Mercurial > repos > pieterlukasse > prims_metabolomics
annotate rankfilterGCMS_tabular.xml @ 57:963684611ccb
fix for xcms support in msclust
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Fri, 12 Dec 2014 12:06:36 +0100 |
| parents | 19d8fd10248e |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="rankfilterGCMS_tabular" name="RIQC-RankFilter GC-MS from tabular file" version="1.0.2"> |
| 2 <description>Convert Retention Time to Retention Index</description> | |
| 3 <command interpreter="python">rankfilter_GCMS/rankfilter.py $input_file</command> | |
| 4 <inputs> | |
| 5 <param format="tabular" name="sample" type="data" label="Sample File" | |
|
21
19d8fd10248e
* Added interface to METEXP data store, including tool to fire queries in batch mode
pieter.lukasse@wur.nl
parents:
20
diff
changeset
|
6 help="Select a tab delimited NIST metabolite identifications file (converted from PDF)" /> |
| 0 | 7 <!-- question: is this calibration file not column specific as it includes RT info?? --> |
|
20
24fb75fedee0
Made calibration file configurable at UI.
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
8 <!-- this one should be input file for now:<param name="calibration" type="select" label="Calibration File" |
| 0 | 9 help="Calibration file with reference masses (e.g. alkanes) with their RT and RI values" |
| 10 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/RankFilter_Calibration_Files")'/> | |
|
20
24fb75fedee0
Made calibration file configurable at UI.
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
11 --> |
|
24fb75fedee0
Made calibration file configurable at UI.
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
12 <param name="calibration" format="any" type="data" label="Calibration File" |
|
24fb75fedee0
Made calibration file configurable at UI.
pieter.lukasse@wur.nl
parents:
0
diff
changeset
|
13 help="Calibration file containing reference masses (e.g. alkanes) with their respective RT and RI values"/> |
| 0 | 14 |
| 15 <param name="analysis_type" type="select" format="text" label="Analysis Type" | |
| 16 help="Select the type of analysis that has been used to generate the sample file"> | |
| 17 <option value="NIST">NIST</option> | |
| 18 <option value="AMDIS">AMDIS</option> | |
| 19 </param> | |
| 20 <param name="model" type="select" format="text" label="Select a model to be used " | |
| 21 help="Both linear and (3rd degree) polynomial models are available "> | |
| 22 <option value="linear">Linear</option> | |
| 23 <option value="poly">Polynomial</option> | |
| 24 </param> | |
| 25 <param name="lib_data" type="select" label="Library" | |
| 26 help="Reference global lookup library file with CAS numbers and respective (previously calculated) RIsvr values" | |
| 27 dynamic_options='get_directory_files("tool-data/shared/PRIMS-metabolomics/RankFilter_lookup_libraries")'/> | |
| 28 | |
| 29 <param name="window" type="float" label="Window" value="10.56" /> | |
| 30 </inputs> | |
| 31 <outputs> | |
| 32 <data format="tabular" label="${tool.name}" name="onefile" /> | |
| 33 </outputs> | |
| 34 <!-- file with implementation of the function get_directory_files() used above --> | |
| 35 <code file="match_library.py" /> | |
| 36 <configfiles> | |
| 37 <configfile name="input_file"> | |
| 38 sample = ${sample} | |
| 39 calibration = ${calibration} | |
| 40 lib_data = ${lib_data} | |
| 41 window = ${window} | |
| 42 analysis_type = ${analysis_type} | |
| 43 tabular = True | |
| 44 onefile = ${onefile} | |
| 45 model = ${model} | |
| 46 </configfile> | |
| 47 </configfiles> | |
| 48 <help> | |
| 49 Basically estimates the experimental RI (RIexp) by building a RI(RT) function based on the | |
| 50 given calibration file. | |
| 51 | |
| 52 It also determines the estimated RI (RIsvr) by looking up for each entry of the given input file (Sample File), | |
| 53 based on its CAS number, its respective RIsvr value in the given global lookup library | |
| 54 (this step is also called the "RankFilter analysis" -see reference below; Sample File may be either from NIST or AMDIS). | |
| 55 This generates an prediction of the RI for | |
| 56 a compound according to the "RankFilter procedure" (RIsvr). | |
| 57 | |
| 58 Output is a tab separated file in which four columns are added: | |
| 59 | |
| 60 - **Rank** Calculated rank | |
| 61 - **RIexp** Experimental Retention Index (RI) | |
| 62 - **RIsvr** Calculated RI based on support vector regression (SVR) | |
| 63 - **%rel.err** Relative RI error (%rel.error = 100 * (RISVR − RIexp) / RIexp) | |
| 64 | |
| 65 .. class:: infomark | |
| 66 | |
| 67 **Notes** | |
| 68 | |
| 69 - The layout of the Calibration file should include the following columns: 'MW', 'R.T.' and 'RI'. | |
| 70 - Selecting 'Polynomial' in the model parameter will calculate a 3rd degree polynomial model that will | |
| 71 be used to convert from XXXX to YYYY. | |
| 72 | |
| 73 ----- | |
| 74 | |
| 75 **References** | |
| 76 | |
| 77 - **RankFilter**: Mihaleva et. al. (2009) *Automated procedure for candidate compound selection in GC-MS | |
| 78 metabolomics based on prediction of Kovats retention index*. Bioinformatics, 25 (2009), pp. 787–794 | |
| 79 </help> | |
| 80 </tool> |