Mercurial > repos > galaxyp > peptideshaker
changeset 61:3ec27b4cee7c draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
| author | galaxyp |
|---|---|
| date | Thu, 12 Aug 2021 14:06:52 +0000 |
| parents | a6ff76e057fd |
| children | |
| files | fasta_cli.xml ident_params.xml macros_basic.xml searchgui.xml |
| diffstat | 4 files changed, 15 insertions(+), 9 deletions(-) [+] |
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--- a/fasta_cli.xml Tue Jul 20 08:55:11 2021 +0000 +++ b/fasta_cli.xml Thu Aug 12 14:06:52 2021 +0000 @@ -46,7 +46,7 @@ <section name="database_processing_options" expanded="true" title="Database Processing Options"> - <param name="decoy_tag" type="text" value="-REVERSED" label="The decoy flag"> + <param name="decoy_tag" type="text" value="_REVERSED" label="The decoy flag"> </param> <param name="decoy_type" type="select" label="Location of the decoy flag: prefix or suffix"> <option value="1">Prefix</option> @@ -74,7 +74,7 @@ Appends decoy sequences to FASTA files. Default format is adequated to be used by SearchGUI and PeptideShaker tools, ie: -* Decoy flag: -REVERSED +* Decoy flag: _REVERSED * Location: suffix
--- a/ident_params.xml Tue Jul 20 08:55:11 2021 +0000 +++ b/ident_params.xml Thu Aug 12 14:06:52 2021 +0000 @@ -525,7 +525,13 @@ ## SPECTRUM ANNOTATION -annotation_level $advanced_options.spectrum_annotation_options.annotation_level + + ## if the user modifies fragment_tol but he does not modify annotation_mz_tolerance, + ## we must overwrite default annotation_mz_tolerance value with fragment_tol value + + #if not ($spectrum_matching_options.fragment_tol != 0.5 and $advanced_options.spectrum_annotation_options.annotation_mz_tolerance == 0.5) -annotation_mz_tolerance $advanced_options.spectrum_annotation_options.annotation_mz_tolerance + #end if -annotation_high_resolution $advanced_options.spectrum_annotation_options.annotation_high_resolution ## TODO: There are still many options from the GUI to be incorporated to the CLI @@ -1203,9 +1209,9 @@ </param> <param name="comet_isotope_correction" label="Comet: Isotope Correction" type="select" help="Controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement"> <option value="0">off</option> - <option value="1" selected="True">0,+1</option> + <option value="1">0,+1</option> <option value="2">0,+1,+2</option> - <option value="3">0,+1,+2,+3</option> + <option value="3" selected="True">0,+1,+2,+3</option> <option value="4">-8,-4,0,+4,+8</option> </param> <param name="comet_min_prec_mass" type="float" value="600.0" @@ -1237,7 +1243,7 @@ <option value="0" selected="True">Summed intensities + flanking</option> <option value="1">Summed intensities</option> </param> - <param name="comet_frag_bin_offset" type="float" value="0.01" + <param name="comet_frag_bin_offset" type="float" value="0" label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" /> </when> </conditional> @@ -1706,7 +1712,7 @@ <param name="annotation_level" label="Percent of the possible annotations relative to the most intensive peak" help="The intensity percentile to consider for annotation, e.g. 0.75 means that the 25% most intense peaks will be annotated, default is 0.75." value="0.75" type="float"> <validator type="in_range" min="0" max="1" /> </param> - <param name="annotation_mz_tolerance" label="Fragment ion annotation accuracy" help=" The m/z tolerance to annotate peaks, default is equal to the search settings MS2 tolerance." value="10" type="float" /> + <param name="annotation_mz_tolerance" label="Fragment ion annotation accuracy" help=" The m/z tolerance to annotate peaks, default is equal to the search settings MS2 tolerance." value="0.5" type="float" /> <param name="annotation_high_resolution" label="High resolution" help="The most accurate peak will be selected within the m/z tolerance if chosen" truevalue="1" falsevalue="0" checked="true" type="boolean"/> </section> @@ -1851,7 +1857,7 @@ </param> <when value="no" /> <when value="yes"> - <param name="decoy_tag" type="text" value="-REVERSED" label="The decoy flag"> + <param name="decoy_tag" type="text" value="_REVERSED" label="The decoy flag"> </param> <param name="decoy_type" type="select" label="Location of the decoy flag: prefix or suffix"> <option value="0">Prefix</option>
--- a/macros_basic.xml Tue Jul 20 08:55:11 2021 +0000 +++ b/macros_basic.xml Thu Aug 12 14:06:52 2021 +0000 @@ -12,7 +12,7 @@ </xml> <token name="@SEARCHGUI_MAJOR_VERSION@">4</token> <token name="@SEARCHGUI_VERSION@">4.0.41</token> - <token name="@SEARCHGUI_VERSION_SUFFIX@">0</token> + <token name="@SEARCHGUI_VERSION_SUFFIX@">1</token> <token name="@PEPTIDESHAKER_VERSION@">2.0.33</token> <token name="@PEPTIDESHAKER_VERSION_SUFFIX@">1</token> <xml name="citations">
--- a/searchgui.xml Tue Jul 20 08:55:11 2021 +0000 +++ b/searchgui.xml Thu Aug 12 14:06:52 2021 +0000 @@ -180,7 +180,7 @@ <!-- Search Engine Selection --> <section name="search_engines_options" expanded="true" title="Search Engine Options"> <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> - <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA might not work into isolated environments like containers. Ms Amanda may not work either when executed into isolated environments based on MacOS X. + <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA might not work into isolated environments like containers. Ms Amanda may not work either when executed into isolated environments based on MacOS X (use SG 4.0.22 to solve any problem running MsAmanda). MetaMorpheus only produce results when using mzML format.</help> <option value="X!Tandem" selected="True">X!Tandem</option> <option value="MSGF" selected="True">MS-GF+</option>