Mercurial > repos > galaxyp > openms_luciphoradapter
diff LuciphorAdapter.xml @ 14:bf2bf60c8af2 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 19:03:21 +0000 |
| parents | cab9b21eabf9 |
| children |
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--- a/LuciphorAdapter.xml Mon Dec 14 16:54:59 2020 +0000 +++ b/LuciphorAdapter.xml Thu Dec 01 19:03:21 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: [ID Processing]--> -<tool id="LuciphorAdapter" name="LuciphorAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05"> +<tool id="LuciphorAdapter" name="LuciphorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Modification site localisation using LuciPHOr2.</description> <macros> <token name="@EXECUTABLE@">LuciphorAdapter</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -45,21 +43,21 @@ <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(dirname \$(realpath \$(which luciphor2)))/luciphor2.jar", "num_threads": "\${GALAXY_SLOTS:-1}", "java_executable": "java", "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 spectrum file" help=" select mzml data sets(s)"/> - <param name="id" argument="-id" type="data" format="idxml" optional="false" label="Protein/peptide identifications file" help=" select idxml data sets(s)"/> - <param name="fragment_method" argument="-fragment_method" display="radio" type="select" optional="false" label="Fragmentation method" help=""> + <param argument="-in" type="data" format="mzml" optional="false" label="Input spectrum file" help=" select mzml data sets(s)"/> + <param argument="-id" type="data" format="idxml" optional="false" label="Protein/peptide identifications file" help=" select idxml data sets(s)"/> + <param argument="-fragment_method" type="select" optional="true" label="Fragmentation method" help=""> <option value="CID" selected="true">CID</option> <option value="HCD">HCD</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="fragment_method"/> </param> - <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Tolerance of the peaks in the fragment spectrum" help=""/> - <param name="fragment_error_units" argument="-fragment_error_units" display="radio" type="select" optional="false" label="Unit of fragment mass tolerance" help=""> + <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Tolerance of the peaks in the fragment spectrum" help=""/> + <param argument="-fragment_error_units" type="select" optional="true" label="Unit of fragment mass tolerance" help=""> <option value="Da" selected="true">Da</option> <option value="ppm">ppm</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="fragment_error_units"/> </param> - <param name="min_mz" argument="-min_mz" type="float" optional="true" value="150.0" label="Do not consider peaks below this value for matching fragment ions" help=""/> - <param name="target_modifications" argument="-target_modifications" multiple="true" type="select" optional="true" label="List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'"> + <param argument="-min_mz" type="float" optional="true" value="150.0" label="Do not consider peaks below this value for matching fragment ions" help=""/> + <param argument="-target_modifications" multiple="true" type="select" optional="true" label="List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'"> <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> @@ -1429,7 +1427,6 @@ <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> @@ -2988,33 +2985,33 @@ <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="target_modifications"/> </param> - <param name="neutral_losses" argument="-neutral_losses" type="text" optional="true" value=""sty -H3PO4 -97.97690"" label="List the types of neutral losses that you want to conside" help="The residue field is case sensitive. For example: lower case 'sty' implies that the neutral loss can only occur if the specified modification is present. Syntax: NL = <RESDIUES> -<NEUTRAL_LOSS_MOLECULAR_FORMULA> <MASS_LOST> (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_string_val"/> - <expand macro="list_string_san"/> + <param argument="-neutral_losses" type="text" optional="true" value=""sty -H3PO4 -97.97690"" label="List the types of neutral losses that you want to conside" help="The residue field is case sensitive. For example: lower case 'sty' implies that the neutral loss can only occur if the specified modification is present. Syntax: NL = <RESDIUES> -<NEUTRAL_LOSS_MOLECULAR_FORMULA> <MASS_LOST> (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val" name="neutral_losses"/> + <expand macro="list_string_san" name="neutral_losses"/> </param> - <param name="decoy_mass" argument="-decoy_mass" type="float" optional="true" min="1.0" value="79.966331" label="How much to add to an amino acid to make it a decoy" help=""/> - <param name="decoy_neutral_losses" argument="-decoy_neutral_losses" type="text" optional="true" value=""X -H3PO4 -97.97690"" label="For handling the neutral loss from a decoy sequence" help="The syntax for this is identical to that of the normal neutral losses given above except that the residue is always 'X'. Syntax: DECOY_NL = X -<NEUTRAL_LOSS_MOLECULAR_FORMULA> <MASS_LOST> (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_string_val"/> - <expand macro="list_string_san"/> + <param argument="-decoy_mass" type="float" optional="true" min="1.0" value="79.966331" label="How much to add to an amino acid to make it a decoy" help=""/> + <param argument="-decoy_neutral_losses" type="text" optional="true" value=""X -H3PO4 -97.97690"" label="For handling the neutral loss from a decoy sequence" help="The syntax for this is identical to that of the normal neutral losses given above except that the residue is always 'X'. Syntax: DECOY_NL = X -<NEUTRAL_LOSS_MOLECULAR_FORMULA> <MASS_LOST> (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val" name="decoy_neutral_losses"/> + <expand macro="list_string_san" name="decoy_neutral_losses"/> </param> - <param name="max_charge_state" argument="-max_charge_state" type="integer" optional="true" min="1" value="5" label="Do not consider PSMs with a charge state above this value" help=""/> - <param name="max_peptide_length" argument="-max_peptide_length" type="integer" optional="true" min="1" value="40" label="Restrict scoring to peptides with a length shorter than this value" help=""/> - <param name="max_num_perm" argument="-max_num_perm" type="integer" optional="true" min="1" value="16384" label="Maximum number of permutations a sequence can have" help=""/> - <param name="modeling_score_threshold" argument="-modeling_score_threshold" type="float" optional="true" min="0.0" value="0.95" label="Minimum score a PSM needs to be considered for modeling" help=""/> - <param name="scoring_threshold" argument="-scoring_threshold" type="float" optional="true" min="0.0" value="0.0" label="PSMs below this value will be discarded" help=""/> - <param name="min_num_psms_model" argument="-min_num_psms_model" type="integer" optional="true" min="1" value="50" label="The minimum number of PSMs you need for any charge state in order to build a model for it" help=""/> - <param name="run_mode" argument="-run_mode" display="radio" type="select" optional="false" label="Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported" help=""> + <param argument="-max_charge_state" type="integer" optional="true" min="1" value="5" label="Do not consider PSMs with a charge state above this value" help=""/> + <param argument="-max_peptide_length" type="integer" optional="true" min="1" value="40" label="Restrict scoring to peptides with a length shorter than this value" help=""/> + <param argument="-max_num_perm" type="integer" optional="true" min="1" value="16384" label="Maximum number of permutations a sequence can have" help=""/> + <param argument="-modeling_score_threshold" type="float" optional="true" min="0.0" value="0.95" label="Minimum score a PSM needs to be considered for modeling" help=""/> + <param argument="-scoring_threshold" type="float" optional="true" min="0.0" value="0.0" label="PSMs below this value will be discarded" help=""/> + <param argument="-min_num_psms_model" type="integer" optional="true" min="1" value="50" label="The minimum number of PSMs you need for any charge state in order to build a model for it" help=""/> + <param argument="-run_mode" type="select" optional="true" label="Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported" help=""> <option value="0" selected="true">0</option> <option value="1">1</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="run_mode"/> </param> - <param name="rt_tolerance" argument="-rt_tolerance" type="float" optional="true" min="0.0" value="0.01" label="Set the retention time tolerance (for the mapping of identifications to spectra in case multiple search engines were used)" help=""/> + <param argument="-rt_tolerance" type="float" optional="true" min="0.0" value="0.01" label="Set the retention time tolerance (for the mapping of identifications to spectra in case multiple search engines were used)" help=""/> <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"> @@ -3027,13 +3024,42 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_LuciphorAdapter"/> - <expand macro="manutest_LuciphorAdapter"/> + <tests><!-- TOPP_LuciphorAdapter_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="LuciphorAdapter_1_input.mzML"/> + <param name="id" value="LuciphorAdapter_1_input.idXML"/> + <output name="out" file="LuciphorAdapter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <param name="fragment_method" value="CID"/> + <param name="fragment_mass_tolerance" value="0.5"/> + <param name="fragment_error_units" value="Da"/> + <param name="min_mz" value="150.0"/> + <param name="target_modifications" value="Phospho (S),Phospho (T),Phospho (Y)"/> + <param name="neutral_losses" value=""sty -H3PO4 -97.97690""/> + <param name="decoy_mass" value="79.966331"/> + <param name="decoy_neutral_losses" value=""X -H3PO4 -97.97690""/> + <param name="max_charge_state" value="5"/> + <param name="max_peptide_length" value="40"/> + <param name="max_num_perm" value="16384"/> + <param name="modeling_score_threshold" value="0.95"/> + <param name="scoring_threshold" value="0.0"/> + <param name="min_num_psms_model" value="1"/> + <param name="run_mode" value="0"/> + <param name="rt_tolerance" value="0.01"/> + <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[Modification site localisation using LuciPHOr2. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_LuciphorAdapter.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_LuciphorAdapter.html]]></help> <expand macro="references"/> </tool>