Mercurial > repos > galaxyp > openms_pepnovoadapter
diff PepNovoAdapter.xml @ 4:533859c7e75f 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 19:18:33 +0000 |
| parents | 3bfc9aba4809 |
| children |
line wrap: on
line diff
--- a/PepNovoAdapter.xml Fri Nov 06 19:54:09 2020 +0000 +++ b/PepNovoAdapter.xml Thu Dec 01 19:18:33 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="PepNovoAdapter" name="PepNovoAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="PepNovoAdapter" name="PepNovoAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format.</description> <macros> <token name="@EXECUTABLE@">PepNovoAdapter</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -41,38 +39,38 @@ <configfile name="hardcoded_json"><![CDATA[{"pepnovo_executable": "pepnovo", "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 argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> <param name="model_directory" argument="-model_directory" type="select" optional="false" label="Name of the directory where the model files are kept" help=""> - <options from_data_table="pepnovo_models"> - <column name="name" index="0"/> - <column name="value" index="2"/> - <filter type="unique_value" name="unique_set" column="0"/> - <validator type="no_options" message="No model directory available"/> - </options> + <options from_data_table="pepnovo_models"> + <column name="name" index="0"/> + <column name="value" index="2"/> + <filter type="unique_value" name="unique_set" column="0"/> + <validator type="no_options" message="No model directory available"/> + </options> </param> - <param name="correct_pm" argument="-correct_pm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find optimal precursor mass and charge values" help=""/> - <param name="use_spectrum_charge" argument="-use_spectrum_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct charge" help=""/> - <param name="use_spectrum_mz" argument="-use_spectrum_mz" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct the precursor m/z value that appears in the file" help=""/> - <param name="no_quality_filter" argument="-no_quality_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not remove low quality spectra" help=""/> - <param name="fragment_tolerance" argument="-fragment_tolerance" type="float" optional="true" value="-1.0" label="The fragment tolerance (between 0 and 0.75 Da" help="Set to -1.0 to use model's default setting)"/> - <param name="pm_tolerance" argument="-pm_tolerance" type="float" optional="true" value="-1.0" label="The precursor mass tolerance (between 0 and 5.0 Da" help="Set to -1.0 to use model's default setting)"/> + <param argument="-correct_pm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find optimal precursor mass and charge values" help=""/> + <param argument="-use_spectrum_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct charge" help=""/> + <param argument="-use_spectrum_mz" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct the precursor m/z value that appears in the file" help=""/> + <param argument="-no_quality_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not remove low quality spectra" help=""/> + <param argument="-fragment_tolerance" type="float" optional="true" value="-1.0" label="The fragment tolerance (between 0 and 0.75 Da" help="Set to -1.0 to use model's default setting)"/> + <param argument="-pm_tolerance" type="float" optional="true" value="-1.0" label="The precursor mass tolerance (between 0 and 5.0 Da" help="Set to -1.0 to use model's default setting)"/> <param name="model" argument="-model" type="select" label="Name of the model that should be used" help=""> - <options from_data_table="pepnovo_models"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="param_value" ref="model_directory" column="2"/> - <filter type="unique_value" column="1"/> - <validator type="no_options" message="No model available"/> - </options> + <options from_data_table="pepnovo_models"> + <column name="name" index="1"/> + <column name="value" index="1"/> + <filter type="param_value" ref="model_directory" column="2"/> + <filter type="unique_value" column="1"/> + <validator type="no_options" message="No model available"/> + </options> </param> - <param name="digest" argument="-digest" display="radio" type="select" optional="false" label="Enzyme used for digestion (default TRYPSIN)" help=""> + <param argument="-digest" type="select" optional="true" label="Enzyme used for digestion (default TRYPSIN)" help=""> <option value="TRYPSIN" selected="true">TRYPSIN</option> <option value="NON_SPECIFIC">NON_SPECIFIC</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="digest"/> </param> - <param name="tag_length" argument="-tag_length" type="integer" optional="true" value="-1" label="Returns peptide sequence of the specified length (only lengths 3-6 are allowed)" help=""/> - <param name="num_solutions" argument="-num_solutions" type="integer" optional="true" min="1" max="2000" value="20" label="Number of solutions to be computed" help=""/> - <param name="fixed_modifications" argument="-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)'"> + <param argument="-tag_length" type="integer" optional="true" value="-1" label="Returns peptide sequence of the specified length (only lengths 3-6 are allowed)" help=""/> + <param argument="-num_solutions" type="integer" optional="true" min="1" max="2000" value="20" label="Number of solutions to be computed" help=""/> + <param argument="-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="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> @@ -1442,7 +1440,6 @@ <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> @@ -3001,9 +2998,9 @@ <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="-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)'"> + <param argument="-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="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> @@ -4373,7 +4370,6 @@ <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> @@ -5932,12 +5928,12 @@ <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> <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"> @@ -5950,13 +5946,23 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_PepNovoAdapter"/> - <expand macro="manutest_PepNovoAdapter"/> - </tests> + <tests><test expect_num_outputs="1"><!-- adapted from (dysfunctional) OMS 3rdParty tests (but model selection + unclear https://github.com/OpenMS/OpenMS/issues/4719)--> + <param name="adv_opts|test" value="true"/> + <param name="in" ftype="mzml" value="PepNovo_1.mzML"/> + <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/> + <param name="model" value="LTQ_COMP"/> + </test> + <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter --> + <param name="adv_opts|test" value="true"/> + <param name="in" ftype="mzml" value="PepNovo_1.mzML"/> + <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/> + <param name="model" value="LTQ_COMP"/> + </test> +</tests> <help><![CDATA[Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PepNovoAdapter.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PepNovoAdapter.html]]></help> <expand macro="references"/> </tool>