Mercurial > repos > fgiacomoni > bih4bloodexposome

annotate bih4bloodexposome.xml @ 0:94eeed7f737f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
author fgiacomoni
date Fri, 27 Nov 2020 10:06:35 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
1 <tool id="bih4bloodexposome" name="BiH4BloodExposome" version="0.1.2">
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
2 <description>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
3 : Utility to detect potential metabolites known or suspected to be part of blood exposome in your peak list.
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
4 </description>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
5 <requirements>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
6 <requirement type="package" version="0.6.3">perl-metabolomics-fragment-annotation</requirement>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
7 </requirements>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
8 <stdio>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
9 <exit_code range="1" level="fatal" />
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
10 </stdio>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
11
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
12 <command><![CDATA[
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
13 perl $__tool_directory__/bih4bloodexposome.pl
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
14 -input $variableMetadata_in
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
15 -mzCol $colmass
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
16
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
17 #if str($has_header.header_choice) == "YES":
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
18 -header "${has_header.header}"
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
19 #end if
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
20
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
21 -ppmError $ppm_error
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
22 -mode $mode
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
23 -outputTab $outputTab
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
24 -outputFull $outFull
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
25 -verbose $verbose
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
26 ]]></command>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
27 <inputs>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
28 <param name="variableMetadata_in" type="data" label="Input file containing a list of mzs (format: tabular)" help="Generally variable metadata file" format="tabular" />
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
29
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
30 <conditional name="has_header">
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
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" />
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
32 <when value="YES">
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
33 <param name="header" type="integer" label="Number of header lines" value="1" min="1" max="10" help="number of lines not containing masses"/>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
34 </when>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
35 <when value="NO"/>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
36 </conditional>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
37
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
38 <param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="variableMetadata_in" accept_default="true" />
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
39
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
40 <param name="verbose" type="select" label="Verbose level" display="radio" help="">
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
41 <option value="1" selected="true">Low</option>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
42 <option value="3" >High</option>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
43 </param>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
44
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
45
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
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"/>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
47
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
48 <param name="mode" label="Molecular Species " type="select" display="radio" help="">
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
49 <option value="POSITIVE">Positif Mode</option>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
50 <option value="NEGATIVE">Negatif Mode</option>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
51 <option value="NEUTRAL">Neutral Mass</option>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
52 </param>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
53
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
54 </inputs>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
55 <outputs>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
56 <data name="outFull" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4BLOODEXPOSOME_Full.tabular" />
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
57 <data name="outputTab" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4BLOODEXPOSOME.tabular" />
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
58 </outputs>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
59 <tests>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
60 <!--test 01 : short input id, mz and rt data -->
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
61 <test>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
62 <param name="variableMetadata_in" value="in_test01_pos.tabular"/>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
63 <param name="header_choice" value="YES"/>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
64 <param name="header" value="1"/>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
65 <param name="colmass" value="2"/>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
66 <param name="ppm_error" value="5"/>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
67 <param name="mode" value="POSITIVE"/>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
68 <param name="verbose" value="3"/>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
69 <output name="outFull" file="outFull_test01.tabular"/>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
70 <output name="outputTab" file="outTab_test01.tabular"/>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
71 </test>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
72 </tests>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
73 <help><![CDATA[
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
74
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
75 .. class:: infomark
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
76
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
77 **Authors**
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
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
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
79
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
80 ---------------------------------------------------
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
81
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
82
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
83 ======================
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
84 bih4BloodExposome
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
85 ======================
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
86
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
87 -----------
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
88 Description
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
89 -----------
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
90
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
91 | detection of potential metabolites in your peak list based on BloodExposome database
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
92
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
93
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
94 Keywords
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
95 ========
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
96
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
97 blood, metabolite, exposome
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
98
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
99
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
100 -----------
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
101 Input files
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
102 -----------
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
103
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
104
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
105 +--------------------------------+-----------+
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
106 | Parameter : num + label | Format |
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
107 +================================+===========+
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
108 | 1 : File with a list of masses | tabular |
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
109 +--------------------------------+-----------+
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
110
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
111 File of masses (Generally variable metadata file) must have at least the following column :
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
112 | Masses : column with all the masses in the tabular input file
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
113 |
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
114
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
115
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
116 ----------
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
117 Parameters
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
118 ----------
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
119
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
120 File of masses
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
121 | see "Input files" section above
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
122 | Tabular file format, Generally variable metadata file
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
123 |
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
124
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
125 Do you have a header
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
126 | YES (default) : parameter **Number of header lines** is visible
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
127 | NO : all lines are considered to contain masses
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
128 |
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
129
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
130 If 'have a header'='YES'
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
131
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
132 Number of header lines
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
133 | Number of lines not containing masses values, these lines will be ignored
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
134 |
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
135
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
136 In all header cases :
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
137
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
138 Column of Masses
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
139 | Specify the column number for the mz in the tabular input file
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
140 |
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
141
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
142
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
143 In all cases :
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
144
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
145 PPM error
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
146 | Specify a delta (in ppm) to apply on annotating mass - This value is a float.
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
147 |
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
148
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
149
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
150 ------------
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
151 Output files
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
152 ------------
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
153
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
154 Two types of files (if you manually enter the masses both files are mingled):
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
155 | BIH4BLOODEXPOSOME_(input.name)_FULL.tabular : for linking with others modules.
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
156 | BIH4BLOODEXPOSOME_(input.name).tabular : an excel-like output will be available.
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
157 |
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
158
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
159
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
160 ---------------------------------------------------
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
161
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
162 ---------------
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
163 Working example
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
164 ---------------
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
165
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
166
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
167 .. class:: warningmark
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
168
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
169 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
170 | Format Data For Postprocessing
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
171 | Perform LCMS Annotations
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
172
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
173 .. class:: warningmark
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
174
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
175 And their "W4M courses 2019":
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
176 | Using Galaxy4Metabolomics - W4M table format for Galaxy
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
177 | Annotation Banks - Annotation
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
178
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
179 ]]></help>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
180 <citations>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
181 <citation type="doi">10.1289/EHP4713</citation>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
182 </citations>
94eeed7f737f planemo upload commit 399d2714dd85043f2ed8bdeff05bb1ccd4c5dd29
fgiacomoni
parents:
diff changeset
183 </tool>