Mercurial > repos > bgruening > openms
comparison FeatureFinderMRM.xml @ 0:3d84209d3178 draft
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| author | bgruening |
|---|---|
| date | Fri, 10 Oct 2014 18:20:03 -0400 |
| parents | |
| children | 6ead64a594bd |
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| -1:000000000000 | 0:3d84209d3178 |
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| 1 <?xml version='1.0' encoding='UTF-8'?> | |
| 2 <tool id="FeatureFinderMRM" name="FeatureFinderMRM" version="1.12.0"> | |
| 3 <description>Detects two-dimensional features in LC-MS data.</description> | |
| 4 <macros> | |
| 5 <token name="@EXECUTABLE@">FeatureFinderMRM</token> | |
| 6 <import>macros.xml</import> | |
| 7 </macros> | |
| 8 <expand macro="stdio"/> | |
| 9 <expand macro="requirements"/> | |
| 10 <command>FeatureFinderMRM | |
| 11 | |
| 12 -in ${param_in} | |
| 13 -out ${param_out} | |
| 14 -threads \${GALAXY_SLOTS:-24} | |
| 15 -algorithm:min_rt_distance ${param_min_rt_distance} | |
| 16 -algorithm:min_signal_to_noise_ratio ${param_min_signal_to_noise_ratio} | |
| 17 #if $adv_opts.adv_opts_selector=='advanced': | |
| 18 -algorithm:min_num_peaks_per_feature ${adv_opts.param_min_num_peaks_per_feature} | |
| 19 ${adv_opts.param_write_debug_files} | |
| 20 ${adv_opts.param_resample_traces} | |
| 21 ${adv_opts.param_write_debuginfo} | |
| 22 #end if | |
| 23 </command> | |
| 24 <inputs> | |
| 25 <param name="param_in" type="data" format="mzML" optional="False" label="input file" help="(-in)"/> | |
| 26 <param name="param_min_rt_distance" type="float" min="0.0" optional="True" value="10.0" label="Minimal distance of MRM features in seconds." help="(-min_rt_distance)"/> | |
| 27 <param name="param_min_signal_to_noise_ratio" type="float" min="0.0" optional="True" value="2.0" label="Minimal S/N ratio a peak must have to be taken into account. Set to zero if the MRM-traces contains mostly signals, and no noise." help="(-min_signal_to_noise_ratio)"/> | |
| 28 <expand macro="advanced_options"> | |
| 29 <param name="param_min_num_peaks_per_feature" type="integer" min="1" optional="True" value="5" label="Minimal number of peaks which are needed for a single feature" help="(-min_num_peaks_per_feature)"/> | |
| 30 <param name="param_write_debug_files" type="boolean" truevalue="-algorithm:write_debug_files true" falsevalue="-algorithm:write_debug_files false" checked="false" optional="True" label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" help="(-write_debug_files)"/> | |
| 31 <param name="param_resample_traces" type="boolean" truevalue="-algorithm:resample_traces true" falsevalue="-algorithm:resample_traces false" checked="false" optional="True" label="If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension" help="(-resample_traces)"/> | |
| 32 <param name="param_write_debuginfo" type="boolean" truevalue="-algorithm:write_debuginfo true" falsevalue="-algorithm:write_debuginfo false" checked="false" optional="True" label="If set to true, debug messages are written, the output can be somewhat lengthy." help="(-write_debuginfo)"/> | |
| 33 </expand> | |
| 34 </inputs> | |
| 35 <outputs> | |
| 36 <data name="param_out" label="output file" format="featureXML"/> | |
| 37 </outputs> | |
| 38 <help>**What it does** | |
| 39 | |
| 40 Detects two-dimensional features in LC-MS data. | |
| 41 | |
| 42 | |
| 43 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMRM.html | |
| 44 | |
| 45 @REFERENCES@ | |
| 46 </help> | |
| 47 </tool> |