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comparison macros.xml @ 0:b96fc0da0a32 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
author tomnl
date Mon, 05 Mar 2018 10:05:57 -0500
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children e2635fa802bd
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-1:000000000000 0:b96fc0da0a32
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="1.4.5" >bioconductor-mspurity</requirement>
6 <requirement type="package" version="1.4.4" >r-optparse</requirement>
7 <yield />
8 </requirements>
9
10 </xml>
11
12 <xml name="offsets">
13 <param name="minoffset" type="float" label="minoffset" value="0.5"
14 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
15 100.0 then the range would be from 999.5 to 100.0"/>
16 <param name="maxoffset" type="float" label="maxoffset" value="0.5"
17 help="Offset to the 'right' for the precursor range e.g. if precursor of interest is
18 100.0 then the range would be from 100.0 to 100.5"/>
19 </xml>
20 <xml name="general_params">
21
22 <param name="ilim" type="float" label="ilim" value="0.05"
23 help="All peaks less than this percentage of the target peak will be removed
24 from the purity calculation, default is 5\% (0.05)"/>
25
26 <param name="iw_norm" type="select" label="Normalisation for isolation efficiency">
27 <option value="gauss" >Gaussian</option>
28 <option value="rcosine" >Raised cosine</option>
29 <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option>
30 <option value="none" selected="true" >No normalisation</option>
31 </param>
32
33 <conditional name="isotopes">
34 <param name="isotopes" type="select" label="Handling of isotopic peaks" >
35 <option value="keep" >Keep isotopes in precursor ion purity calculation</option>
36 <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option>
37 <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option>
38 </param>
39 <when value="keep">
40 </when>
41 <when value="exclude_default">
42 </when>
43 <when value="user">
44 <param name="im" type="data" format="tabular" label="Isotope matrix" help="
45 tabular file composing of columns:
46 ['isotope_id', 'mass diff', 'abundance of isotope', 'ppm tol for mz', 'abundance buffer',
47 'charge', 'relative atomic mass (int)', 'xflag'].
48 The xflag indicates if the larger (mass) isotope is the most abundant or less abundant.
49 e.g. for c12 to c13, the c13 is less abundant so we flag as 1 for Li6 to Li7, the Li7 is more abundant
50 so we would flag as 0.
51 Example row: For C13 isotope (single charge) the row could be [1, 1.003355, 1.07, 4, 0.1, 1, 12, 1]"/>
52 </when>
53 </conditional>
54 </xml>
55
56
57
58
59
60
61
62 <xml name="fileload">
63 <conditional name="file_load_conditional">
64 <param name="file_load_select" type="select" label="Resubmit your dataset"
65 help="Use only if you get a message which say that your original dataset or
66 dataset collection can not be found the server." >
67 <option value="no" >no need</option>
68 <option value="yes" >yes</option>
69 </param>
70 <when value="no">
71 </when>
72 <when value="yes">
73 <param name="input" type="data_collection" collection_type="list" format="mzxml,mzml,mzdata,netcdf"
74 multiple="true" label="File(s) from your history containing your chromatograms"
75 help="Select the dataset collection containing the files that were used
76 for processing" />
77 </when>
78 </conditional>
79 </xml>
80
81
82
83 <xml name="citations">
84 <citations>
85 <citation type="doi">10.1021/acs.analchem.6b04358</citation>
86 <yield />
87 </citations>
88 </xml>
89
90 </macros>