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comparison createMSP.xml @ 0:df2efceff4cd draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
author tomnl
date Fri, 24 May 2019 09:06:56 -0400
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children 6d1312ad450c
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-1:000000000000 0:df2efceff4cd
1 <tool id="mspurity_createmsp" name="msPurity.createMSP" version="0.2.0">
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 <stdio>
9 <exit_code range="1:" />
10 </stdio>
11 <command interpreter="Rscript" ><![CDATA[
12 createMSP.R
13 --rdata_input "$rdata_input"
14 --method "$method"
15
16 #if $metadata_cond.metadata_select == "true"
17 --metadata "$metadata_cond.metadata"
18 --metadata_cols "$metadata_cond.metadata_cols"
19 --adduct_split "$metadata_cond.adduct_split"
20 #end if
21
22 #if $xcms_group_cond.xcms_group_select == "true"
23 --xcms_groupids "$xcms_group_cond.xcms_groupids"
24 #end if
25
26 $filter
27
28 --msp_schema "$msp_schema"
29 --intensity_ra "$intensity_ra"
30
31 --out_dir '.'
32 ]]></command>
33 <inputs>
34 <param name="rdata_input" type="data" format="rdata" label="msPurity purityA dataset" argument="--purity_dataset"
35 help="RData file containing the purityA object following frag4feature and/or averageFragmentation"/>
36 <param name="method" type="select" label="How to choose fragmentation spectra (if precursor was fragmented in >1 scans per XCMS group feature)"
37 help="'Average all' will use the averaged MS/MS spectra of the XCMS grouped feature, ignoring inter and intra file relationships,
38 'Average' (intra)' will use the intra file (within file) averaged MS/MS spectra of the XCMS grouped feature,
39 'Average (inter)' will use the inter file (across file) MS/MS averaged spectra,
40 'All scans' will export all matching MS/MS spectra to XCMS grouped features,
41 'Max intensity' will choose the most MS/MS spectra with the most intense precursor ion for each XCMS grouped feature"
42 argument="--method">
43 <option value="av_all" selected="true">Average (all)</option>
44 <option value="av_intra">Average (intra)</option>
45 <option value="av_inter">Average (inter)</option>
46 <option value="all">All scans</option>
47 <option value="max" >Max intensity</option>
48 </param>
49
50 <conditional name="metadata_cond">
51 <param name="metadata_select" type="boolean" label="Use additional metadata?" />
52 <when value="true">
53 <param type="data" name="metadata" label="Metadata for each feature" format="tsv,tabular"
54 help="Metadata for each grouped XCMS feature, the data will be added to the MSP metadata.
55 Using the MassBank format e.g. https://github.com/MassBank/MassBank-data/blob/master/MetaboLights/ML003001.txt "/>
56
57 <param name="metadata_cols" type="text" label="Metadata columns for name" value="CH$NAME, MS$FOCUSED_ION: PRECURSOR_TYPE" help="Comma separated string of column names where the corresponding values in the metadata will be used for the MSP spectra name"/>
58 <param name="adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?" help="If either 'adduct' or 'MS$FOCUSED_ION: PRECURSOR_TYPE'
59 column is in metadata then each adduct will have it's own MSP spectra.
60 (Useful, if the MSP file will be used for further annotation)" />
61 </when>
62 <when value="false">
63 </when>
64 </conditional>
65
66 <conditional name="xcms_group_cond">
67 <param name="xcms_group_select" type="boolean" label="Select XCMS groups?" help="if set to no, all XCMS group features will be used" />
68 <when value="true">
69 <param name="xcms_groupids" type="text" label="XCMS peak group ids" value=""
70 help="Comma separated string of XCMS group ids to export MSP spectra for. If blank all XCMS peak groups will be used"/>
71 </when>
72 <when value="false">
73 </when>
74 </conditional>
75
76 <param name="intensity_ra" type="select" label="Include intensity, relative abundanace or both in the MSP file"
77 argument="--intensity_ra">
78 <option value="intensity_ra" selected="true">Both intensity and relative abundance</option>
79 <option value="intensity">Intensity only</option>
80 <option value="ra">Relative abundance only</option>
81 </param>
82
83 <param name="msp_schema" type="select" label="MSP schema to use for files"
84 argument="--msp_schema">
85 <option value="massbank" selected="true">MassBank (Europe)</option>
86 <option value="mona">MoNA</option>
87
88 </param>
89
90 <param name="filter" type="boolean" checked="true" truevalue="--filter" falsevalue="" label="Filter peaks that have been flagged in prior processing steps" help="" />
91
92 </inputs>
93 <outputs>
94 <data name="createMSP_output" format="msp" from_work_dir="lcmsms_spectra.msp" label="${tool.name} on ${on_string}: msp"/>
95 </outputs>
96 <tests>
97 <test>
98 <param name="method" value="all"/>
99 <param name="rdata_input" value="frag4feature_output.RData"/>
100 <output name="createMSP_output" file="createMSP_output_scans_all.msp"/>
101 </test>
102 <test>
103 <param name="method" value="av_all"/>
104 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
105 <output name="createMSP_output" file="createMSP_output_av_all.msp"/>
106 </test>
107 <test>
108 <param name="method" value="av_all"/>
109 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
110 <param name="metadata_cond|metadata_select" value="true"/>
111 <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/>
112 <param name="metadata_cond|metadata_cols" value="AC$CHROMATOGRAPHY: COLUMN_NAME, AC$MASS_SPECTROMETRY: ION_MODE, AC$MASS_SPECTROMETRY: MS_TYPE, CH$LINK: INCHIKEY, CH$LINK: PUBCHEM CH$NAME
113 "/>
114 <param name="xcms_group_cond|xcms_group_select" value="true"/>
115 <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
116 <param name="metadata_cond|adduct_split" value="true"/>
117 <output name="createMSP_output" file="createMSP_output_av_all_metadata.msp"/>
118 </test>
119 <test>
120 <param name="method" value="av_all"/>
121 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
122 <param name="xcms_group_cond|xcms_group_select" value="true"/>
123 <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
124 <output name="createMSP_output" file="createMSP_output_av_all_and_all_xcms.msp"/>
125 </test>
126 <test>
127 <param name="method" value="av_intra"/>
128 <param name="rdata_input" value="averageFragSpectra_output_intra.RData"/>
129 <output name="createMSP_output" file="createMSP_output_av_intra.msp"/>
130 </test>
131 <test>
132 <param name="method" value="av_inter"/>
133 <param name="rdata_input" value="averageFragSpectra_output_inter.RData"/>
134 <output name="createMSP_output" file="createMSP_output_av_inter.msp"/>
135 </test>
136 <test>
137 <param name="method" value="max"/>
138 <param name="rdata_input" value="frag4feature_output.RData"/>
139 <output name="createMSP_output" file="createMSP_output_max.msp"/>
140 </test>
141 </tests>
142 <help><![CDATA[
143 ------------------------------
144 Create MSP Files from msPurity
145 ------------------------------
146
147 Description
148 -----------
149
150 | This tool will extract the MSMS spectra data from an msPurity-frag4feature object into a file with MSP data format.
151
152
153
154
155 Developers and contributors
156 ---------------------------
157
158 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
159 - **Andris Jankevics (a.jankevics@bham.ac.uk) - University of Birmingham (UK)**
160 - **Thomas N. Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)**
161 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
162
163 ]]></help>
164
165 <expand macro="citations" />
166
167 </tool>