Mercurial > repos > pieterlukasse > prims_metabolomics
comparison msclust.xml @ 49:f772a5caa86a
Added more options and better documentation.
Added MsClust support for parsing XCMS alignment results.
Improved output reports for XCMS wrappers.
New tools.
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Wed, 10 Dec 2014 22:03:27 +0100 |
| parents | 26b93438f30e |
| children |
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| 48:26b93438f30e | 49:f772a5caa86a |
|---|---|
| 1 <tool name="MsClust" id="msclust2" version="2.0.6"> | 1 <tool name="MsClust" id="msclust2" version="2.0.7"> |
| 2 <description>Extracts fragmentation spectra from aligned data</description> | 2 <description>Extracts fragmentation spectra from aligned data</description> |
| 3 <!-- | 3 <!-- |
| 4 For remote debugging start you listener on port 8000 and use the following as command interpreter: | 4 For remote debugging start you listener on port 8000 and use the following as command interpreter: |
| 5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 | 5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 |
| 6 ////////////////////////// | 6 ////////////////////////// |
| 13 -dataType $dataType | 13 -dataType $dataType |
| 14 -imputationMethod $imputationMethod.type | 14 -imputationMethod $imputationMethod.type |
| 15 #if $imputationMethod.type == "valueRange" | 15 #if $imputationMethod.type == "valueRange" |
| 16 -rangeUpperLimit $imputationMethod.rangeUpperLimit | 16 -rangeUpperLimit $imputationMethod.rangeUpperLimit |
| 17 #end if | 17 #end if |
| 18 -plInputFormat "metalign" | 18 -plInputFormat $plInputFormat |
| 19 -potDensFuncType $potDensFuncType.type | 19 -potDensFuncType $potDensFuncType.type |
| 20 -centerSelectionType $centerSelectionType.type | 20 -centerSelectionType $centerSelectionType.type |
| 21 -clusteringType $clusteringType.type | 21 -clusteringType $clusteringType.type |
| 22 -neighborhoodWindowSize $potDensFuncType.pdf_neighborhoodWindowSize | 22 -neighborhoodWindowSize $potDensFuncType.pdf_neighborhoodWindowSize |
| 23 -clusterSearchStopCriterium $centerSelectionType.cs_stop_criterion | 23 -clusterSearchStopCriterium $centerSelectionType.cs_stop_criterion |
| 66 #end if | 66 #end if |
| 67 | 67 |
| 68 </command> | 68 </command> |
| 69 <inputs> | 69 <inputs> |
| 70 | 70 |
| 71 <param name="inputPeaks" type="data" format="txt" label="Ion-wise aligned data (e.g. MetAlign output data)" /> | 71 <param name="inputPeaks" type="data" format="txt" label="Ion-wise aligned data (e.g. MetAlign or XCMS/metaMS output data)" /> |
| 72 <param name="plInputFormat" type="select" size="30" label="Data format"> | |
| 73 <option value="metalign" selected="true">MetAlign</option> | |
| 74 <option value="xcms">XCMS/metaMS (beta)</option> | |
| 75 </param> | |
| 72 <param name="dataType" type="select" size="30" label="Data type"> | 76 <param name="dataType" type="select" size="30" label="Data type"> |
| 73 <option value="gcms" selected="true">GC-MS</option> | 77 <option value="gcms" selected="true">GC-MS</option> |
| 74 <option value="lcms">LC-MS</option> | 78 <option value="lcms">LC-MS</option> |
| 75 </param> | 79 </param> |
| 76 <conditional name="imputationMethod"> | 80 <conditional name="imputationMethod"> |
| 77 <param name="type" type="select" size="30" label="Select the approach used for imputing missing values (optional)" help="select how you generated the values to fill in the data gaps"> | 81 <param name="type" type="select" size="30" label="Select the approach used for imputing missing values (optional)" help="select how you generated the values to fill in the data gaps"> |
| 78 <option value="none" >none</option> | 82 <option value="none" >none</option> |
| 79 <option value="metot" selected="true">MeTot</option> | 83 <option value="metot" selected="true">MeTot</option> |
| 80 <option value="valueRange">Values range</option> | 84 <option value="valueRange">Values range</option> |
| 93 </param> | 97 </param> |
| 94 <when value="original"> | 98 <when value="original"> |
| 95 <param name="pdf_neighborhoodWindowSize" type="integer" size="10" value="200" label="Effective Peaks" /> | 99 <param name="pdf_neighborhoodWindowSize" type="integer" size="10" value="200" label="Effective Peaks" /> |
| 96 <conditional name="rt_dist_tol_unit"> | 100 <conditional name="rt_dist_tol_unit"> |
| 97 <param name="type" type="select" size="30" label="Peak time unit"> | 101 <param name="type" type="select" size="30" label="Peak time unit"> |
| 98 <option value="1" selected="true">scan nr</option> | 102 <option value="1" selected="true">scan nr (MetAlign)</option> |
| 99 <option value="2" >(average) micro minutes</option> | 103 <option value="2" >(average) micro minutes (MetAlign)</option> |
| 104 <option value="3" >(average) minutes (XCMS)</option> | |
| 100 </param> | 105 </param> |
| 101 <when value="1"> | 106 <when value="1"> |
| 102 <param name="pdf_rt_toler" type="float" size="10" value="10" label="Peak Width, in scans" /> | 107 <param name="pdf_rt_toler" type="float" size="10" value="10" label="Peak Width, in scans" /> |
| 103 </when> | 108 </when> |
| 104 <when value="2"> | 109 <when value="2"> |
| 105 <param name="pdf_rt_toler" type="float" size="10" value="100000" label="Peak Width, in micro minutes" help="e.g. 100,000=6 seconds" /> | 110 <param name="pdf_rt_toler" type="float" size="10" value="100000" label="Peak Width, in micro minutes" help="e.g. 100,000=6 seconds" /> |
| 111 </when> | |
| 112 <when value="3"> | |
| 113 <param name="pdf_rt_toler" type="float" size="10" value="0.1" label="Peak Width, in minutes" help="e.g. 0.1=6 seconds" /> | |
| 106 </when> | 114 </when> |
| 107 </conditional> | 115 </conditional> |
| 108 <param name="pdf_scan_conf" type="float" size="10" value="80" label="Peak Width confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" /> | 116 <param name="pdf_scan_conf" type="float" size="10" value="80" label="Peak Width confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" /> |
| 109 <param name="pdf_pears_treshold" type="float" size="10" value="0.8" label="Correlation threshold (0.0 - 1.0)" /> | 117 <param name="pdf_pears_treshold" type="float" size="10" value="0.8" label="Correlation threshold (0.0 - 1.0)" /> |
| 110 <param name="pdf_pears_conf" type="float" size="10" value="98.0" label="Correlation threshold confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" /> | 118 <param name="pdf_pears_conf" type="float" size="10" value="98.0" label="Correlation threshold confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" /> |