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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:17:28 +0000
parents 3a8e53c6b9d6
children
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15:2d24eaa25373 16:cd9449dbe4e4
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="CompNovo" name="CompNovo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="CompNovo" name="CompNovo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Performs a de novo peptide identification using the CompNovo engine.</description> 5 <description>Performs a de novo peptide identification using the CompNovo engine.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">CompNovo</token> 7 <token name="@EXECUTABLE@">CompNovo</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@
39 <configfiles> 37 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 38 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 40 </configfiles>
43 <inputs> 41 <inputs>
44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file in mzML format" help=" select mzml data sets(s)"/> 42 <param argument="-in" type="data" format="mzml" optional="false" label="input file in mzML format" help=" select mzml data sets(s)"/>
45 <section name="algorithm" title="Algorithm section" help="" expanded="false"> 43 <section name="algorithm" title="Algorithm section" help="" expanded="false">
46 <param name="max_number_aa_per_decomp" argument="-algorithm:max_number_aa_per_decomp" type="integer" optional="true" value="4" label="maximal amino acid frequency per decomposition" help=""/> 44 <param name="max_number_aa_per_decomp" argument="-algorithm:max_number_aa_per_decomp" type="integer" optional="true" value="4" label="maximal amino acid frequency per decomposition" help=""/>
47 <param name="tryptic_only" argument="-algorithm:tryptic_only" type="text" optional="true" value="true" label="if set to true only tryptic peptides are reported" help=""> 45 <param name="tryptic_only" argument="-algorithm:tryptic_only" type="boolean" truevalue="true" falsevalue="false" checked="true" label="if set to true only tryptic peptides are reported" help=""/>
48 <expand macro="list_string_san"/>
49 </param>
50 <param name="precursor_mass_tolerance" argument="-algorithm:precursor_mass_tolerance" type="float" optional="true" value="1.5" label="precursor mass tolerance" help=""/> 46 <param name="precursor_mass_tolerance" argument="-algorithm:precursor_mass_tolerance" type="float" optional="true" value="1.5" label="precursor mass tolerance" help=""/>
51 <param name="fragment_mass_tolerance" argument="-algorithm:fragment_mass_tolerance" type="float" optional="true" value="0.3" label="fragment mass tolerance" help=""/> 47 <param name="fragment_mass_tolerance" argument="-algorithm:fragment_mass_tolerance" type="float" optional="true" value="0.3" label="fragment mass tolerance" help=""/>
52 <param name="max_number_pivot" argument="-algorithm:max_number_pivot" type="integer" optional="true" value="9" label="maximal number of pivot ions to be used" help=""/> 48 <param name="max_number_pivot" argument="-algorithm:max_number_pivot" type="integer" optional="true" value="9" label="maximal number of pivot ions to be used" help=""/>
53 <param name="max_subscore_number" argument="-algorithm:max_subscore_number" type="integer" optional="true" value="40" label="maximal number of solutions of a subsegment that are kept" help=""/> 49 <param name="max_subscore_number" argument="-algorithm:max_subscore_number" type="integer" optional="true" value="40" label="maximal number of solutions of a subsegment that are kept" help=""/>
54 <param name="decomp_weights_precision" argument="-algorithm:decomp_weights_precision" type="float" optional="true" value="0.01" label="precision used to calculate the decompositions, this only affects cache usage!" help=""/> 50 <param name="decomp_weights_precision" argument="-algorithm:decomp_weights_precision" type="float" optional="true" value="0.01" label="precision used to calculate the decompositions, this only affects cache usage!" help=""/>
61 <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" value="1" label="maximal number of missed cleavages allowed per peptide" help=""/> 57 <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" value="1" label="maximal number of missed cleavages allowed per peptide" help=""/>
62 <param name="number_of_hits" argument="-algorithm:number_of_hits" type="integer" optional="true" value="100" label="maximal number of hits which are reported per spectrum" help=""/> 58 <param name="number_of_hits" argument="-algorithm:number_of_hits" type="integer" optional="true" value="100" label="maximal number of hits which are reported per spectrum" help=""/>
63 <param name="estimate_precursor_mz" argument="-algorithm:estimate_precursor_mz" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If set to true, the precursor charge will be estimated" help="e.g. from the precursor peaks of the ETD spectrum.. The input is believed otherwise"/> 59 <param name="estimate_precursor_mz" argument="-algorithm:estimate_precursor_mz" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If set to true, the precursor charge will be estimated" help="e.g. from the precursor peaks of the ETD spectrum.. The input is believed otherwise"/>
64 <param name="number_of_prescoring_hits" argument="-algorithm:number_of_prescoring_hits" type="integer" optional="true" value="250" label="how many sequences are kept after first rough scoring for better scoring" help=""/> 60 <param name="number_of_prescoring_hits" argument="-algorithm:number_of_prescoring_hits" type="integer" optional="true" value="250" label="how many sequences are kept after first rough scoring for better scoring" help=""/>
65 <param name="fixed_modifications" argument="-algorithm: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)'"> 61 <param name="fixed_modifications" argument="-algorithm: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)'">
66 <option value="">default (nothing chosen)</option>
67 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 62 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
68 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 63 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
69 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 64 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
70 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 65 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
71 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 66 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
1430 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 1425 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
1431 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 1426 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
1432 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 1427 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
1433 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 1428 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
1434 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 1429 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
1435 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1436 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 1430 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
1437 <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> 1431 <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>
1438 <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> 1432 <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>
1439 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 1433 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
1440 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 1434 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
2990 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 2984 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
2991 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 2985 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
2992 <option value="ZGB (K)">ZGB (K)</option> 2986 <option value="ZGB (K)">ZGB (K)</option>
2993 <option value="ZGB (N-term)">ZGB (N-term)</option> 2987 <option value="ZGB (N-term)">ZGB (N-term)</option>
2994 <option value="ZQG (K)">ZQG (K)</option> 2988 <option value="ZQG (K)">ZQG (K)</option>
2995 <expand macro="list_string_san"/> 2989 <expand macro="list_string_san" name="fixed_modifications"/>
2996 </param> 2990 </param>
2997 <param name="variable_modifications" argument="-algorithm: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)'"> 2991 <param name="variable_modifications" argument="-algorithm: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)'">
2998 <option value="">default (nothing chosen)</option>
2999 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> 2992 <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
3000 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> 2993 <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option>
3001 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> 2994 <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option>
3002 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option> 2995 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
3003 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option> 2996 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
4362 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option> 4355 <option value="Glu-&gt;Lys (E)">Glu-&gt;Lys (E)</option>
4363 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option> 4356 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
4364 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option> 4357 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
4365 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option> 4358 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
4366 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option> 4359 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
4367 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4368 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option> 4360 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
4369 <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> 4361 <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>
4370 <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> 4362 <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>
4371 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option> 4363 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
4372 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option> 4364 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
5922 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option> 5914 <option value="Xlink:SMCC[237] (Protein N-term)">Xlink:SMCC[237] (Protein N-term)</option>
5923 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option> 5915 <option value="Xlink:SMCC[321] (C)">Xlink:SMCC[321] (C)</option>
5924 <option value="ZGB (K)">ZGB (K)</option> 5916 <option value="ZGB (K)">ZGB (K)</option>
5925 <option value="ZGB (N-term)">ZGB (N-term)</option> 5917 <option value="ZGB (N-term)">ZGB (N-term)</option>
5926 <option value="ZQG (K)">ZQG (K)</option> 5918 <option value="ZQG (K)">ZQG (K)</option>
5927 <expand macro="list_string_san"/> 5919 <expand macro="list_string_san" name="variable_modifications"/>
5928 </param> 5920 </param>
5929 <param name="residue_set" argument="-algorithm:residue_set" type="text" optional="true" value="Natural19WithoutI" label="The predefined amino acid set that should be used, see doc of ResidueDB for possible residue sets" help=""> 5921 <param name="residue_set" argument="-algorithm:residue_set" type="text" optional="true" value="Natural19WithoutI" label="The predefined amino acid set that should be used, see doc of ResidueDB for possible residue sets" help="">
5930 <expand macro="list_string_san"/> 5922 <expand macro="list_string_san" name="residue_set"/>
5931 </param> 5923 </param>
5932 </section> 5924 </section>
5933 <expand macro="adv_opts_macro"> 5925 <expand macro="adv_opts_macro">
5934 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 5926 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
5935 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 5927 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
5936 <expand macro="list_string_san"/> 5928 <expand macro="list_string_san" name="test"/>
5937 </param> 5929 </param>
5938 </expand> 5930 </expand>
5939 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 5931 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
5940 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 5932 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
5941 </param> 5933 </param>
5944 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 5936 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
5945 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 5937 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
5946 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 5938 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
5947 </data> 5939 </data>
5948 </outputs> 5940 </outputs>
5949 <tests> 5941 <tests><!-- TOPP_CompNovo_1 -->
5950 <expand macro="autotest_CompNovo"/> 5942 <test expect_num_outputs="2">
5951 <expand macro="manutest_CompNovo"/> 5943 <section name="adv_opts">
5944 <param name="force" value="false"/>
5945 <param name="test" value="true"/>
5946 </section>
5947 <param name="in" value="CompNovo_1_input.mzML"/>
5948 <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
5949 <section name="algorithm">
5950 <param name="max_number_aa_per_decomp" value="4"/>
5951 <param name="tryptic_only" value="true"/>
5952 <param name="precursor_mass_tolerance" value="0.3"/>
5953 <param name="fragment_mass_tolerance" value="0.3"/>
5954 <param name="max_number_pivot" value="9"/>
5955 <param name="max_subscore_number" value="40"/>
5956 <param name="decomp_weights_precision" value="0.01"/>
5957 <param name="double_charged_iso_threshold" value="0.6"/>
5958 <param name="max_mz" value="2000.0"/>
5959 <param name="min_mz" value="200.0"/>
5960 <param name="max_isotope_to_score" value="3"/>
5961 <param name="max_decomp_weight" value="450.0"/>
5962 <param name="max_isotope" value="3"/>
5963 <param name="missed_cleavages" value="1"/>
5964 <param name="number_of_hits" value="1"/>
5965 <param name="estimate_precursor_mz" value="true"/>
5966 <param name="number_of_prescoring_hits" value="250"/>
5967 <param name="fixed_modifications"/>
5968 <param name="variable_modifications"/>
5969 <param name="residue_set" value="Natural19WithoutI"/>
5970 </section>
5971 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
5972 <output name="ctd_out" ftype="xml">
5973 <assert_contents>
5974 <is_valid_xml/>
5975 </assert_contents>
5976 </output>
5977 </test>
5952 </tests> 5978 </tests>
5953 <help><![CDATA[Performs a de novo peptide identification using the CompNovo engine. 5979 <help><![CDATA[Performs a de novo peptide identification using the CompNovo engine.
5954 5980
5955 5981
5956 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_CompNovo.html]]></help> 5982 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_CompNovo.html]]></help>
5957 <expand macro="references"/> 5983 <expand macro="references"/>
5958 </tool> 5984 </tool>