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comparison rankfilterGCMS_tabular.xml @ 0:9d5f4f5f764b

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author pieter.lukasse@wur.nl
date Thu, 16 Jan 2014 13:10:00 +0100
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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>