="missing_decoy_action" value="warn"/>
6353 <param name="write_protein_sequence" value="false"/>
6354 <param name="write_protein_description" value="false"/>
6355 <param name="keep_unreferenced_proteins" value="false"/>
6356 <param name="unmatched_action" value="error"/>
6357 <param name="aaa_max" value="3"/>
6358 <param name="mismatches_max" value="0"/>
6359 <param name="IL_equivalent" value="false"/>
6360 <section name="enzyme">
6361 <param name="name" value="auto"/>
6362 <param name="specificity" value="auto"/>
6363 </section>
6364 </section>
6365 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
6366 <output name="ctd_out" ftype="xml">
6367 <assert_contents>
6368 <is_valid_xml/>
6369 </assert_contents>
6370 </output>
6371 </test>
6372 <!-- TOPP_CometAdapter_4 -->
6373 <test expect_num_outputs="2">
6374 <section name="adv_opts">
6375 <param name="use_A_ions" value="false"/>
6376 <param name="use_B_ions" value="true"/>
6377 <param name="use_C_ions" value="false"/>
6378 <param name="use_X_ions" value="false"/>
6379 <param name="use_Y_ions" value="true"/>
6380 <param name="use_Z_ions" value="false"/>
6381 <param name="use_NL_ions" value="false"/>
6382 <param name="second_enzyme"/>
6383 <param name="digest_mass_range" value="600:1200"/>
6384 <param name="max_precursor_charge" value="5"/>
6385 <param name="spectrum_batch_size" value="20000"/>
6386 <param name="mass_offsets" value="0.0"/>
6387 <param name="minimum_peaks" value="10"/>
6388 <param name="minimum_intensity" value="0.0"/>
6389 <param name="remove_precursor_peak" value="no"/>
6390 <param name="remove_precursor_tolerance" value="1.5"/>
6391 <param name="clear_mz_range" value="0:0"/>
6392 <param name="max_variable_mods_in_peptide" value="3"/>
6393 <param name="require_variable_mod" value="false"/>
6394 <param name="force" value="false"/>
6395 <param name="test" value="true"/>
6396 </section>
6397 <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/>
6398 <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
6399 <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/>
6400 <param name="precursor_mass_tolerance" value="5.0"/>
6401 <param name="precursor_error_units" value="ppm"/>
6402 <param name="isotope_error" value="off"/>
6403 <param name="fragment_mass_tolerance" value="0.01"/>
6404 <param name="fragment_error_units" value="Da"/>
6405 <param name="fragment_bin_offset" value="0.0"/>
6406 <param name="instrument" value="high_res"/>
6407 <param name="enzyme" value="Trypsin"/>
6408 <param name="num_enzyme_termini" value="fully"/>
6409 <param name="missed_cleavages" value="3"/>
6410 <param name="min_peptide_length" value="5"/>
6411 <param name="max_peptide_length" value="63"/>
6412 <param name="num_hits" value="5"/>
6413 <param name="precursor_charge" value="0:0"/>
6414 <param name="override_charge" value="keep known search unknown"/>
6415 <param name="ms_level" value="2"/>
6416 <param name="activation_method" value="ALL"/>
6417 <param name="max_fragment_charge" value="3"/>
6418 <param name="clip_nterm_methionine" value="false"/>
6419 <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
6420 <param name="variable_modifications" value="Met-loss (Protein N-term M)"/>
6421 <param name="binary_modifications" value=""/>
6422 <param name="reindex" value="true"/>
6423 <section name="PeptideIndexing">
6424 <param name="decoy_string" value=""/>
6425 <param name="decoy_string_position" value="prefix"/>
6426 <param name="missing_decoy_action" value="warn"/>
6427 <param name="write_protein_sequence" value="false"/>
6428 <param name="write_protein_description" value="false"/>
6429 <param name="keep_unreferenced_proteins" value="false"/>
6430 <param name="unmatched_action" value="error"/>
6431 <param name="aaa_max" value="3"/>
6432 <param name="mismatches_max" value="0"/>
6433 <param name="IL_equivalent" value="false"/>
6434 <section name="enzyme">
6435 <param name="name" value="auto"/>
6436 <param name="specificity" value="auto"/>
6437 </section>
6438 </section>
6439 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
6440 <output name="ctd_out" ftype="xml">
6441 <assert_contents>
6442 <is_valid_xml/>
6443 </assert_contents>
6444 </output>
6445 </test>
6079 </tests> 6446 </tests>
6080 <help><![CDATA[Annotates MS/MS spectra using Comet. 6447 <help><![CDATA[Annotates MS/MS spectra using Comet.
6081 6448
6082 6449
6083 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_CometAdapter.html]]></help> 6450 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_CometAdapter.html]]></help>
6084 <expand macro="references"/> 6451 <expand macro="references"/>
6085 </tool> 6452 </tool>