Mercurial > repos > pieterlukasse > prims_metabolomics
comparison msclust.xml @ 19:c068ed713eb9
fixes on <when> tags
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Fri, 31 Jan 2014 12:21:51 +0100 |
| parents | 777c1c2a17a2 |
| children | 19d8fd10248e |
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| 18:278680d76d71 | 19:c068ed713eb9 |
|---|---|
| 78 <option value="valueRange">Values range</option> | 78 <option value="valueRange">Values range</option> |
| 79 </param> | 79 </param> |
| 80 <when value="valueRange"> | 80 <when value="valueRange"> |
| 81 <param name="rangeUpperLimit" type="integer" size="10" value="0" label="Range upper limit" help="values up to this limit will be considered 'generated' values" /> | 81 <param name="rangeUpperLimit" type="integer" size="10" value="0" label="Range upper limit" help="values up to this limit will be considered 'generated' values" /> |
| 82 </when> | 82 </when> |
| 83 <when value="metot"> | |
| 84 </when> | |
| 85 <when value="none"> | |
| 86 </when> | |
| 83 </conditional> | 87 </conditional> |
| 84 <conditional name="potDensFuncType"> | 88 <conditional name="potDensFuncType"> |
| 85 <param name="type" type="select" size="30" label="Select PD function type ====================================================="> | 89 <param name="type" type="select" size="30" label="Select PD function type ====================================================="> |
| 86 <option value="original" selected="true">Original</option> | 90 <option value="original" selected="true">Original</option> |
| 87 </param> | 91 </param> |
| 109 <option value="fuzzyCMeans">(experimental) Fuzzy C-Means - Fuzzy clustering, optimize centers</option> | 113 <option value="fuzzyCMeans">(experimental) Fuzzy C-Means - Fuzzy clustering, optimize centers</option> |
| 110 </param> | 114 </param> |
| 111 <when value="original"> | 115 <when value="original"> |
| 112 <!-- nothing --> | 116 <!-- nothing --> |
| 113 </when> | 117 </when> |
| 118 <!-- one idea would be to have clustering specific tolerance values, not reusing the centrotype selection ones | |
| 114 <when value="originalNewTol"> | 119 <when value="originalNewTol"> |
| 115 <param name="clust_scan_toler" type="float" size="10" value="10" label="Peak Width, in scans" /> | 120 <param name="clust_scan_toler" type="float" size="10" value="10" label="Peak Width, in scans" /> |
| 116 <param name="clust_scan_slope" type="float" size="10" value="2" label="Peak Width margin softness" /> | 121 <param name="clust_scan_slope" type="float" size="10" value="2" label="Peak Width margin softness" /> |
| 117 </when> | 122 </when> |
| 123 --> | |
| 118 <when value="fuzzyCMeans"> | 124 <when value="fuzzyCMeans"> |
| 119 <param name="fcmMembershipWeightingExponent" type="float" size="10" value="2.0" label="Membership Weighting Exponent" help="Influences cluster center repositioning in the iterations 1.1 (exploratory) to around 3.0 (conservative)" /> | 125 <param name="fcmMembershipWeightingExponent" type="float" size="10" value="2.0" label="Membership Weighting Exponent" help="Influences cluster center repositioning in the iterations 1.1 (exploratory) to around 3.0 (conservative)" /> |
| 120 <param name="fcmStopCriterion" type="float" size="10" value="0.05" label="Stop Criterion" help="When convergence is 'reached' (e.g. 0.05 means memberships only changed with 5% in last iteration)" /> | 126 <param name="fcmStopCriterion" type="float" size="10" value="0.05" label="Stop Criterion" help="When convergence is 'reached' (e.g. 0.05 means memberships only changed with 5% in last iteration)" /> |
| 121 <param name="fcmCorrelationWeight" type="float" size="10" value="2" label="Correlation weight factor" help="Increase this if you think the correlation is reliable (e.g. you have a high number of samples)" /> | 127 <param name="fcmCorrelationWeight" type="float" size="10" value="2" label="Correlation weight factor" help="Increase this if you think the correlation is reliable (e.g. you have a high number of samples)" /> |
| 122 <conditional name="finalClusterAssembly"> | 128 <conditional name="finalClusterAssembly"> |
| 167 <param name="simAbsenseThreshold" optional="true" type="float" size="10" label="SIM absence threshold (%)" help="Maximum % of samples in which a SIM candidate peak may be absent. If the candidate peak exceeds this threshold, then another peak is chosen. If no peak can be found meeting this criteria, mass 0 is reported" /> | 173 <param name="simAbsenseThreshold" optional="true" type="float" size="10" label="SIM absence threshold (%)" help="Maximum % of samples in which a SIM candidate peak may be absent. If the candidate peak exceeds this threshold, then another peak is chosen. If no peak can be found meeting this criteria, mass 0 is reported" /> |
| 168 | 174 |
| 169 <param name="micMembershipThreshold" optional="true" type="float" size="10" label="MIC membership threshold" help="Minimum membership a peak should have to be counted in the MIC sum. E.g. 0.8 " /> | 175 <param name="micMembershipThreshold" optional="true" type="float" size="10" label="MIC membership threshold" help="Minimum membership a peak should have to be counted in the MIC sum. E.g. 0.8 " /> |
| 170 | 176 |
| 171 </when> | 177 </when> |
| 178 <when value="No"> | |
| 179 </when> | |
| 172 </conditional> | 180 </conditional> |
| 173 | 181 |
| 174 | 182 |
| 175 </inputs> | 183 </inputs> |
| 176 <outputs> | 184 <outputs> |