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comparison macros.xml @ 5:f2683ec717fe draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a164f06c09dc1614c2909c247ebf390aab433527-dirty
author tomnl
date Wed, 18 Sep 2019 05:46:09 -0400
parents 769ec2496d14
children
comparison
equal deleted inserted replaced
4:769ec2496d14 5:f2683ec717fe
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="1.7.7" >bioconductor-mspurity</requirement>
6 <yield />
7 </requirements>
8
9 </xml>
10
11 <xml name="offsets">
12 <param name="minoffset" type="float" label="minoffset" value="0.5"
13 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
14 100.0 then the range would be from 999.5 to 100.0"/>
15 <param name="maxoffset" type="float" label="maxoffset" value="0.5"
16 help="Offset to the 'right' for the precursor range e.g. if precursor of interest is
17 100.0 then the range would be from 100.0 to 100.5"/>
18 </xml>
19 <xml name="general_params">
20
21 <param name="ilim" type="float" label="ilim" value="0.05"
22 help="All peaks less than this percentage of the target peak will be removed
23 from the purity calculation, default is 5\% (0.05)"/>
24
25 <param name="iw_norm" type="select" label="Normalisation for isolation efficiency">
26 <option value="gauss" >Gaussian</option>
27 <option value="rcosine" >Raised cosine</option>
28 <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option>
29 <option value="none" selected="true" >No normalisation</option>
30 </param>
31
32 <conditional name="isotopes">
33 <param name="isotopes" type="select" label="Handling of isotopic peaks" >
34 <option value="keep" >Keep isotopes in precursor ion purity calculation</option>
35 <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option>
36 <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option>
37 </param>
38 <when value="keep">
39 </when>
40 <when value="exclude_default">
41 </when>
42 <when value="user">
43 <param name="im" type="data" format="tabular" label="Isotope matrix" help="
44 tabular file composing of columns:
45 ['isotope_id', 'mass diff', 'abundance of isotope', 'ppm tol for mz', 'abundance buffer',
46 'charge', 'relative atomic mass (int)', 'xflag'].
47 The xflag indicates if the larger (mass) isotope is the most abundant or less abundant.
48 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
49 so we would flag as 0.
50 Example row: For C13 isotope (single charge) the row could be [1, 1.003355, 1.07, 4, 0.1, 1, 12, 1]"/>
51 </when>
52 </conditional>
53 </xml>
54
55
56 <xml name="camera_xcms">
57 <param name="camera_xcms" type="select" label="Use CAMERA object or XCMS object from RData?"
58 help="Within the RData file there should be either an XCMS object called xset or a CAMERA object called
59 xa (or both). The XCMS object is nested within the CAMERA object so either can be used">
60 <option value="xcms" selected="true" >XCMS (xset)</option>
61 <option value="camera" >CAMERA (xa)</option>
62 </param>
63 </xml>
64
65
66 <xml name="fileload">
67 <conditional name="file_load_conditional">
68 <param name="file_load_select" type="select" label="Resubmit your dataset"
69 help="Use only if you get a message which say that your original dataset or
70 dataset collection can not be found the server." >
71 <option value="no" >no need</option>
72 <option value="yes" >yes</option>
73 </param>
74 <when value="no">
75 </when>
76 <when value="yes">
77 <param name="input" type="data_collection" collection_type="list" format="mzxml,mzml,mzdata,netcdf"
78 multiple="true" label="File(s) from your history containing your chromatograms"
79 help="Select the dataset collection containing the files that were used
80 for processing" />
81 </when>
82 </conditional>
83 </xml>
84
85 <xml name="grp_peaklist">
86 <conditional name="grp_peaklist_opt">
87 <param name="grp_peaklist_opt" type="select" label="Add a different grouped peaklist to database?">
88 <option value="yes" >Provide group peaklist </option>
89 <option value="no" selected="true">Use default grouped peaklist</option>
90 </param>
91 <when value="no">
92 </when>
93 <when value="yes">
94 <param type="data" name="grp_peaklist" label="grouped peaklist"
95 help="User supplied grouped peaklist to add to the database (if additional columns required e.g.
96 CAMERA annotations" format="tsv,tabular"/>
97 </when>
98 </conditional>
99 </xml>
100
101 <xml name="citations">
102 <citations>
103 <citation type="doi">10.1021/acs.analchem.6b04358</citation>
104 <yield />
105 </citations>
106 </xml>
107
108 </macros>