Mercurial > repos > tomnl > create_sqlite_db

annotate macros.xml @ 28:be54f396ecfe draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
author tomnl
date Wed, 18 Jul 2018 05:47:49 -0400
parents 0d59d313d3f8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
1 <?xml version="1.0"?>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
2 <macros>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
3 <xml name="requirements">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
4 <requirements>
27
0d59d313d3f8 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6
tomnl
parents: 26
diff changeset
5 <requirement type="package" version="1.7.7" >bioconductor-mspurity</requirement>
0
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
6 <yield />
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
7 </requirements>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
8
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
9 </xml>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
10
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
11 <xml name="offsets">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
12 <param name="minoffset" type="float" label="minoffset" value="0.5"
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
13 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
14 100.0 then the range would be from 999.5 to 100.0"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
15 <param name="maxoffset" type="float" label="maxoffset" value="0.5"
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
16 help="Offset to the 'right' for the precursor range e.g. if precursor of interest is
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
17 100.0 then the range would be from 100.0 to 100.5"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
18 </xml>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
19 <xml name="general_params">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
20
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
21 <param name="ilim" type="float" label="ilim" value="0.05"
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
22 help="All peaks less than this percentage of the target peak will be removed
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
23 from the purity calculation, default is 5\% (0.05)"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
24
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
25 <param name="iw_norm" type="select" label="Normalisation for isolation efficiency">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
26 <option value="gauss" >Gaussian</option>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
27 <option value="rcosine" >Raised cosine</option>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
28 <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
29 <option value="none" selected="true" >No normalisation</option>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
30 </param>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
31
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
32 <conditional name="isotopes">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
33 <param name="isotopes" type="select" label="Handling of isotopic peaks" >
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
34 <option value="keep" >Keep isotopes in precursor ion purity calculation</option>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
35 <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
36 <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
37 </param>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
38 <when value="keep">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
39 </when>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
40 <when value="exclude_default">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
41 </when>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
42 <when value="user">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
43 <param name="im" type="data" format="tabular" label="Isotope matrix" help="
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
44 tabular file composing of columns:
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
45 ['isotope_id', 'mass diff', 'abundance of isotope', 'ppm tol for mz', 'abundance buffer',
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
46 'charge', 'relative atomic mass (int)', 'xflag'].
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
47 The xflag indicates if the larger (mass) isotope is the most abundant or less abundant.
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
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
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
49 so we would flag as 0.
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
50 Example row: For C13 isotope (single charge) the row could be [1, 1.003355, 1.07, 4, 0.1, 1, 12, 1]"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
51 </when>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
52 </conditional>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
53 </xml>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
54
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
55
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
56 <xml name="camera_xcms">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
57 <param name="camera_xcms" type="select" label="Use CAMERA object or XCMS object from RData?"
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
58 help="Within the RData file there should be either an XCMS object called xset or a CAMERA object called
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
59 xa (or both). The XCMS object is nested within the CAMERA object so either can be used">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
60 <option value="xcms" selected="true" >XCMS (xset)</option>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
61 <option value="camera" >CAMERA (xa)</option>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
62 </param>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
63 </xml>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
64
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
65
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
66 <xml name="fileload">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
67 <conditional name="file_load_conditional">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
68 <param name="file_load_select" type="select" label="Resubmit your dataset"
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
69 help="Use only if you get a message which say that your original dataset or
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
70 dataset collection can not be found the server." >
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
71 <option value="no" >no need</option>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
72 <option value="yes" >yes</option>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
73 </param>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
74 <when value="no">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
75 </when>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
76 <when value="yes">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
77 <param name="input" type="data_collection" collection_type="list" format="mzxml,mzml,mzdata,netcdf"
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
78 multiple="true" label="File(s) from your history containing your chromatograms"
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
79 help="Select the dataset collection containing the files that were used
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
80 for processing" />
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
81 </when>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
82 </conditional>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
83 </xml>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
84
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
85 <xml name="grp_peaklist">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
86 <conditional name="grp_peaklist_opt">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
87 <param name="grp_peaklist_opt" type="select" label="Add a different grouped peaklist to database?">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
88 <option value="yes" >Provide group peaklist </option>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
89 <option value="no" selected="true">Use default grouped peaklist</option>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
90 </param>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
91 <when value="no">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
92 </when>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
93 <when value="yes">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
94 <param type="data" name="grp_peaklist" label="grouped peaklist"
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
95 help="User supplied grouped peaklist to add to the database (if additional columns required e.g.
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
96 CAMERA annotations" format="tsv,tabular"/>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
97 </when>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
98 </conditional>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
99 </xml>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
100
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
101 <xml name="citations">
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
102 <citations>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
103 <citation type="doi">10.1021/acs.analchem.6b04358</citation>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
104 <yield />
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
105 </citations>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
106 </xml>
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
107
fe7d7cc95ca5 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
tomnl
parents:
diff changeset
108 </macros>