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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef commit d4b6dd6bf42d2e8faa335bcd77b681938e56a9e4"
author galaxyp
date Fri, 06 Mar 2020 07:16:26 -0500
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1 <tool id="diapysef" name="diapysef library generation" version="0.3.5.0">
2 <description>generates spectral library for DIA analysis</description>
3 <requirements>
4 <requirement type="package" version="0.3.5">diapysef</requirement>
5 <requirement type="package" version="1.0.1">pandas</requirement>
6 </requirements>
7 <command detect_errors="aggressive">
8 <![CDATA[
9
10 python '${diapysef_script}'
11
12 ]]>
13 </command>
14 <configfiles>
15 <configfile name="diapysef_script"><![CDATA[
16
17 import diapysef as dp
18 import pandas as pd
19
20 msms = pd.read_csv("$input_msms", sep="\t")
21 evidence = pd.read_csv("$input_evidence", sep="\t")
22 irt = pd.read_csv("$input_irtassays", sep="\t")
23 ptsv = dp.pasef_to_tsv(evidence, msms, irt_file=irt, ion_mobility=None, rt_alignment="$alignment")
24 ptsv.to_csv("$output_tabular", sep="\t", index=False)
25
26
27 ]]></configfile>
28 </configfiles>
29 <inputs>
30 <param name="input_msms" type="data" format="tabular" label="MaxQuant output file msms.txt" help="" />
31 <param name="input_evidence" type="data" format="tabular" label="MaxQuant output file evidence.txt" help="" />
32 <param name="input_irtassays" type="data" format="tabular" label="Retention time alignment peptides" help="tabular file containing peptides for the alignment, e.g. iRTs or ciRTs" />
33 <param name="alignment" type="select" display="radio" label="RT alignment method" help="" >
34 <option value="linear" selected="True">linear</option>
35 <option value="nonlinear">lowess</option>
36 </param>
37 </inputs>
38 <outputs>
39 <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: spectral library" from_work_dir="mqout.tabular" />
40 <data name="output_pdf" format="pdf" label="${tool.name} on ${on_string}: RT calibration curves" from_work_dir="rtcalibration.pdf" />
41 </outputs>
42 <tests>
43 <test>
44 <param name="input_msms" value="msms_cut.tabular" ftype="tabular" />
45 <param name="input_evidence" value="evidence_cut.tabular" ftype="tabular" />
46 <param name="input_irtassays" value="irtassays.tabular" ftype="tabular" />
47 <param name="alignment" value="linear" />
48 <output name="output_pdf" file="rtcalibration1.pdf" compare="sim_size"/>
49 </test>
50 <test>
51 <param name="input_msms" value="msms_cut.tabular" ftype="tabular" />
52 <param name="input_evidence" value="evidence_cut.tabular" ftype="tabular" />
53 <param name="input_irtassays" value="irtassays.tabular" ftype="tabular" />
54 <param name="alignment" value="nonlinear" />
55 <output name="output_pdf" file="rtcalibration2.pdf" compare="sim_size"/>
56 </test>
57 <test>
58 <param name="input_msms" value="msms_cut.tabular" ftype="tabular" />
59 <param name="input_evidence" value="evidence_cut.tabular" ftype="tabular" />
60 <param name="input_irtassays" value="irtassays.tabular" ftype="tabular" />
61 <param name="alignment" value="nonlinear" />
62 <output name="output_tabular" >
63 <assert_contents>
64 <has_text text="transition_group_id" />
65 <has_text text="LibraryIntensity" />
66 <has_text text="(Acetylation)DGLDAASYYAPVR" />
67 <has_text text="sp|Biognosys_pep-h|iRT-Kit_WR_fusion" />
68 <has_text text="sp|Biognosys_pep-k|iRT-Kit_WR_fusion" />
69 <has_n_columns n="11" />
70 </assert_contents>
71 </output>
72 </test>
73 </tests>
74 <help>
75 <![CDATA[
76
77
78 Diapysef enables generating a DIA library. For more information: http://openswath.org/en/latest/docs/librarygeneration.html
79
80 For most data-independent acquisition (DIA) analysis, a well-represented spectral library is required for precursors, peptide, and protein identifications. Currently, we support library generation with the diapysef package directly from a MaxQuant analysis of several DDA runs.
81
82 **Inputs**
83
84 - msms.txt and evidence.txt (output files from MaxQuant)
85 - peptides used for retention time alignment e.g. iRTs or ciRTs
86
87 - Tabular file with at least three columns for precursor charge, normalized retention time and modified peptide sequence
88 - The headers of the columns must be named "PrecursorCharge" "NormalizedRetentionTime" "ModifiedPeptideSequence"
89
90
91 ::
92
93 PrecursorCharge NormalizedRetentionTime ModifiedPeptideSequence
94 2 53.2 ADVTPADFSEWSK
95 3 52.9 ADVTPADFSEWSK
96 2 43.6 DGLDAASYYAPVR
97 ...
98 ...
99
100
101 **Potential next Steps**
102
103 After generating the spectral library with diapysef, the tabular file can be imported into OpenSwathAssayGenerator and OpenSwathDecoyGenerator to refine the library.
104
105
106 ]]>
107 </help>
108 <citations>
109 <citation type="doi">10.1038/nbt.2841</citation>
110 </citations>
111 </tool>