Mercurial > repos > galaxyp > msms_extractor
comparison msms_extractor.xml @ 0:4bef80b09854 draft default tip
"planemo upload commit 498440b547e1feaa6a81764b55ac8208626d70a8"
author | galaxyp |
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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> |