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