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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">
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2 <description>Extract MS/MS scans from the mzML file(s) based on PSM report</description>
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3 <requirements>
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4 <requirement type="package" version="3_0_9992">proteowizard</requirement>
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5 <requirement type="package" version="3.7.3">python</requirement>
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6 <requirement type="package" version="4.1.2">pyteomics</requirement>
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7 <requirement type="package" version="0.25.2">pandas</requirement>
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8 </requirements>
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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>
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10 <inputs>
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11 <param name="spectrumfile" type="data" format="mzml" label="Input mzML File"/>
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12 <param name="psmreportfile" type="data" format="tabular" label="Input PSM Report File"/>
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13
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14 <conditional name="removeretain">
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15 <param name="doremoveretain" type="select" display="radio" label="Retain or Remove the MS/MS scans that were identified in PSM report">
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16 <option value="remove" selected="True">Remove the scans reported in the PSM Report File</option>
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17 <option value="retain">Retain the scans reported in the PSM Report File </option>
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18 </param>
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19
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20 <when value="remove">
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21 <param name="num_random_scans" type="hidden" value="0" />
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22 </when>
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23 <when value="retain">
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24 <param name="num_random_scans" type="integer" label="Add N random scans in addition to those in the list" value="0" optional="true" />
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25 </when>
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26 </conditional>
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27
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28 </inputs>
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29
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30 <outputs>
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31 <data format="mzml" name="output" label="${spectrumfile.name.rsplit('.',1)[0]}.mzml" />
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32 </outputs>
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33
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34 <tests>
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35 <test>
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36 <param name="spectrumfile" value="Mo_Tai_iTRAQ_f1.mzml"/>
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37 <param name="psmreportfile" value="test_psmreport.tabular"/>
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38 <conditional name="removeretain">
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39 <param name="doremoveretain" value="retain"/>
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40 <param name="num_random_scans" value="5"/>
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41 </conditional>
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42 <output name="output">
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43 <assert_contents>
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44 <has_text text="Mo_Tai_iTRAQ_f1" />
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45 </assert_contents>
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46 </output>
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47 </test>
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48 </tests>
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49
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50 <help>
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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.
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52
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53 ----
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54
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55 REMOVE option:
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56
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57 Creates a new mzml file with all the unidentified scans (removes those that are in the PSM report).
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58
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59
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60 RETAIN option:
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61
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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.
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63
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64 ----
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65
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66 Please Note: This tool currently works only with PeptideShaker generated PSM report file.
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67
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68
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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).
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70
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71 </help>
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72 <citations>
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73 <citation type="bibtex">
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74 @misc{A cross-platform toolkit for mass spectrometry and proteomics,
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75 author={Matt Chambers et al.},
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76 year={2012},
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77 title={ProteoWizard}
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78 }
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79 </citation>
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80 </citations>
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81 </tool>