Mercurial > repos > galaxyp > dia_umpire

annotate dia_umpire_macros.xml @ 3:6caa9011f245 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
author galaxyp
date Mon, 04 Mar 2019 11:49:18 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
1 <macros>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
2 <token name="@VERSION@">2.1.3</token>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
3 <xml name="requirements">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
4 <requirements>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
5 <requirement type="package" version="2.1.3">dia_umpire</requirement>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
6 </requirements>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
7 </xml>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
8 <xml name="stdio">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
9 <stdio>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
10 <exit_code range="1:" />
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
11 </stdio>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
12 </xml>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
13 <xml name="citations">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
14 <citations>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
15 <citation type="doi">10.1038/nmeth.3255</citation>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
16 <yield />
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
17 </citations>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
18 </xml>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
19
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
20 <xml name="common_se_params">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
21 <param name="SE_Resolution" type="integer" value="" optional="true" label="Resolution" >
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
22 <help>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
23 SE.Resolution: Used only if the input spectra are stored in profile mode (i.e. not centroided, e.g. by using "Peak Picking" option in MSConvert when converting raw spectral data to mzXML format).
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
24 Profile spectra will be centroided using a sliding window. The window is moved across the entire mass range of a spectrum. Only the most intense peak in the window centered at the peak m/z is kept, others are discarded. The window width is calculated based on this parameter as: width = mz / para.Resolution.
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
25 Recommended value: Depends on the instrument and acquisition settings. Either check raw data to see the real average resolution of peaks in spectra or consult vendor specifications for the instrument. For AB SCIEX TripleTOF 5600 we use 15000-20000.
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
26 </help>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
27 </param>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
28
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
29 <param name="SE_StartCharge" type="integer" value="1" min="1" max="10" optional="true" label="StartCharge">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
30 <help>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
31 SE.StartCharge: The minimum charge state for MS1 precursor ion to be detected during isotopic peak grouping.
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
32 </help>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
33 </param>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
34
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
35 <param name="SE_EndCharge" type="integer" value="5" min="1" max="10" optional="true" label="EndCharge">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
36 <help>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
37 SE.EndCharge: The maximum charge state for MS1 precursor ion to be detected during isotopic peak grouping.
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
38 Recommended value: it is not recommended to set this parameter higher than 5 for typical proteomic experiments, as it is unlikely to observe peptides of higher charge states.
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
39 </help>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
40 </param>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
41
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
42 <param name="SE_MS2StartCharge" type="integer" value="1" min="1" max="10" optional="true" label="MS2StartCharge">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
43 <help>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
44 SE.MS2StartCharge: The minimum charge state for MS2 unfragmented precursor ion to be detected during isotopic peak grouping.
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
45 </help>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
46 </param>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
47
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
48 <param name="SE_MS2EndCharge" type="integer" value="5" min="1" max="10" optional="true" label="MS2EndCharge">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
49 <help>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
50 SE.MS2EndCharge: The maximum charge state for MS2 unfragmented precursor ion to be detected during isotopic peak grouping.
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
51 Recommended value: it is not recommended to set this parameter higher than 5 for typical proteomic experiments, as it is unlikely to observe peptides of higher charge states.
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
52 </help>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
53 </param>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
54 </xml>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
55
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
56 <xml name="se_window_params">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
57 <conditional name="window">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
58 <param name="WindowType" type="select" label="WindowType">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
59 <option value="SWATH">SWATH - fixed window size</option>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
60 <option value="V_SWATH">V_SWATH - variable window size</option>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
61 <option value="MSX">MSX - 2Da isolation window, its position is shuffled randomly until the whole MS1 range is covered</option>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
62 <option value="MSE">MSE - as originally implemented in Waters instruments. The full MS1 range is being fragmented at once.</option>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
63 </param>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
64 <when value="SWATH">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
65 <param name="WindowSize" type="integer" value="" optional="true" label="WindowSize">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
66 <help>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
67 WindowSize: Isolation window size setting for fixed window SWATH. (Please skip this part if the data is from Thermo instrument)
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
68 Note: The window size is to be specified including overlapping regions. I.e. if your windows are: 399.5-425.5, 424.5 - 450.5, etc., then the window size should be set to 26.
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
69 </help>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
70 </param>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
71 </when>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
72 <when value="V_SWATH">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
73 <!-- should allow a dataset here as well -->
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
74 <conditional name="window_list">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
75 <param name="window_list_src" type="select" label="">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
76 <option value="history"></option>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
77 <option value="text_entry"></option>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
78 </param>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
79 <when value="history">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
80 <param name="WindowListFile" type="data" format="tabular" label="WindowList">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
81 <help><![CDATA[
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
82 The format should be a tab-delimited list of m/z low and high values, one window per line. Example:
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
83 <pre>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
84 400 451<br>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
85 449 600<br>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
86 </pre>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
87 ]]>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
88 </help>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
89 </param>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
90 </when>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
91 <when value="text_entry">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
92 <param name="WindowList" type="text" area="True" size="40x40" value="" label="WindowList">
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
93 <help><![CDATA[
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
94 The format should be a tab-delimited list of m/z low and high values, one window per line. Example:
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
95 <pre>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
96 400 451<br>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
97 449 600<br>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
98 </pre>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
99 ]]>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
100 </help>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
101 </param>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
102 </when>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
103 </conditional>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
104 </when>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
105 <when value="MSX"/>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
106 <when value="MSE"/>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
107 </conditional>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
108 </xml>
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
109
6caa9011f245 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
galaxyp
parents:
diff changeset
110 </macros>