Mercurial > repos > galaxyp > openms_mascotadapter
diff MascotAdapter.xml @ 14:087b9d721a08 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp |
|---|---|
| date | Fri, 14 Jun 2024 21:43:35 +0000 |
| parents | 27e308170367 |
| children |
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--- a/MascotAdapter.xml Thu Dec 01 19:12:19 2022 +0000 +++ b/MascotAdapter.xml Fri Jun 14 21:43:35 2024 +0000 @@ -1,8 +1,7 @@ -<?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]--> +<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]--> <tool id="MascotAdapter" name="MascotAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Annotates MS/MS spectra using Mascot.</description> + <description>Annotates MS/MS spectra using Mascot</description> <macros> <token name="@EXECUTABLE@">MascotAdapter</token> <import>macros.xml</import> @@ -15,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call @@ -39,18 +38,19 @@ <configfile name="hardcoded_json"><![CDATA[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="mascotxml,mzdata" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/> - <param argument="-out_type" display="radio" type="select" optional="false" label="output file type (for TOPPAS)" help=""> + <param argument="-in" type="data" format="mascotxml,mzdata" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/> + <param argument="-out_type" type="select" label="output file type (for TOPPAS)" help=""> <option value="idXML">idxml</option> <option value="mgf">mgf</option> + <validator type="expression" message="A value needs to be selected">value != "select a value"</validator> <expand macro="list_string_san" name="out_type"/> </param> - <param argument="-instrument" type="text" optional="true" value="Default" label="the instrument that was used to measure the spectra" help=""> + <param argument="-instrument" type="text" value="Default" label="the instrument that was used to measure the spectra" help=""> <expand macro="list_string_san" name="instrument"/> </param> - <param argument="-precursor_mass_tolerance" type="float" optional="true" value="2.0" label="the precursor mass tolerance" help=""/> - <param argument="-peak_mass_tolerance" type="float" optional="true" value="1.0" label="the peak mass tolerance" help=""/> - <param argument="-taxonomy" type="select" optional="true" label="the taxonomy" help=""> + <param argument="-precursor_mass_tolerance" type="float" value="2.0" label="the precursor mass tolerance" help=""/> + <param argument="-peak_mass_tolerance" type="float" value="1.0" label="the peak mass tolerance" help=""/> + <param argument="-taxonomy" type="select" label="the taxonomy" help=""> <option value="All entries" selected="true">All entries</option> <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option> <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option> @@ -126,17 +126,17 @@ <expand macro="list_string_val" name="variable_modifications"/> <expand macro="list_string_san" name="variable_modifications"/> </param> - <param argument="-charges" type="text" optional="true" value="1+ 2+ 3+" label="the different charge states" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <param argument="-charges" type="text" value="1+ 2+ 3+" label="the different charge states" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_string_val" name="charges"/> <expand macro="list_string_san" name="charges"/> </param> - <param argument="-db" type="text" optional="true" value="MSDB" label="the database to search in" help=""> + <param argument="-db" type="text" value="MSDB" label="the database to search in" help=""> <expand macro="list_string_san" name="db"/> </param> - <param argument="-hits" type="text" optional="true" value="AUTO" label="the number of hits to report" help=""> + <param argument="-hits" type="text" value="AUTO" label="the number of hits to report" help=""> <expand macro="list_string_san" name="hits"/> </param> - <param argument="-cleavage" type="select" optional="true" 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)"> + <param argument="-cleavage" type="select" 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)"> <option value="Trypsin" selected="true">Trypsin</option> <option value="Arg-C">Arg-C</option> <option value="Asp-N">Asp-N</option> @@ -158,27 +158,27 @@ <option value="None">None</option> <expand macro="list_string_san" name="cleavage"/> </param> - <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="0" label="number of allowed missed cleavages" help=""/> - <param argument="-sig_threshold" type="float" optional="true" value="0.05" label="significance threshold" help=""/> - <param argument="-pep_homol" type="float" optional="true" value="1.0" label="peptide homology threshold" help=""/> - <param argument="-pep_ident" type="float" optional="true" value="1.0" label="peptide ident threshold" help=""/> - <param argument="-pep_rank" type="integer" optional="true" value="1" label="peptide rank" help=""/> - <param argument="-prot_score" type="float" optional="true" value="1.0" label="protein score" help=""/> - <param argument="-pep_score" type="float" optional="true" value="1.0" label="peptide score" help=""/> - <param argument="-pep_exp_z" type="integer" optional="true" value="1" label="peptide expected charge" help=""/> - <param argument="-show_unassigned" type="integer" optional="true" value="1" label="show_unassigned" help=""/> - <param argument="-first_dim_rt" type="float" optional="true" value="0.0" label="additional information which is added to every peptide identification as metavalue if set > 0" help=""/> + <param argument="-missed_cleavages" type="integer" min="0" value="0" label="number of allowed missed cleavages" help=""/> + <param argument="-sig_threshold" type="float" value="0.05" label="significance threshold" help=""/> + <param argument="-pep_homol" type="float" value="1.0" label="peptide homology threshold" help=""/> + <param argument="-pep_ident" type="float" value="1.0" label="peptide ident threshold" help=""/> + <param argument="-pep_rank" type="integer" value="1" label="peptide rank" help=""/> + <param argument="-prot_score" type="float" value="1.0" label="protein score" help=""/> + <param argument="-pep_score" type="float" value="1.0" label="peptide score" help=""/> + <param argument="-pep_exp_z" type="integer" value="1" label="peptide expected charge" help=""/> + <param argument="-show_unassigned" type="integer" value="1" label="show_unassigned" help=""/> + <param argument="-first_dim_rt" type="float" value="0.0" label="additional information which is added to every peptide identification as metavalue if set > 0" help=""/> <param argument="-boundary" type="text" optional="true" value="" label="MIME boundary for mascot output format" help=""> <expand macro="list_string_san" name="boundary"/> </param> - <param argument="-mass_type" type="select" optional="true" label="mass type" help=""> + <param argument="-mass_type" type="select" label="mass type" help=""> <option value="Monoisotopic" selected="true">Monoisotopic</option> <option value="Average">Average</option> <expand macro="list_string_san" name="mass_type"/> </param> <expand macro="adv_opts_macro"> <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=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -196,14 +196,15 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_MascotAdapter_1 --> + <tests> + <!-- TOPP_MascotAdapter_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="MascotAdapter_1_input.mzData"/> - <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta_frac="0.7"/> + <output name="out" value="MascotAdapter_1_output.mascot_in" compare="sim_size" delta_frac="0.7"/> <param name="out_type" value="mgf"/> <param name="instrument" value="ESI-TRAP"/> <param name="precursor_mass_tolerance" value="1.3"/> @@ -233,6 +234,9 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_MascotAdapter_2 --> <test expect_num_outputs="2"> @@ -241,14 +245,12 @@ <param name="test" value="true"/> </section> <param name="in" value="MascotAdapter_2_input.mascotXML"/> - <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <output name="out" value="MascotAdapter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> <param name="out_type" value="idXML"/> <param name="instrument" value="Default"/> <param name="precursor_mass_tolerance" value="2.0"/> <param name="peak_mass_tolerance" value="1.0"/> <param name="taxonomy" value="All entries"/> - <param name="modifications" value=""/> - <param name="variable_modifications" value=""/> <param name="charges" value=""1+" "2+" "3+""/> <param name="db" value="MSDB"/> <param name="hits" value="AUTO"/> @@ -271,11 +273,14 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> </tests> <help><![CDATA[Annotates MS/MS spectra using Mascot. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MascotAdapter.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MascotAdapter.html]]></help> <expand macro="references"/> </tool>