Mercurial > repos > pieterlukasse > prims_metabolomics
changeset 30:60b53f2aa48a
Small fixes, added microminutes support to MsClust, removed TIC or MsClust output
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Sat, 30 Aug 2014 16:14:18 +0200 |
| parents | 0d534bce8e84 |
| children | 31e6e2242d33 |
| files | MsClust.jar msclust.xml query_mass_repos.py query_metexp.xml test/test_library_lookup.py |
| diffstat | 5 files changed, 25 insertions(+), 11 deletions(-) [+] |
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--- a/msclust.xml Fri May 09 17:11:11 2014 +0200 +++ b/msclust.xml Sat Aug 30 16:14:18 2014 +0200 @@ -64,9 +64,7 @@ </command> <inputs> - <!-- <param name="rankingWeightConfig" type="text" area="true" size="11x70" label="NB - TEST VERSION" -value="VERSION BEING TESTED AT THIS MOMENT...NOT READY FOR USE..."/> - --> + <param name="inputPeaks" type="data" format="txt" label="Ion-wise aligned data (e.g. MetAlign output data)" /> <param name="dataType" type="select" size="30" label="Data type"> <option value="gcms" selected="true">GC-MS</option> @@ -222,6 +220,20 @@ ----- +**Input** + +The input file should contain the following columns (in this order), followed by the sample intensity columns (one column with the +intensity value for each sample): + +*ScanNR +*Ret(umin) +*Mass(uD) +*(Optional)retentionMean +*(only required if retentionMean is present)retentionSD +*N sample intensity columns... + +----- + **Output** This tools returns a number of ouptut files and a small report.
--- a/query_mass_repos.py Fri May 09 17:11:11 2014 +0200 +++ b/query_mass_repos.py Sat Aug 30 16:14:18 2014 +0200 @@ -276,7 +276,7 @@ # Query data against repository : enriched_data = _query_and_add_data(input_data, molecular_mass_col, repository_dblink, error_margin, margin_unit) headers = input_data.keys() + ['SEARCH hits for ','SEARCH hits: db-names', 'SEARCH hits: molecular-formulas ', - 'SEARCH hits: ids','SEARCH hits: descriptions', 'Link to SEARCH hits'] + 'SEARCH hits: ids','SEARCH hits: descriptions', 'Link to SEARCH hits'] #TODO - add min and max formula weigth columns _save_data(enriched_data, headers, output_result)
--- a/query_metexp.xml Fri May 09 17:11:11 2014 +0200 +++ b/query_metexp.xml Sat Aug 30 16:14:18 2014 +0200 @@ -1,7 +1,7 @@ <tool id="query_metexp" name="METEXP - Query Database " version="0.1.0"> - <description>Query a set of identifications against the METabolomics EXPlorer database</description> + <description>Query a set of identifications against the METabolomics EXPeriments database</description> <command interpreter="python"> query_metexp.py $input_file @@ -18,6 +18,12 @@ label="Input file" help="Select a tabular file containing the entries to be queried/verified in the MetExp DB"/> + <param name="separation_method" type="select" label="Data type to query"> + <option value="GC" selected="True">GC</option> + <option value="LC">LC</option> + </param> + + <param name="casid_col" type="text" size="50" label="CAS ID column name" value="CAS" @@ -35,11 +41,7 @@ help="Select the MetExp Database/backend which should be queried" dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/MetExp_Databases")'/> - <param name="separation_method" type="select" label="Data type to query"> - <option value="GC" selected="True">GC</option> - <option value="LC">LC</option> - </param> - + </inputs> <outputs> <data name="output_result" format="tabular" label="${tool.name} on ${on_string}" />
--- a/test/test_library_lookup.py Fri May 09 17:11:11 2014 +0200 +++ b/test/test_library_lookup.py Sat Aug 30 16:14:18 2014 +0200 @@ -149,7 +149,7 @@ ''' riqc_libs_dir = resource_filename(__name__, "../repositories/PRIMS-metabolomics/RI_DB_libraries") get_library_files_output = match_library.get_directory_files(riqc_libs_dir) - self.assertEqual(1, len(get_library_files_output)) + self.assertEqual(2, len(get_library_files_output)) self.assertEqual("Library_RI_DB_capillary_columns-noDuplicates", get_library_files_output[0][0]) #TODO change assert below to assert that the result is a file, so the test can run on other dirs as well: #self.assertEqual("E:\\workspace\\PRIMS-metabolomics\\python-tools\\tools\\GCMS\\test\\data\\riqc_libs\\RI DB library (capillary columns) Dec.2012.txt", get_library_files_output[0][1])