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planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
author eschen42
date Sun, 29 Oct 2017 09:41:21 -0400
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1 <tool id="w4mjoinpn" name="Join +/- Ions" version="0.98.1">
2 <description>Join positive and negative ionization-mode W4M datasets for the same samples</description>
3 <requirements>
4 <requirement type="package" version="8.25">coreutils</requirement>
5 <requirement type="package" version="4.2.3.dev0">sed</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" level="fatal" />
9 </stdio>
10 <command><![CDATA[
11 echo "These are the the paths to the tools used by this script:" 1>&2 ;
12 which cut sed head paste cat cp bash test 1>&2 ;
13 $__tool_directory__/w4mjoinpn.sh
14 dmneg $dmneg
15 dmpos $dmpos
16 dmout $dmout
17 smneg $smneg
18 smpos $smpos
19 smout $smout
20 vmneg $vmneg
21 vmpos $vmpos
22 vmout $vmout
23 ]]></command>
24 <inputs>
25 <param name="dmpos" label="Data matrix positive" type="data" format="tabular" help="Positive ionization-mode: Features x samples (tabular data - decimal: '.'; missing: NA; mode: numerical; separator: tab character)" />
26 <param name="smpos" label="Sample metadata positive" type="data" format="tabular" help="Positive ionization-mode: Samples x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
27 <param name="vmpos" label="Variable metadata positive" type="data" format="tabular" help="Positive ionization-mode: Features x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
28 <param name="dmneg" label="Data matrix negative" type="data" format="tabular" help="Negative ionization-mode: Features x samples (tabular data - decimal: '.'; missing: NA; mode: numerical; separator: tab character)" />
29 <param name="smneg" label="Sample metadata negative" type="data" format="tabular" help="Negative ionization-mode: Samples x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
30 <param name="vmneg" label="Variable metadata negative" type="data" format="tabular" help="Negative ionization-mode: Features x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
31 </inputs>
32 <outputs>
33 <data name="dmout" label="${dmneg.name}.posneg" format="tabular" ></data>
34 <data name="smout" label="${smneg.name}.posneg" format="tabular" ></data>
35 <data name="vmout" label="${vmneg.name}.posneg" format="tabular" ></data>
36 </outputs>
37 <help><![CDATA[
38 **Join positive and negative ionization-mode W4M datasets for the same samples**
39 --------------------------------------------------------------------------------
40
41 **Author** - Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
42
43
44 Motivation
45 ----------
46
47 Workflow4Metabolomics (W4M, Giacomoni *et al.*, 2014; http://workflow4metabolomics.org; https://github.com/workflow4metabolomics)
48 provides a suite of Galaxy tools for processing and analyzing metabolomics data.
49
50 W4M uses the XCMS package (Smith *et al.*, 2006) to extract features and align
51 their retention times among multiple samples.
52
53 After peak extraction and alignment, W4M uses the CAMERA package (Kuhl *et al.*, 2012)
54 "to postprocess XCMS feature lists and to collect all features related to a compound into a compound spectrum."
55
56 Both of these steps are done using data collected in a single ionization mode (i.e., only negative or only positive)
57 because it would not make sense to attempt to use CAMERA otherwise.
58
59 However, performing and interpreting statistical analysis would be more convenient and statistically powerful
60 with all variables (features), negative and positive, combined for one analysis.
61
62
63 Description
64 -----------
65
66 This tool joins two sets of MS1 datasets for **exactly** the same set of samples, where one was gathered in positive ionization
67 mode and the other in negative ionization-mode, for reasons set forth above. These datasets must be post-XCMS and post-CAMERA.
68
69 This tool will fail:
70
71 * when the samples are not listed in exactly the same order in the negative-mode dataMatrix and the positive-mode dataMatrix
72 * when the samples are not listed in exactly the same order in the negative-mode sampleMetadata and the positive-mode sampleMetadata
73
74 Otherwise:
75
76 * the two dataMatrix files are concatenated, and the names of features identified from positive ionization-mode data are prefixed with "P"; negative, with "N".
77 * the two variableMetadata files are concatenated, and the names of features are prefixed in the same way.
78 * if sampleMetadata has a polarity column, its value is set to "posneg" in the output. (In fact, the sampleMetadata file in the output is copied from the negative ionization-mode sampleMetadata, with the polarity replaced.)
79
80 Workflow Position
81 -----------------
82
83 * Upstream tool category: Preprocessing
84 * Downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort
85
86 Working example
87 ---------------
88
89 **Input files**
90
91 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
92 | Input File | Download from URL |
93 +=============================================+=======================================================================================================================+
94 | Data matrix, negative ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_dataMatrix_neg.tsv |
95 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
96 | Sample metadata, negative ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_sampleMetadata_neg.tsv |
97 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
98 | Variable metadata, negative ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_variableMetadata_neg.tsv |
99 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
100 | Data matrix, positive ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_dataMatrix_pos.tsv |
101 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
102 | Sample metadata, positive ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_sampleMetadata_pos.tsv |
103 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
104 | Variable metadata, positive ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_variableMetadata_pos.tsv |
105 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
106
107 **Output files**
108
109 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
110 | Output File | Download from URL |
111 +=============================================+=======================================================================================================================+
112 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/output_dataMatrix.tsv |
113 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
114 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/output_sampleMetadata.tsv |
115 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
116 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/output_variableMetadata.tsv |
117 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
118
119 ]]></help>
120 <citations>
121 <citation type="doi">10.5281/zenodo.1038289</citation>
122 <!--
123 <citation type="bibtex">
124 @misc{
125 w4mjoinpn_galaxy_wrapper,
126 author = {Eschenlauer, Arthur},
127 year = {2017},
128 title = {w4mjoinpn_galaxy_wrapper},
129 publisher = {GitHub},
130 journal = {GitHub repository},
131 url = {https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper},
132 doi = 10.5281/zenodo.1038290
133 }
134 </citation>
135 -->
136 <!-- Giacomoni, 2014 Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics -->
137 <citation type="doi">10.1093/bioinformatics/btu813</citation>
138 <!-- Kuhl et al., 2012 -->
139 <citation type="doi">10.1021/ac202450g</citation>
140 <!-- Smith, 2006 XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification. -->
141 <citation type="doi">10.1021/ac051437y</citation>
142 </citations>
143 </tool>