Mercurial > repos > galaxyp > openms_compnovo
diff CompNovo.xml @ 16:cd9449dbe4e4 draft default tip
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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--- a/CompNovo.xml Fri Nov 06 20:05:59 2020 +0000 +++ b/CompNovo.xml Thu Dec 01 19:17:28 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="CompNovo" name="CompNovo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="CompNovo" name="CompNovo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Performs a de novo peptide identification using the CompNovo engine.</description> <macros> <token name="@EXECUTABLE@">CompNovo</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -41,12 +39,10 @@ <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="algorithm" title="Algorithm section" help="" expanded="false"> <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=""/> - <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=""> - <expand macro="list_string_san"/> - </param> + <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=""/> <param name="precursor_mass_tolerance" argument="-algorithm:precursor_mass_tolerance" type="float" optional="true" value="1.5" label="precursor mass tolerance" help=""/> <param name="fragment_mass_tolerance" argument="-algorithm:fragment_mass_tolerance" type="float" optional="true" value="0.3" label="fragment mass tolerance" help=""/> <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=""/> @@ -63,7 +59,6 @@ <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"/> <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=""/> <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)'"> - <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> @@ -1433,7 +1428,6 @@ <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> @@ -2992,10 +2986,9 @@ <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="-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)'"> - <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> @@ -4365,7 +4358,6 @@ <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> @@ -5924,16 +5916,16 @@ <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="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=""> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="residue_set"/> </param> </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"> @@ -5946,13 +5938,47 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_CompNovo"/> - <expand macro="manutest_CompNovo"/> + <tests><!-- TOPP_CompNovo_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="CompNovo_1_input.mzML"/> + <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <section name="algorithm"> + <param name="max_number_aa_per_decomp" value="4"/> + <param name="tryptic_only" value="true"/> + <param name="precursor_mass_tolerance" value="0.3"/> + <param name="fragment_mass_tolerance" value="0.3"/> + <param name="max_number_pivot" value="9"/> + <param name="max_subscore_number" value="40"/> + <param name="decomp_weights_precision" value="0.01"/> + <param name="double_charged_iso_threshold" value="0.6"/> + <param name="max_mz" value="2000.0"/> + <param name="min_mz" value="200.0"/> + <param name="max_isotope_to_score" value="3"/> + <param name="max_decomp_weight" value="450.0"/> + <param name="max_isotope" value="3"/> + <param name="missed_cleavages" value="1"/> + <param name="number_of_hits" value="1"/> + <param name="estimate_precursor_mz" value="true"/> + <param name="number_of_prescoring_hits" value="250"/> + <param name="fixed_modifications"/> + <param name="variable_modifications"/> + <param name="residue_set" value="Natural19WithoutI"/> + </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[Performs a de novo peptide identification using the CompNovo engine. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_CompNovo.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_CompNovo.html]]></help> <expand macro="references"/> </tool>