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"planemo upload commit 498440b547e1feaa6a81764b55ac8208626d70a8"
author galaxyp
date Tue, 29 Oct 2019 11:09:46 -0400
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1 <tool id="msms_extractor" name="msms_extractor" version="1.0.0">
2 <description>Extract MS/MS scans from the mzML file(s) based on PSM report</description>
3 <requirements>
4 <requirement type="package" version="3_0_9992">proteowizard</requirement>
5 <requirement type="package" version="3.7.3">python</requirement>
6 <requirement type="package" version="4.1.2">pyteomics</requirement>
7 <requirement type="package" version="0.25.2">pandas</requirement>
8 </requirements>
9 <command detect_errors="aggressive"><![CDATA[python '$__tool_directory__/msms_extractor.py' '$spectrumfile' '$psmreportfile' '$output' ${spectrumfile.name.rsplit('.',1)[0]} '$removeretain.doremoveretain' '$removeretain.num_random_scans']]></command>
10 <inputs>
11 <param name="spectrumfile" type="data" format="mzml" label="Input mzML File"/>
12 <param name="psmreportfile" type="data" format="tabular" label="Input PSM Report File"/>
13
14 <conditional name="removeretain">
15 <param name="doremoveretain" type="select" display="radio" label="Retain or Remove the MS/MS scans that were identified in PSM report">
16 <option value="remove" selected="True">Remove the scans reported in the PSM Report File</option>
17 <option value="retain">Retain the scans reported in the PSM Report File </option>
18 </param>
19
20 <when value="remove">
21 <param name="num_random_scans" type="hidden" value="0" />
22 </when>
23 <when value="retain">
24 <param name="num_random_scans" type="integer" label="Add N random scans in addition to those in the list" value="0" optional="true" />
25 </when>
26 </conditional>
27
28 </inputs>
29
30 <outputs>
31 <data format="mzml" name="output" label="${spectrumfile.name.rsplit('.',1)[0]}.mzml" />
32 </outputs>
33
34 <tests>
35 <test>
36 <param name="spectrumfile" value="Mo_Tai_iTRAQ_f1.mzml"/>
37 <param name="psmreportfile" value="test_psmreport.tabular"/>
38 <conditional name="removeretain">
39 <param name="doremoveretain" value="retain"/>
40 <param name="num_random_scans" value="5"/>
41 </conditional>
42 <output name="output">
43 <assert_contents>
44 <has_text text="Mo_Tai_iTRAQ_f1" />
45 </assert_contents>
46 </output>
47 </test>
48 </tests>
49
50 <help>
51 msms_extractor reads scan numbers from the PSM report (scan numbers with identified PSM) and gives option to create a new mzml file, either with those scans or without those scans.
52
53 ----
54
55 REMOVE option:
56
57 Creates a new mzml file with all the unidentified scans (removes those that are in the PSM report).
58
59
60 RETAIN option:
61
62 Creates a new mzml file with only those scans that is present in the PSM report. In addition to this, it also has an option to add N number of randomly selected scans to the output mzml file.
63
64 ----
65
66 Please Note: This tool currently works only with PeptideShaker generated PSM report file.
67
68
69 This tool uses msconvert from ProteoWizard: Chambers, M.C., MacLean, B., Burke, R., Amode, D., Ruderman, D.L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T.A., Brusniak, M.-Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S.L., Nuwaysir, L.M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E.W., Moritz, R.L., Katz, J.E., Agus, D.B., MacCoss, M., Tabb, D.L. and Mallick, P. A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology 30, 918-920 (2012).
70
71 </help>
72 <citations>
73 <citation type="bibtex">
74 @misc{A cross-platform toolkit for mass spectrometry and proteomics,
75 author={Matt Chambers et al.},
76 year={2012},
77 title={ProteoWizard}
78 }
79 </citation>
80 </citations>
81 </tool>