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comparison create_msp.xml @ 0:4b417094bf71 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
author tomnl
date Wed, 02 May 2018 13:09:23 -0400
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1 <tool id="create_msp" name="Create MSP Files from msPurity" version="0.1.1">
2 <description> </description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 </expand>
8
9
10 <command interpreter="Rscript" ><![CDATA[
11 create_msp.R
12 --purity "$purity"
13 --mode "$mode"
14 --ppm "$ppm"
15 ]]></command>
16 <inputs>
17 <param name="purity" type="data" format="rdata" label="msPurity frag4feature dataset" argument="--purity"/>
18 <param name="mode" type="select" label="Spectra use mode (if precursor was fragmented in >1 scans)" help='WARNING: The averaging and max options are still being developed and will likely fail' argument="--mode">
19 <option value="max" >Max Intensity</option>
20 <option value="average">Weighted Average</option>
21 <option value="all" selected="true">All</option>
22 </param>
23 <param name="ppm" optional="true" type="float" label="Allowed mass deviation between fragment MZs for spectra averaging (in ppm)" argument="--ppm"/>
24 </inputs>
25 <outputs>
26 <data name="output" format="txt" label="log" />
27 <data name="msp_out" format="msp" from_work_dir="outfile.msp" label="${purity.name} MSP file"/>
28 </outputs>
29 <tests>
30 <test>
31 <param name="mode" value="all"/>
32 <param name="purity" value="lightpurity.RData"/>
33 <output name="msp_out" file="input.msp"/>
34 </test>
35
36 </tests>
37 <help><![CDATA[
38 ------------------------------
39 Create MSP Files from msPurity
40 ------------------------------
41
42 * TO-DO: Averaging functionality
43 * TO-DO: Add citation for MSP
44 * TO-DO: Add PRECURSORTYPE if adducts available
45 * TO-DO: Create MSP from xcms/mzml files
46
47 Description
48 -----------
49
50 | This tool will extract the MSMS spectra data from an msPurity-frag4feature object into a file with MSP data format.
51 | Linking each precursor with its corresponding fragmentation spectra and associating the index within the msPurity object as the name UID.
52 | Currently, there are three different methods for extracting the data in case that more than one MSMS scan was acquired for the same precursor m/z. See Parameters.
53
54 Parameters
55 ----------
56
57 **\1. msPurity frag4feature dataset**
58
59 Result object from msPurity purityA-frag4feature functions.
60
61 **\2. Spectra use mode (if precursor was fragmented in >1 scans)**
62
63 * "Max Intensity" will only use the scan where the precursor m/z signal was maximal.
64
65 * "Weighted Average" will merge all the scans, group fragment m/z using a PPM deviation (see 3.) and weight the intensities based on the precursor intensity of that scan.
66
67 * "All" will generate a single entry in the MSP file for each MSMS scan independently.
68
69 **\3. PPM deviation for fragmentation spectra averaging**
70
71 Set the value only if you selected "Weighted Average" above, the PPM value is used to define the limits for m/z grouping into a single fragment.
72 The weighting is based on the precursor intensity, meaning that the more intense the precursor signal was, the more intensity will its fragments contribute to the averaged spectra.
73
74
75 Developers and contributors
76 ---------------------------
77
78 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
79 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
80
81 ]]></help>
82
83 <expand macro="citations" >
84 <citation type="doi">10.1186/s13321-016-0115-9</citation>
85 </expand>
86
87 </tool>