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date Fri, 27 Nov 2020 10:06:35 +0000
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1 <tool id="bih4bloodexposome" name="BiH4BloodExposome" version="0.1.2">
2 <description>
3 : Utility to detect potential metabolites known or suspected to be part of blood exposome in your peak list.
4 </description>
5 <requirements>
6 <requirement type="package" version="0.6.3">perl-metabolomics-fragment-annotation</requirement>
7 </requirements>
8 <stdio>
9 <exit_code range="1" level="fatal" />
10 </stdio>
11
12 <command><![CDATA[
13 perl $__tool_directory__/bih4bloodexposome.pl
14 -input $variableMetadata_in
15 -mzCol $colmass
16
17 #if str($has_header.header_choice) == "YES":
18 -header "${has_header.header}"
19 #end if
20
21 -ppmError $ppm_error
22 -mode $mode
23 -outputTab $outputTab
24 -outputFull $outFull
25 -verbose $verbose
26 ]]></command>
27 <inputs>
28 <param name="variableMetadata_in" type="data" label="Input file containing a list of mzs (format: tabular)" help="Generally variable metadata file" format="tabular" />
29
30 <conditional name="has_header">
31 <param name="header_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Do you have a header?" help="if 'YES' is selected then enter your number of header lines" />
32 <when value="YES">
33 <param name="header" type="integer" label="Number of header lines" value="1" min="1" max="10" help="number of lines not containing masses"/>
34 </when>
35 <when value="NO"/>
36 </conditional>
37
38 <param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="variableMetadata_in" accept_default="true" />
39
40 <param name="verbose" type="select" label="Verbose level" display="radio" help="">
41 <option value="1" selected="true">Low</option>
42 <option value="3" >High</option>
43 </param>
44
45
46 <param name="ppm_error" label="Tolerance in ppm used during annotation step" type="float" value="5" min="0" max="300000" help="Default value is 5 ppm"/>
47
48 <param name="mode" label="Molecular Species " type="select" display="radio" help="">
49 <option value="POSITIVE">Positif Mode</option>
50 <option value="NEGATIVE">Negatif Mode</option>
51 <option value="NEUTRAL">Neutral Mass</option>
52 </param>
53
54 </inputs>
55 <outputs>
56 <data name="outFull" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4BLOODEXPOSOME_Full.tabular" />
57 <data name="outputTab" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4BLOODEXPOSOME.tabular" />
58 </outputs>
59 <tests>
60 <!--test 01 : short input id, mz and rt data -->
61 <test>
62 <param name="variableMetadata_in" value="in_test01_pos.tabular"/>
63 <param name="header_choice" value="YES"/>
64 <param name="header" value="1"/>
65 <param name="colmass" value="2"/>
66 <param name="ppm_error" value="5"/>
67 <param name="mode" value="POSITIVE"/>
68 <param name="verbose" value="3"/>
69 <output name="outFull" file="outFull_test01.tabular"/>
70 <output name="outputTab" file="outTab_test01.tabular"/>
71 </test>
72 </tests>
73 <help><![CDATA[
74
75 .. class:: infomark
76
77 **Authors**
78 | Franck Giacomoni - FLAME ; PFEM ; INRAE ; MetaboHUB (for original version and development of this Perl script and for xml interface and Perl wrapper) - based on the Perl CPAN package Metabolomics::Fragmentation::Annotation
79
80 ---------------------------------------------------
81
82
83 ======================
84 bih4BloodExposome
85 ======================
86
87 -----------
88 Description
89 -----------
90
91 | detection of potential metabolites in your peak list based on BloodExposome database
92
93
94 Keywords
95 ========
96
97 blood, metabolite, exposome
98
99
100 -----------
101 Input files
102 -----------
103
104
105 +--------------------------------+-----------+
106 | Parameter : num + label | Format |
107 +================================+===========+
108 | 1 : File with a list of masses | tabular |
109 +--------------------------------+-----------+
110
111 File of masses (Generally variable metadata file) must have at least the following column :
112 | Masses : column with all the masses in the tabular input file
113 |
114
115
116 ----------
117 Parameters
118 ----------
119
120 File of masses
121 | see "Input files" section above
122 | Tabular file format, Generally variable metadata file
123 |
124
125 Do you have a header
126 | YES (default) : parameter **Number of header lines** is visible
127 | NO : all lines are considered to contain masses
128 |
129
130 If 'have a header'='YES'
131
132 Number of header lines
133 | Number of lines not containing masses values, these lines will be ignored
134 |
135
136 In all header cases :
137
138 Column of Masses
139 | Specify the column number for the mz in the tabular input file
140 |
141
142
143 In all cases :
144
145 PPM error
146 | Specify a delta (in ppm) to apply on annotating mass - This value is a float.
147 |
148
149
150 ------------
151 Output files
152 ------------
153
154 Two types of files (if you manually enter the masses both files are mingled):
155 | BIH4BLOODEXPOSOME_(input.name)_FULL.tabular : for linking with others modules.
156 | BIH4BLOODEXPOSOME_(input.name).tabular : an excel-like output will be available.
157 |
158
159
160 ---------------------------------------------------
161
162 ---------------
163 Working example
164 ---------------
165
166
167 .. class:: warningmark
168
169 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto
170 | Format Data For Postprocessing
171 | Perform LCMS Annotations
172
173 .. class:: warningmark
174
175 And their "W4M courses 2019":
176 | Using Galaxy4Metabolomics - W4M table format for Galaxy
177 | Annotation Banks - Annotation
178
179 ]]></help>
180 <citations>
181 <citation type="doi">10.1289/EHP4713</citation>
182 </citations>
183 </tool>