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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:19:07 +0000
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-1:000000000000 0:eeb5d343374c
1 <tool id="mspurity_createmsp" name="msPurity.createMSP" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
2 <description>Create MSP files from msPurity processed data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 </expand>
8 <command detect_errors="exit_code"><![CDATA[
9 Rscript '$__tool_directory__/createMSP.R'
10 --rdata_input '$rdata_input'
11 --method '$method'
12
13 #if $metadata_cond.metadata_select == "true"
14 --metadata '$metadata_cond.metadata'
15 --metadata_cols '$metadata_cond.metadata_cols'
16 --metadata_cols_filter '$metadata_cond.metadata_cols_filter'
17
18 #end if
19
20 #if $xcms_group_cond.xcms_group_select == "true"
21 --xcms_groupids '$xcms_group_cond.xcms_groupids'
22 #end if
23
24 $filter
25 $adduct_split
26
27 --msp_schema $msp_schema
28 --intensity_ra $intensity_ra
29 --include_adducts $include_adducts
30 #if $include_adducts_custom
31 --include_adducts_custom "$include_adducts_custom"
32 #end if
33
34 --out_dir '.'
35 ]]></command>
36 <inputs>
37 <param argument="--rdata_input" type="data" format="rdata" label="msPurity purityA dataset"
38 help="RData file containing the purityA object following frag4feature and/or averageFragmentation"/>
39 <param argument="--method" type="select" label="How to choose fragmentation spectra (if precursor was fragmented in >1 scans per XCMS group feature)"
40 help="'Average all' will use the averaged MS/MS spectra of the XCMS grouped feature, ignoring inter and intra file relationships,
41 'Average' (intra)' will use the intra file (within file) averaged MS/MS spectra of the XCMS grouped feature,
42 'Average (inter)' will use the inter file (across file) MS/MS averaged spectra,
43 'All scans' will export all matching MS/MS spectra to XCMS grouped features,
44 'Max intensity' will choose the most MS/MS spectra with the most intense precursor ion for each XCMS grouped feature"
45 >
46 <option value="av_all" selected="true">Average (all)</option>
47 <option value="av_intra">Average (intra)</option>
48 <option value="av_inter">Average (inter)</option>
49 <option value="all">All scans</option>
50 <option value="max" >Max intensity</option>
51 </param>
52
53 <conditional name="metadata_cond">
54 <param name="metadata_select" type="boolean" label="Use additional metadata?" />
55 <when value="true">
56 <param argument="--metadata" type="data" label="Metadata for each feature" format="tsv,tabular"
57 help="Metadata for each grouped XCMS feature, e.g. could be the adduct calculated from CAMERA "/>
58
59 <param argument="--metadata_cols_filter" type="text" label="Metadata columns to use" value=""
60 help="Comma separated string of column names where the corresponding values in the metadata will be used"/>
61
62 <param argument="--metadata_cols" type="text" label="Metadata columns for MSP spectra name" value=""
63 help="Comma separated string of column names where the corresponding values in the metadata will be used
64 for MSP spectra name"/>
65
66 </when>
67 <when value="false">
68 </when>
69 </conditional>
70
71 <conditional name="xcms_group_cond">
72 <param name="xcms_group_select" type="boolean" label="Select XCMS groups?" help="if set to no, all XCMS group features will be used" />
73 <when value="true">
74 <param argument="--xcms_groupids" type="text" label="XCMS peak group ids" value=""
75 help="Comma separated string of XCMS group ids to export MSP spectra for. If blank all XCMS peak groups will be used"/>
76 </when>
77 <when value="false">
78 </when>
79 </conditional>
80
81 <param argument="--intensity_ra" type="select" label="Include intensity, relative abundanace or both in the MSP file">
82 <option value="intensity_ra" selected="true">Both intensity and relative abundance</option>
83 <option value="intensity">Intensity only</option>
84 <option value="ra">Relative abundance only</option>
85 </param>
86
87 <param argument="--msp_schema" type="select" label="MSP schema to use for files">
88 <option value="massbank" selected="true">MassBank (Europe)</option>
89 <option value="mona">MoNA</option>
90
91 </param>
92
93 <param argument="--filter" type="boolean" checked="true" truevalue="--filter" falsevalue=""
94 label="Filter peaks that have been flagged in prior processing steps" help="" />
95
96
97 <param argument="--include_adducts" type="select" label="Always include the following adduct descriptions in the MSP file"
98 help="Additional adducts to include, can be useful for downstream processing" multiple="true">
99 <option value="[M+H]+">[M+H]+</option>
100 <option value="[M+Na]+">[M+Na]+</option>
101 <option value="[M+NH4]+">[M+NH4]+</option>
102 <option value="[M+K]+" >[M+K]+</option>
103 <option value="[M+CH3OH+H]+">[M+CH3OH+H]+</option>
104 <option value="[M+ACN+H]+">[M+ACN+H]+</option>
105 <option value="[M+ACN+Na]+">[M+ACN+Na]+</option>
106 <option value="[M+2ACN+H]+">[M+2ACN+H]+</option>
107 <option value="[M-H]-">[M-H]-</option>
108 <option value="[M+HCOO]-" >[M+HCOO]-</option>
109 <option value="[M+CH3COO]-" >[M+CH3COO]-</option>
110 <option value="[M-H+CH3COOH]-" >[M-H+CH3COOH]-</option>
111 </param>
112 <param argument="--include_adducts_custom" type="text" label="Always include the following custom adducts"
113 help="Additional custom adducts to include, should be comma separated" optional="true">
114 <expand macro="text-adduct-regex-validator"/>
115 </param>
116
117 <param argument="--adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?"
118 help="Useful if the MSP file will be used for further annotation" truevalue="--adduct_split" falsevalue=""/>
119
120 </inputs>
121 <outputs>
122 <data name="createMSP_output" format="msp" from_work_dir="lcmsms_spectra.msp" label="${tool.name} on ${on_string}: msp"/>
123 </outputs>
124 <tests>
125
126 <test>
127 <!-- Test all average with metadata -->
128 <param name="method" value="av_all"/>
129 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
130 <param name="metadata_cond|metadata_select" value="true"/>
131 <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/>
132 <param name="xcms_group_cond|xcms_group_select" value="true"/>
133 <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
134 <param name="metadata_cond|adduct_split" value="true"/>
135 <output name="createMSP_output" file="createMSP_output_av_all_metadata.msp"/>
136 </test>
137
138 <test>
139 <!-- Test custom adducts average with metadata -->
140 <param name="method" value="av_all"/>
141 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
142 <param name="metadata_cond|metadata_select" value="true"/>
143 <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/>
144 <param name="xcms_group_cond|xcms_group_select" value="true"/>
145 <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
146 <param name="metadata_cond|adduct_split" value="true"/>
147 <param name="include_adducts_custom" value="[M+]+,[M-H]-,[M+TEST SPACE+]+"/>
148 <output name="createMSP_output" file="createMSP_output_av_all_metadata_custom_adducts.msp"/>
149 </test>
150
151
152
153 </tests>
154 <help><![CDATA[
155 ------------------------------
156 Create MSP Files from msPurity
157 ------------------------------
158
159 Description
160 -----------
161
162 | This tool will extract the MSMS spectra data from an msPurity-frag4feature object into a file with MSP data format.
163
164
165
166
167 Developers and contributors
168 ---------------------------
169
170 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
171 - **Andris Jankevics (a.jankevics@bham.ac.uk) - University of Birmingham (UK)**
172 - **Thomas N. Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)**
173 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
174
175 ]]></help>
176
177 <expand macro="citations" />
178
179 </tool>