Mercurial > repos > lecorguille > ipo
comparison ipo4xcmsSet.xml @ 5:d63c80d54b24 draft
planemo upload commit ed7e37099389cdc575d4163ed277b882a0043e5a-dirty
| author | lecorguille |
|---|---|
| date | Thu, 29 Sep 2016 16:55:16 -0400 |
| parents | 9fa5856f6184 |
| children | 03fdfbd914ab |
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| 4:9fa5856f6184 | 5:d63c80d54b24 |
|---|---|
| 1 <tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="0.0.3"> | 1 <tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="0.0.3"> |
| 2 | 2 |
| 3 <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description> | 3 <description>IPO optimization process for xcms.xcmsSet</description> |
| 4 | 4 |
| 5 <macros> | 5 <macros> |
| 6 <import>macros.xml</import> | 6 <import>macros.xml</import> |
| 7 </macros> | 7 </macros> |
| 8 | 8 |
| 85 <option value="hide" selected="true">hide</option> | 85 <option value="hide" selected="true">hide</option> |
| 86 </param> | 86 </param> |
| 87 <when value="show"> | 87 <when value="show"> |
| 88 <param name="snthresh" type="text" value="10" label="Range for Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff (ex: 10 or 5,15)" /> | 88 <param name="snthresh" type="text" value="10" label="Range for Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff (ex: 10 or 5,15)" /> |
| 89 <param name="mzdiff" type="text" value="-0.001" label="Range for Min m/z difference" help="[mzdiff] Min m/z difference for peaks with overlapping RT (ex: -0.001 or -0.001,0.010)" /> | 89 <param name="mzdiff" type="text" value="-0.001" label="Range for Min m/z difference" help="[mzdiff] Min m/z difference for peaks with overlapping RT (ex: -0.001 or -0.001,0.010)" /> |
| 90 <param name="integrate" type="select" label="Peak limits method" help="[integrate]" multiple="true" > | 90 <param name="integrate" type="select" label="Peak limits method" help="[integrate]" > |
| 91 <option value="1">1 - peak limits based on smoothed 2nd derivative (less precise)</option> | 91 <option value="1">1 - peak limits based on smoothed 2nd derivative (less precise)</option> |
| 92 <option value="2">2 - peak limits based on real data (more sensitive to noise)</option> | 92 <option value="2">2 - peak limits based on real data (more sensitive to noise)</option> |
| 93 </param> | 93 </param> |
| 94 <param name="prefilter" type="text" value="3" label="Range for the k value for the Prefilter step for the first phase" help="[prefilter] Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’ (ex: 3 or 2,3)"/> | 94 <param name="prefilter" type="text" value="3" label="Range for the k value for the Prefilter step for the first phase" help="[prefilter] Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’ (ex: 3 or 2,3)"/> |
| 95 <param name="prefilter_value" type="text" value="100" label="Range for the I value for the Prefilter step for the first phase" help="[prefilter_value] Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’ (ex: 100 or 95,105)"/> | 95 <param name="prefilter_value" type="text" value="100" label="Range for the I value for the Prefilter step for the first phase" help="[prefilter_value] Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’ (ex: 100 or 95,105)"/> |