Mercurial > repos > tomnl > mspurity_averagefragspectra

comparison averageFragSpectra.xml @ 12:e0b1da3ed06b draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
author tomnl
date Fri, 13 Sep 2019 11:52:29 -0400
parents 36f2d807c2b8
children 42bfb67c3b62
comparison
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11:36f2d807c2b8 12:e0b1da3ed06b
31 ]]></command> 31 ]]></command>
32 <inputs> 32 <inputs>
33 <param name="pa" type="data" label="purityA object" format="rdata" 33 <param name="pa" type="data" label="purityA object" format="rdata"
34 help="purityA object saved as 'pa' in a RData file (output from frag4feature tool)"/> 34 help="purityA object saved as 'pa' in a RData file (output from frag4feature tool)"/>
35 35
36 <conditional name="av">
37 <param name="level" type="select" label="Average and filter fragmentation spectra for each XCMS feature" help="">
38 <option value="intra" selected="true">within a MS data file</option>
39 <option value="inter">accross MS data files</option>
40 <option value="all">within and accross MS data files (ignoring intra and inter relationships)</option>
41 </param>
42 <when value="intra">
43 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
44 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
45 </when>
46 <when value="inter">
47 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
48 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
49 </when>
50 <when value="all">
51 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
52 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
53 </when>
54 </conditional>
55 36
56 <param name="av_level" type="select" label="Average and filter fragmentation spectra for each XCMS feature" help=""> 37 <param name="av_level" type="select" label="Average and filter fragmentation spectra for each XCMS feature" help="">
57 <option value="intra" selected="true">within a MS data file</option> 38 <option value="intra" selected="true">within a MS data file</option>
58 <option value="inter">accross MS data files</option> 39 <option value="inter">across MS data files</option>
59 <option value="all">within and accross MS data files (ignoring intra and inter relationships)</option> 40 <option value="all">within and across MS data files (ignoring intra and inter relationships)</option>
60 </param> 41 </param>
42
43
61 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" /> 44 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
62 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" /> 45 <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
63 <param name="minfrac" type="float" min="0.0" max="1.0" value="0.5" label="Minimum fraction (i.e. percentage) of (averaged) scans a fragment peak has to be present in." help="" /> 46 <param name="minfrac" type="float" min="0.0" max="1.0" value="0.5" label="Minimum fraction (i.e. percentage) of (averaged) scans a fragment peak has to be present in." help="" />
64 <param name="minnum" type="integer" value="1" label="Minimum number of (averaged) fragmentation scans for a fragmentation event (precursor)." help="" /> 47 <param name="minnum" type="integer" value="1" label="Minimum number of (averaged) fragmentation scans for a fragmentation event (precursor)." help="" />
65 <param name="ppm" type="float" value="5.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation in parts per million." /> 48 <param name="ppm" type="float" value="5.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation in parts per million." />