Mercurial > repos > galaxyp > openms_mascotadapteronline
diff MascotAdapterOnline.xml @ 13:3f3d33920f90 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:16:04 +0000 |
| parents | 92476035066d |
| children | 5f9e1383f6e4 |
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--- a/MascotAdapterOnline.xml Fri Nov 06 20:13:11 2020 +0000 +++ b/MascotAdapterOnline.xml Thu Dec 01 19:16:04 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: [Identification]--> -<tool id="MascotAdapterOnline" name="MascotAdapterOnline" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="MascotAdapterOnline" name="MascotAdapterOnline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Annotates MS/MS spectra using Mascot.</description> <macros> <token name="@EXECUTABLE@">MascotAdapterOnline</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -41,46 +39,45 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file in mzML format.." help=" select mzml data sets(s)"/> + <param argument="-in" type="data" format="mzml" optional="false" label="input file in mzML format.." help=" select mzml data sets(s)"/> <section name="Mascot_parameters" title="Mascot parameters used for searching" help="" expanded="false"> <param name="database" argument="-Mascot_parameters:database" type="text" optional="true" value="MSDB" label="Name of the sequence database" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="database"/> </param> - <param name="search_type" argument="-Mascot_parameters:search_type" display="radio" type="select" optional="false" label="Name of the search type for the query" help=""> + <param name="search_type" argument="-Mascot_parameters:search_type" type="select" optional="true" label="Name of the search type for the query" help=""> <option value="MIS" selected="true">MIS</option> <option value="SQ">SQ</option> <option value="PMF">PMF</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="search_type"/> </param> <param name="enzyme" argument="-Mascot_parameters:enzyme" type="text" optional="true" value="Trypsin" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)"> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="enzyme"/> </param> <param name="instrument" argument="-Mascot_parameters:instrument" type="text" optional="true" value="Default" label="Instrument definition which specifies the fragmentation rules" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="instrument"/> </param> <param name="missed_cleavages" argument="-Mascot_parameters:missed_cleavages" type="integer" optional="true" min="0" value="1" label="Number of missed cleavages allowed for the enzyme" help=""/> <param name="precursor_mass_tolerance" argument="-Mascot_parameters:precursor_mass_tolerance" type="float" optional="true" min="0.0" value="3.0" label="Tolerance of the precursor peaks" help=""/> - <param name="precursor_error_units" argument="-Mascot_parameters:precursor_error_units" display="radio" type="select" optional="false" label="Units of the precursor mass tolerance" help=""> + <param name="precursor_error_units" argument="-Mascot_parameters:precursor_error_units" type="select" optional="true" label="Units of the precursor mass tolerance" help=""> <option value="%">%</option> <option value="ppm">ppm</option> <option value="mmu">mmu</option> <option value="Da" selected="true">Da</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="precursor_error_units"/> </param> <param name="fragment_mass_tolerance" argument="-Mascot_parameters:fragment_mass_tolerance" type="float" optional="true" min="0.0" value="0.3" label="Tolerance of the peaks in the fragment spectrum" help=""/> - <param name="fragment_error_units" argument="-Mascot_parameters:fragment_error_units" display="radio" type="select" optional="false" label="Units of the fragment peaks tolerance" help=""> + <param name="fragment_error_units" argument="-Mascot_parameters:fragment_error_units" type="select" optional="true" label="Units of the fragment peaks tolerance" help=""> <option value="mmu">mmu</option> <option value="Da" selected="true">Da</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="fragment_error_units"/> </param> <param name="charges" argument="-Mascot_parameters:charges" type="text" optional="true" value="1,2,3" label="Charge states to consider, given as a comma separated list of integers (only used for spectra without precursor charge information)" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="charges"/> </param> <param name="taxonomy" argument="-Mascot_parameters:taxonomy" type="text" optional="true" value="All entries" label="Taxonomy specification of the sequences" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="taxonomy"/> </param> <param name="fixed_modifications" argument="-Mascot_parameters:fixed_modifications" multiple="true" type="select" optional="true" label="List of fixed modifications, according to UniMod definitions" 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> @@ -1450,7 +1447,6 @@ <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> @@ -3009,10 +3005,9 @@ <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="fixed_modifications"/> </param> <param name="variable_modifications" argument="-Mascot_parameters:variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications given as UniMod definitions" 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> @@ -4382,7 +4377,6 @@ <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> @@ -5941,69 +5935,70 @@ <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="variable_modifications"/> </param> <param name="special_modifications" argument="-Mascot_parameters:special_modifications" type="text" optional="true" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)" label="Modifications with specificity groups that are used by Mascot and have to be treated specially" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="special_modifications"/> </param> - <param name="mass_type" argument="-Mascot_parameters:mass_type" display="radio" type="select" optional="false" label="Defines the mass type, either monoisotopic or average" help=""> + <param name="mass_type" argument="-Mascot_parameters:mass_type" type="select" optional="true" label="Defines the mass type, either monoisotopic or average" help=""> <option value="monoisotopic" selected="true">monoisotopic</option> <option value="average">average</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="mass_type"/> </param> <param name="number_of_hits" argument="-Mascot_parameters:number_of_hits" type="integer" optional="true" min="0" value="0" label="Number of hits which should be returned, if 0 AUTO mode is enabled" help=""/> <param name="skip_spectrum_charges" argument="-Mascot_parameters:skip_spectrum_charges" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sometimes precursor charges are given for each spectrum but are wrong, setting this to 'true' does not write any charge information to the spectrum, the general charge information is however kept" help=""/> + <param name="decoy" argument="-Mascot_parameters:decoy" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to true if mascot should generate the decoy database" help=""/> <param name="search_title" argument="-Mascot_parameters:search_title" type="text" optional="true" value="OpenMS_search" label="Sets the title of the search" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="search_title"/> </param> <param name="username" argument="-Mascot_parameters:username" type="text" optional="true" value="OpenMS" label="Sets the username which is mentioned in the results file" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="username"/> </param> <param name="email" argument="-Mascot_parameters:email" type="text" optional="true" value="" label="Sets the email which is mentioned in the results file" help="Note: Some server require that a proper email is provided"> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="email"/> </param> </section> <section name="Mascot_server" title="Mascot server details" help="" expanded="false"> <param name="hostname" argument="-Mascot_server:hostname" type="text" optional="true" value="" label="Address of the host where Mascot listens" help="e.g. 'mascot-server' or '127.0.0.1'"> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="hostname"/> </param> <param name="host_port" argument="-Mascot_server:host_port" type="integer" optional="true" min="0" value="80" label="Port where the Mascot server listens, 80 should be a good guess" help=""/> <param name="server_path" argument="-Mascot_server:server_path" type="text" optional="true" value="mascot" label="Path on the server where Mascot server listens, 'mascot' should be a good guess" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="server_path"/> </param> <param name="timeout" argument="-Mascot_server:timeout" type="integer" optional="true" min="0" value="1500" label="Timeout in seconds, after which the query is declared as failed.This is NOT the whole time the search takes, but the time in between two progress steps" help="Some Mascot servers freeze during this (unstable network etc) and idle forever, the connection is killed. Set this to 0 to disable timeout!"/> <param name="boundary" argument="-Mascot_server:boundary" type="text" optional="true" value="GZWgAaYKjHFeUaLOLEIOMq" label="Boundary for the MIME section" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="boundary"/> </param> <param name="use_proxy" argument="-Mascot_server:use_proxy" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag which enables the proxy usage for the HTTP requests, please specify at least 'proxy_host' and 'proxy_port'" help=""/> <param name="proxy_host" argument="-Mascot_server:proxy_host" type="text" optional="true" value="" label="Host where the proxy server runs on" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="proxy_host"/> </param> <param name="proxy_port" argument="-Mascot_server:proxy_port" type="integer" optional="true" min="0" value="0" label="Port where the proxy server listens" help=""/> <param name="proxy_username" argument="-Mascot_server:proxy_username" type="text" optional="true" value="" label="Login name for the proxy server, if needed" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="proxy_username"/> </param> <param name="proxy_password" argument="-Mascot_server:proxy_password" type="text" optional="true" value="" label="Login password for the proxy server, if needed" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="proxy_password"/> </param> <param name="login" argument="-Mascot_server:login" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag which should be set 'true' if Mascot security is enabled; also set 'username' and 'password' then" help=""/> <param name="username" argument="-Mascot_server:username" type="text" optional="true" value="" label="Name of the user if login is used (Mascot security must be enabled!)" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="username"/> </param> <param name="password" argument="-Mascot_server:password" type="text" optional="true" value="" label="Password of the user if login is used (Mascot security must be enabled!)" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="password"/> </param> <param name="use_ssl" argument="-Mascot_server:use_ssl" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag indicating whether you want to send requests to an HTTPS server or not (HTTP)" help="Requires OpenSSL to be installed (see openssl.org)"/> <param name="export_params" argument="-Mascot_server:export_params" type="text" optional="true" value="_ignoreionsscorebelow=0&_sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0" label="Adjustable export parameters (passed to Mascot's 'export_dat_2.pl' script)" help="Generally only parameters that control which hits to export are safe to adjust/add. Many settings that govern what types of information to include are required by OpenMS and cannot be changed. Note that setting 'query_master' to 1 may lead to incorrect protein references for peptides"> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="export_params"/> </param> <param name="skip_export" argument="-Mascot_server:skip_export" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For use with an external Mascot Percolator (via GenericWrapper): Run the Mascot search, but do not export the results" help="The output file produced by MascotAdapterOnline will contain only the Mascot search number"/> + <param name="batch_size" argument="-Mascot_server:batch_size" type="integer" optional="true" min="0" value="50000" label="Number of spectra processed in one batch by Mascot (default 50000)" help=""/> </section> <expand macro="adv_opts_macro"> - <param name="keep_protein_links" argument="-keep_protein_links" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The Mascot response file usually returns incomplete/wrong protein hits, so re-indexing the peptide hits is required" help="To avoid confusion why there are so few protein hits and force re-indexing, no proteins should be reported. To see the original (wrong) list, enable this flag"/> - <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"> @@ -6016,13 +6011,124 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_MascotAdapterOnline"/> - <expand macro="manutest_MascotAdapterOnline"/> + <tests><!-- TOPP_MascotAdapterOnline_1 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="spectra_comet.mzML"/> + <output name="out" file="MascotAdapterOnline_1_out.idXML" compare="sim_size" delta_frac="0.7" 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"/> + <param name="variable_modifications"/> + <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="decoy" 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"/> + <param name="batch_size" value="50000"/> + </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_MascotAdapterOnline_2 --> + <test expect_num_outputs="2"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="spectra_comet.mzML"/> + <output name="out" file="MascotAdapterOnline_2_out.idXML" compare="sim_size" delta_frac="0.7" 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"/> + <param name="variable_modifications"/> + <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="decoy" value="true"/> + <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"/> + <param name="batch_size" value="50000"/> + </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[Annotates MS/MS spectra using Mascot. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MascotAdapterOnline.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MascotAdapterOnline.html]]></help> <expand macro="references"/> </tool>