Mercurial > repos > galaxyp > openms_simplesearchengine
diff SimpleSearchEngine.xml @ 13:da78f97a6dda draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:17:17 +0000 |
| parents | 1b56031ac321 |
| children | a1724438d580 |
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--- a/SimpleSearchEngine.xml Fri Nov 06 20:11:01 2020 +0000 +++ b/SimpleSearchEngine.xml Thu Dec 01 19:17:17 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: [Utilities]--> -<tool id="SimpleSearchEngine" name="SimpleSearchEngine" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="SimpleSearchEngine" name="SimpleSearchEngine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Annotates MS/MS spectra using SimpleSearchEngine.</description> <macros> <token name="@EXECUTABLE@">SimpleSearchEngine</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -45,65 +43,65 @@ <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" help=" select mzml data sets(s)"/> - <param name="database" argument="-database" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/> + <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> + <param argument="-database" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/> <section name="Search" title="" help="" expanded="false"> - <param name="enzyme" argument="-Search:enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help=""> + <param name="enzyme" argument="-Search:enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help=""> <option value="Trypsin" selected="true">Trypsin</option> - <option value="Lys-C/P">Lys-C/P</option> - <option value="PepsinA">PepsinA</option> - <option value="TrypChymo">TrypChymo</option> - <option value="Trypsin/P">Trypsin/P</option> - <option value="no cleavage">no cleavage</option> - <option value="unspecific cleavage">unspecific cleavage</option> - <option value="Arg-C/P">Arg-C/P</option> - <option value="V8-DE">V8-DE</option> - <option value="V8-E">V8-E</option> - <option value="leukocyte elastase">leukocyte elastase</option> - <option value="proline endopeptidase">proline endopeptidase</option> - <option value="Arg-C">Arg-C</option> - <option value="Chymotrypsin/P">Chymotrypsin/P</option> - <option value="CNBr">CNBr</option> - <option value="Formic_acid">Formic_acid</option> - <option value="Lys-C">Lys-C</option> - <option value="Lys-N">Lys-N</option> + <option value="staphylococcal protease/D">staphylococcal protease/D</option> <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> <option value="Glu-C+P">Glu-C+P</option> <option value="PepsinA + P">PepsinA + P</option> <option value="cyanogen-bromide">cyanogen-bromide</option> <option value="Clostripain/P">Clostripain/P</option> <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> + <option value="CNBr">CNBr</option> + <option value="Formic_acid">Formic_acid</option> + <option value="Lys-C">Lys-C</option> + <option value="Arg-C/P">Arg-C/P</option> + <option value="Asp-N">Asp-N</option> + <option value="Asp-N/B">Asp-N/B</option> + <option value="PepsinA">PepsinA</option> + <option value="TrypChymo">TrypChymo</option> + <option value="Trypsin/P">Trypsin/P</option> + <option value="V8-DE">V8-DE</option> + <option value="V8-E">V8-E</option> + <option value="leukocyte elastase">leukocyte elastase</option> + <option value="proline endopeptidase">proline endopeptidase</option> + <option value="no cleavage">no cleavage</option> + <option value="unspecific cleavage">unspecific cleavage</option> <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> <option value="Alpha-lytic protease">Alpha-lytic protease</option> <option value="2-iodobenzoate">2-iodobenzoate</option> <option value="iodosobenzoate">iodosobenzoate</option> - <option value="staphylococcal protease/D">staphylococcal protease/D</option> - <option value="Asp-N">Asp-N</option> - <option value="Asp-N/B">Asp-N/B</option> + <option value="Arg-C">Arg-C</option> + <option value="Lys-N">Lys-N</option> + <option value="Lys-C/P">Lys-C/P</option> <option value="Asp-N_ambic">Asp-N_ambic</option> <option value="Chymotrypsin">Chymotrypsin</option> - <expand macro="list_string_san"/> + <option value="Chymotrypsin/P">Chymotrypsin/P</option> + <expand macro="list_string_san" name="enzyme"/> </param> <param name="decoys" argument="-Search:decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Should decoys be generated?" help=""/> <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false"> - <param name="mass_tolerance" argument="-Search:precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/> - <param name="mass_tolerance_unit" argument="-Search:precursor:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help=""> + <param name="mass_tolerance" argument="-Search:precursor:mass_tolerance" type="float" optional="true" value="10.0" label="+/- tolerance for precursor mass" help=""/> + <param name="mass_tolerance_unit" argument="-Search:precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help=""> <option value="ppm" selected="true">ppm</option> <option value="Da">Da</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="mass_tolerance_unit"/> </param> <param name="min_charge" argument="-Search:precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/> <param name="max_charge" argument="-Search:precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/> <param name="isotopes" argument="-Search:precursor:isotopes" type="text" optional="true" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_integer_valsan"/> + <expand macro="list_integer_valsan" name="isotopes"/> </param> </section> <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false"> <param name="mass_tolerance" argument="-Search:fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance" help=""/> - <param name="mass_tolerance_unit" argument="-Search:fragment:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of fragment m" help=""> + <param name="mass_tolerance_unit" argument="-Search:fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment m" help=""> <option value="ppm" selected="true">ppm</option> <option value="Da">Da</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="mass_tolerance_unit"/> </param> </section> <section name="modifications" title="Modifications Options" help="" expanded="false"> @@ -1477,7 +1475,6 @@ <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> @@ -3036,7 +3033,7 @@ <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"/> </param> <param name="variable" argument="-Search:modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'"> <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> @@ -4408,7 +4405,6 @@ <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> @@ -5967,16 +5963,18 @@ <option value="ZGB (K)">ZGB (K)</option> <option value="ZGB (N-term)">ZGB (N-term)</option> <option value="ZQG (K)">ZQG (K)</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="variable"/> </param> <param name="variable_max_per_peptide" argument="-Search:modifications:variable_max_per_peptide" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/> </section> <section name="annotate" title="Annotation Options" help="" expanded="false"> <param name="PSM" argument="-Search:annotate:PSM" multiple="true" type="select" optional="true" label="Annotations added to each PSM" help=""> - <option value="">default (nothing chosen)</option> + <option value="ALL" selected="true">ALL</option> <option value="fragment_mz_error_median_ppm">fragment_mz_error_median_ppm</option> <option value="precursor_mz_error_ppm">precursor_mz_error_ppm</option> - <expand macro="list_string_san"/> + <option value="matched_prefix_ions_fraction">matched_prefix_ions_fraction</option> + <option value="matched_suffix_ions_fraction">matched_suffix_ions_fraction</option> + <expand macro="list_string_san" name="PSM"/> </param> </section> <section name="peptide" title="Peptide Options" help="" expanded="false"> @@ -5984,7 +5982,7 @@ <param name="max_size" argument="-Search:peptide:max_size" type="integer" optional="true" value="40" label="Maximum size a peptide must have after digestion to be considered in the search (0 = disabled)" help=""/> <param name="missed_cleavages" argument="-Search:peptide:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/> <param name="motif" argument="-Search:peptide:motif" type="text" optional="true" value="" label="If set, only peptides that contain this motif (provided as RegEx) will be considered" help=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="motif"/> </param> </section> <section name="report" title="Reporting Options" help="" expanded="false"> @@ -5992,9 +5990,9 @@ </section> </section> <expand macro="adv_opts_macro"> - <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"> @@ -6007,13 +6005,106 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_SimpleSearchEngine"/> - <expand macro="manutest_SimpleSearchEngine"/> + <tests><!-- UTILS_SimpleSearchEngine_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="SimpleSearchEngine_1.mzML"/> + <param name="database" value="SimpleSearchEngine_1.fasta"/> + <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <section name="Search"> + <param name="enzyme" value="Trypsin"/> + <param name="decoys" value="false"/> + <section name="precursor"> + <param name="mass_tolerance" value="5.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + <param name="min_charge" value="2"/> + <param name="max_charge" value="5"/> + <param name="isotopes" value="0 1"/> + </section> + <section name="fragment"> + <param name="mass_tolerance" value="0.3"/> + <param name="mass_tolerance_unit" value="Da"/> + </section> + <section name="modifications"> + <param name="fixed"/> + <param name="variable" value="Oxidation (M)"/> + <param name="variable_max_per_peptide" value="2"/> + </section> + <section name="annotate"> + <param name="PSM" value="ALL"/> + </section> + <section name="peptide"> + <param name="min_size" value="7"/> + <param name="max_size" value="40"/> + <param name="missed_cleavages" value="1"/> + <param name="motif" value=""/> + </section> + <section name="report"> + <param name="top_hits" value="1"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- UTILS_SimpleSearchEngine_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="SimpleSearchEngine_1.mzML"/> + <param name="database" value="SimpleSearchEngine_1.fasta"/> + <output name="out" file="SimpleSearchEngine_2_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <section name="Search"> + <param name="enzyme" value="Trypsin"/> + <param name="decoys" value="false"/> + <section name="precursor"> + <param name="mass_tolerance" value="10.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + <param name="min_charge" value="2"/> + <param name="max_charge" value="5"/> + <param name="isotopes" value="0 1"/> + </section> + <section name="fragment"> + <param name="mass_tolerance" value="10.0"/> + <param name="mass_tolerance_unit" value="ppm"/> + </section> + <section name="modifications"> + <param name="fixed" value="Carbamidomethyl (C)"/> + <param name="variable" value="Oxidation (M)"/> + <param name="variable_max_per_peptide" value="2"/> + </section> + <section name="annotate"> + <param name="PSM" value="ALL"/> + </section> + <section name="peptide"> + <param name="min_size" value="7"/> + <param name="max_size" value="40"/> + <param name="missed_cleavages" value="1"/> + <param name="motif" value=""/> + </section> + <section name="report"> + <param name="top_hits" value="1"/> + </section> + </section> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Annotates MS/MS spectra using SimpleSearchEngine. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SimpleSearchEngine.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SimpleSearchEngine.html]]></help> <expand macro="references"/> </tool>