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comparison bih4maconda.xml @ 0:de13e2c45971 draft

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Init repository for bih4maconda
author fgiacomoni
date Tue, 21 Jan 2020 15:49:00 -0500
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children 2744d20c830a
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-1:000000000000 0:de13e2c45971
1 <tool id="bih4maconda" name="Bih4MaConDa" version="0.1.3">
2 <description>
3 : Utility to detect potential contaminants in your peak list based on MaConDa database
4 </description>
5 <requirements>
6 <requirement type="package" version="0.2.0">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__/bih4maconda.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]}.BIH4MACONDA_Full.tabular" />
57 <data name="outputTab" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4MACONDA.tabular" />
58 </outputs>
59
60 <help><![CDATA[
61
62 .. class:: infomark
63
64 **Authors**
65 | Franck Giacomoni - FLAME ; PFEM ; INRA ; MetaboHUB (for original version and development of this Perl script and for xml interface and Perl wrapper)
66
67 ---------------------------------------------------
68
69
70 ======================
71 bih4MaDonDa
72 ======================
73
74 -----------
75 Description
76 -----------
77
78 | detection of potential contaminants in your peak list based on MaConDa database
79
80
81 Keywords
82 ========
83
84 contaminants
85
86
87 -----------------
88 Workflow position
89 -----------------
90
91
92 .. image::
93 :width: 800
94
95
96 -----------
97 Input files
98 -----------
99
100
101 +--------------------------------+-----------+
102 | Parameter : num + label | Format |
103 +================================+===========+
104 | 1 : File with a list of masses | tabular |
105 +--------------------------------+-----------+
106
107 File of masses (Generally variable metadata file) must have at least the following column :
108 | Masses : column with all the masses in the tabular input file
109 |
110
111
112 ----------
113 Parameters
114 ----------
115
116 File of masses
117 | see "Input files" section above
118 | Tabular file format, Generally variable metadata file
119 |
120
121 Do you have a header
122 | YES (default) : parameter **Number of header lines** is visible
123 | NO : all lines are considered to contain masses
124 |
125
126 If 'have a header'='YES'
127
128 Number of header lines
129 | Number of lines not containing masses values, these lines will be ignored
130 |
131
132 In all header cases :
133
134 Column of Masses
135 | Specify the column number for the mz in the tabular input file
136 |
137
138
139 In all cases :
140
141 PPM error
142 | Specify a delta (in ppm) to apply on annotating mass - This value is a float.
143 |
144
145
146 ------------
147 Output files
148 ------------
149
150 Two types of files (if you manually enter the masses both files are mingled):
151 | BIH4MACONDA_(input.name)_FULL.tabular : for linking with others modules.
152 | BIH4MACONDA_(input.name).tabular : an excel-like output will be available.
153 |
154
155
156 ---------------------------------------------------
157
158 ---------------
159 Working example
160 ---------------
161
162
163 .. class:: warningmark
164
165 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto
166 | Format Data For Postprocessing
167 | Perform LCMS Annotations
168
169 .. class:: warningmark
170
171 And their "W4M courses 2018":
172 | Using Galaxy4Metabolomics - W4M table format for Galaxy
173 | Annotation Banks - Annotation
174
175 ]]></help>
176 <citations>
177 <citation type="doi">10.1093/bioinformatics/bts527</citation>
178 </citations>
179 </tool>