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comparison secimtools/compound_identification.xml @ 0:b54326490b4d draft

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Upload 21.3.4.2 release
author malex
date Mon, 08 Mar 2021 20:55:03 +0000
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1 <tool id="secimtools_compound_identification" name="Compound Identification" version="@WRAPPER_VERSION@">
2 <description>based on m/z ratio and retention time.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 compound_identification.py
9 --anno $anno
10 --uniqID $uniqID
11 --mzID $mzID
12 --rtID $rtID
13 --library $library
14 --libuniqID $libuniqID
15 --libmzID $libmzID
16 --librtID $librtID
17 --output $output
18 ]]></command>
19 <inputs>
20 <param name="anno" type="data" format="tabular" label="Target Annotation File" help="Input tab-separated dataset in wide format. If not tab separated see TIP below."/>
21 <param name="uniqID" type="text" size="30" value="" optional="false" label="Target Annotation Unique Feature ID column" help="Name of the column in your target annotation file containing unique identifiers."/>
22 <param name="mzID" type="text" size="30" value="" optional="false" label="Target Annotation Mass/Charge column." help="Name of the column in your target annotation file containing m/z ratios."/>
23 <param name="rtID" type="text" size="30" value="" optional="false" label="Target Annotation Retention Time" help="Name of the column in your target annotation file containing retention times."/>
24 <param name="library" type="data" format="tabular" label="Library File" help="Library dataset. If not tab separated see TIP below."/>
25 <param name="libuniqID" type="text" size="30" value="" optional="false" label="Library compound name column" help="Name of the column in your library file containing the compound/adduct names to use for identification."/>
26 <param name="libmzID" type="text" size="30" value="" optional="false" label="Library Mass/Charge column" help="Name of the column in your library file containing m/z ratios."/>
27 <param name="librtID" type="text" size="30" value="" optional="false" label="Library Retention Time column" help="Name of the column in your library file containing the retention times."/>
28 </inputs>
29 <outputs>
30 <data format="tabular" name="output" label="identified_compounds_adducts_on_${anno.name}"/>
31 </outputs>
32 <tests>
33 <test>
34 <param name="anno" value="TEST0000_mzrt_first.tsv"/>
35 <param name="uniqID" value="rowID_first"/>
36 <param name="mzID" value="MZ_first" />
37 <param name="rtID" value="RT_first" />
38 <param name="library" value="TEST0000_database.tsv"/>
39 <param name="libuniqID" value="name_database"/>
40 <param name="libmzID" value="MZ_database" />
41 <param name="librtID" value="RT_database" />
42 <output name="output" file="TEST0000_compound_identification_output.tsv" />
43 </test>
44 </tests>
45 <help><![CDATA[
46
47 @TIP_AND_WARNING@
48
49 **Tool Description**
50
51 This tool is primarily intended for identification of compounds in a target file given a mass spectroscopy library file.
52
53 Each metabolite (feature) is characterized by a mass to charge (m/z) ratio and retention time (RT).
54
55 This tool matches two files: (1) a mass spectroscopy library file and (2) a target annotation file.
56
57 The library file (in tsv format) contains a list of compounds and their associated m/z ratios and RTs.
58
59 The target annotation file (in tsv format) contains the m/z ratios and RTs for the experimental samples.
60
61 --------------------------------------------------------------------------------
62
63 **Input**
64
65 - Two input datasets are required, a library file and an annotation target file.
66
67 @MZRTFILE@
68
69 **Target Annotation Unique Feature ID column**
70
71 - Name of the column in your target annotation file containing unique ID.
72
73
74 **Annotation Mass/Charge column**
75
76 - Name of the column in your target annotation file containing the m/z ratio.
77
78 **Annotation Retention Time**
79
80 - Name of the column in your target annotation file containing Retention Times.
81
82 **Library File**
83
84 **Library compound name colum**
85
86 - Name of the column in your library file containing the compound names to use.
87
88 **Library Mass/Charge column**
89
90 - Name of the column in your library file containing the m/z ratios.
91
92 **Library Retention Time column**
93
94 - Name of the column in your library file containing Retention Times.
95
96
97 --------------------------------------------------------------------------------
98
99 **Output**
100
101 A TSV file containing the original target annotation input file plus an additional column containing the name of any compounds that were matched using the m/z ratio and RT.
102
103 ]]></help>
104 <expand macro="citations"/>
105 </tool>