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planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit 919fba0dbfcdb553bbb6e1c765c3a8c9f26a47f9
author eschen42
date Wed, 08 Aug 2018 19:40:57 -0400
parents 948bac693947
children
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0:948bac693947 1:dcfaffec48c8
1 <tool id="w4mjoinpn" name="Join +/- Ions" version="0.98.1"> 1 <tool id="w4mjoinpn" name="Join +/- Ions" version="0.98.2">
2 <description>Join positive and negative ionization-mode W4M datasets for the same samples</description> 2 <description>Join positive and negative ionization-mode W4M datasets for the same samples</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="8.25">coreutils</requirement> 4 <requirement type="package" version="8.25">coreutils</requirement>
5 <requirement type="package" version="4.2.3.dev0">sed</requirement> 5 <!--
6 </requirements> 6 <requirement type="package" version="4.2.3.dev0">sed</requirement>
7 <stdio> 7 -->
8 <exit_code range="1:" level="fatal" /> 8 <requirement type="package" version="4.4">sed</requirement>
9 </stdio> 9 </requirements>
10 <command><![CDATA[ 10 <stdio>
11 echo "These are the the paths to the tools used by this script:" 1>&2 ; 11 <exit_code range="1:" level="fatal" />
12 which cut sed head paste cat cp bash test 1>&2 ; 12 </stdio>
13 $__tool_directory__/w4mjoinpn.sh 13 <command detect_errors="aggressive"><![CDATA[
14 dmneg $dmneg 14 pwd
15 dmpos $dmpos 15 ;
16 dmout $dmout 16 echo $__tool_directory__/w4mjoinpn.sh
17 smneg $smneg 17 vmneg $vmneg
18 smpos $smpos 18 vmpos $vmpos
19 smout $smout 19 vmout $vmout
20 vmneg $vmneg 20 dmneg $dmneg
21 vmpos $vmpos 21 dmpos $dmpos
22 vmout $vmout 22 dmout $dmout
23 ]]></command> 23 smneg $smneg
24 <inputs> 24 smpos $smpos
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)" /> 25 smout $smout
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)" /> 26 ;
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)" /> 27 $__tool_directory__/w4mjoinpn.sh
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)" /> 28 vmneg $vmneg
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)" /> 29 vmpos $vmpos
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)" /> 30 vmout $vmout
31 </inputs> 31 dmneg $dmneg
32 <outputs> 32 dmpos $dmpos
33 <data name="dmout" label="${dmneg.name}.posneg" format="tabular" ></data> 33 dmout $dmout
34 <data name="smout" label="${smneg.name}.posneg" format="tabular" ></data> 34 smneg $smneg
35 <data name="vmout" label="${vmneg.name}.posneg" format="tabular" ></data> 35 smpos $smpos
36 </outputs> 36 smout $smout
37 <help><![CDATA[ 37 ]]></command>
38 <inputs>
39 <param name="dmpos" label="Data matrix positive" type="data" format="tabular"
40 help="Positive ionization-mode: variables &#10006; samples" />
41 <param name="smpos" label="Sample metadata positive" type="data" format="tabular"
42 help="Positive ionization-mode: sample metadata, one row per sample" />
43 <param name="vmpos" label="Variable metadata positive" type="data" format="tabular"
44 help="Positive ionization-mode: variable metadata, one row per variable" />
45 <param name="dmneg" label="Data matrix negative" type="data" format="tabular"
46 help="Negative ionization-mode: variables &#10006; samples" />
47 <param name="smneg" label="Sample metadata negative" type="data" format="tabular"
48 help="Negative ionization-mode: sample metadata, one row per sample" />
49 <param name="vmneg" label="Variable metadata negative" type="data" format="tabular"
50 help="Negative ionization-mode: variable metadata, one row per variable" />
51 </inputs>
52 <outputs>
53 <data name="dmout" label="${dmneg.name}.posneg" format="tabular" ></data>
54 <data name="smout" label="${smneg.name}.posneg" format="tabular" ></data>
55 <data name="vmout" label="${vmneg.name}.posneg" format="tabular" ></data>
56 </outputs>
57 <tests>
58 <!-- test 1 -->
59 <test>
60 <param name="dmpos" value="input_dataMatrix_pos.tsv"/>
61 <param name="dmneg" value="input_dataMatrix_neg.tsv"/>
62 <param name="smpos" value="input_sampleMetadata_pos.tsv"/>
63 <param name="smneg" value="input_sampleMetadata_neg.tsv"/>
64 <param name="vmpos" value="input_variableMetadata_pos.tsv"/>
65 <param name="vmneg" value="input_variableMetadata_neg.tsv"/>
66 <output name="dmout">
67 <assert_contents>
68 <has_text text="NM295T781" />
69 <has_text text="1177836.83774999" />
70 <has_text text="3552840.90153851" />
71 </assert_contents>
72 </output>
73 <output name="vmout">
74 <assert_contents>
75 <has_text text="NM295T781" />
76 <has_text text="M295.125T780.95" />
77 <has_text text="780.953277587891" />
78 </assert_contents>
79 </output>
80 <output name="smout">
81 <assert_contents>
82 <has_text text="Y5_1_RA4_01_212" />
83 <has_text text="posneg" />
84 <has_text text="Y13_1_RA6_01_214" />
85 </assert_contents>
86 </output>
87 </test>
88 <!-- test 2 -->
89 <test>
90 <param name="dmpos" value="input_dataMatrix_pos.tsv"/>
91 <param name="dmneg" value="input_dataMatrix_neg.tsv"/>
92 <param name="smpos" value="input_sampleMetadata_pos.tsv"/>
93 <param name="smneg" value="input_sampleMetadata_neg_4col.tsv"/>
94 <param name="vmpos" value="input_variableMetadata_pos.tsv"/>
95 <param name="vmneg" value="input_variableMetadata_neg.tsv"/>
96 <output name="dmout">
97 <assert_contents>
98 <has_text text="NM295T781" />
99 <has_text text="1177836.83774999" />
100 <has_text text="3552840.90153851" />
101 </assert_contents>
102 </output>
103 <output name="vmout">
104 <assert_contents>
105 <has_text text="NM295T781" />
106 <has_text text="M295.125T780.95" />
107 <has_text text="780.953277587891" />
108 </assert_contents>
109 </output>
110 <output name="smout">
111 <assert_contents>
112 <has_text text="Y5_1_RA4_01_212" />
113 <has_text text="posneg" />
114 <has_text text="y5" />
115 <has_text text="bar" />
116 </assert_contents>
117 </output>
118 </test>
119 </tests>
120 <help><![CDATA[
38 **Join positive and negative ionization-mode W4M datasets for the same samples** 121 **Join positive and negative ionization-mode W4M datasets for the same samples**
39 -------------------------------------------------------------------------------- 122 --------------------------------------------------------------------------------
40 123
41 **Author** - Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu) 124 **Author** - Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
42 125
44 Motivation 127 Motivation
45 ---------- 128 ----------
46 129
47 Workflow4Metabolomics (W4M, Giacomoni *et al.*, 2014; http://workflow4metabolomics.org; https://github.com/workflow4metabolomics) 130 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. 131 provides a suite of Galaxy tools for processing and analyzing metabolomics data.
49 132
50 W4M uses the XCMS package (Smith *et al.*, 2006) to extract features and align 133 W4M uses the XCMS package (Smith *et al.*, 2006) to extract features and align
51 their retention times among multiple samples. 134 their retention times among multiple samples.
52 135
53 After peak extraction and alignment, W4M uses the CAMERA package (Kuhl *et al.*, 2012) 136 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." 137 "to postprocess XCMS feature lists and to collect all features related to a compound into a compound spectrum."
86 Working example 169 Working example
87 --------------- 170 ---------------
88 171
89 **Input files** 172 **Input files**
90 173
91 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ 174 +---------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
92 | Input File | Download from URL | 175 | Input File | Download from URL |
93 +=============================================+=======================================================================================================================+ 176 +=============================================+==========================================================================================================================================+
94 | Data matrix, negative ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_dataMatrix_neg.tsv | 177 | Data matrix, negative ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/tools/w4mjoinpn/test-data/input_dataMatrix_neg.tsv |
95 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ 178 +---------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
96 | Sample metadata, negative ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_sampleMetadata_neg.tsv | 179 | Sample metadata, negative ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/tools/w4mjoinpn/test-data/input_sampleMetadata_neg.tsv |
97 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ 180 +---------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
98 | Variable metadata, negative ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_variableMetadata_neg.tsv | 181 | Variable metadata, negative ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/tools/w4mjoinpn/test-data/input_variableMetadata_neg.tsv |
99 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ 182 +---------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
100 | Data matrix, positive ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_dataMatrix_pos.tsv | 183 | Data matrix, positive ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/tools/w4mjoinpn/test-data/input_dataMatrix_pos.tsv |
101 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ 184 +---------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
102 | Sample metadata, positive ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_sampleMetadata_pos.tsv | 185 | Sample metadata, positive ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/tools/w4mjoinpn/test-data/input_sampleMetadata_pos.tsv |
103 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ 186 +---------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
104 | Variable metadata, positive ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_variableMetadata_pos.tsv | 187 | Variable metadata, positive ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/tools/w4mjoinpn/test-data/input_variableMetadata_pos.tsv |
105 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ 188 +---------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
106 189
107 **Output files** 190 **Output files**
108 191
109 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ 192 +---------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
110 | Output File | Download from URL | 193 | Output File | Download from URL |
111 +=============================================+=======================================================================================================================+ 194 +=============================================+==========================================================================================================================================+
112 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/output_dataMatrix.tsv | 195 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/tools/w4mjoinpn/test-data/expected_dataMatrix.tsv |
113 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ 196 +---------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
114 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/output_sampleMetadata.tsv | 197 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/tools/w4mjoinpn/test-data/expected_sampleMetadata.tsv |
115 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ 198 +---------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
116 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/output_variableMetadata.tsv | 199 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/tools/w4mjoinpn/test-data/expected_variableMetadata.tsv |
117 +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ 200 +---------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------+
118 201
119 ]]></help> 202 ]]></help>
120 <citations> 203 <citations>
121 <citation type="doi">10.5281/zenodo.1038289</citation> 204 <!-- Giacomoni, 2014 Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics -->
205 <citation type="doi">10.1093/bioinformatics/btu813</citation>
206 <!-- Kuhl et al., 2012 CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of LC-MS Data Sets -->
207 <citation type="doi">10.1021/ac202450g</citation>
208 <!-- Smith, 2006 XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification. -->
209 <citation type="doi">10.1021/ac051437y</citation>
210 </citations>
122 <!-- 211 <!--
123 <citation type="bibtex"> 212 vim:et:sw=4:ts=4
124 @misc{ 213 --> </tool>
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>