Mercurial > repos > galaxyp > openms_peakpickerhires
diff PeakPickerHiRes.xml @ 0:2741adc39601 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 09:58:38 -0500 |
| parents | |
| children | 8d74240aafb9 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PeakPickerHiRes.xml Wed Mar 01 09:58:38 2017 -0500 @@ -0,0 +1,134 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Signal processing and preprocessing]--> +<tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="2.1.0"> + <description>Finds mass spectrometric peaks in profile mass spectra.</description> + <macros> + <token name="@EXECUTABLE@">PeakPickerHiRes</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>PeakPickerHiRes + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_algorithm_signal_to_noise: + -algorithm:signal_to_noise $param_algorithm_signal_to_noise +#end if + +#if $rep_param_algorithm_ms_levels: +-algorithm:ms_levels + #for token in $rep_param_algorithm_ms_levels: + #if " " in str(token): + "$token.param_algorithm_ms_levels" + #else + $token.param_algorithm_ms_levels + #end if + #end for +#end if +#if $param_algorithm_report_FWHM: + -algorithm:report_FWHM +#end if +#if $param_algorithm_report_FWHM_unit: + -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit" +#end if +#if $param_algorithm_SignalToNoise_win_len: + -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len +#end if +#if $param_algorithm_SignalToNoise_bin_count: + -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count +#end if +#if $param_algorithm_SignalToNoise_min_required_elements: + -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements +#end if +#if $param_algorithm_SignalToNoise_write_log_messages: + -algorithm:SignalToNoise:write_log_messages $param_algorithm_SignalToNoise_write_log_messages +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_processOption: + -processOption $adv_opts.param_processOption +#end if + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_spacing_difference_gap: + -algorithm:spacing_difference_gap $adv_opts.param_algorithm_spacing_difference_gap +#end if + #if $adv_opts.param_algorithm_spacing_difference: + -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference +#end if + #if $adv_opts.param_algorithm_missing: + -algorithm:missing $adv_opts.param_algorithm_missing +#end if + #if $adv_opts.param_algorithm_SignalToNoise_max_intensity: + -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity +#end if + #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor: + -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor +#end if + #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile: + -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile +#end if + #if $adv_opts.param_algorithm_SignalToNoise_auto_mode: + -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode +#end if + #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window: + -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window +#end if +#end if +</command> + <inputs> + <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/> + <param name="param_algorithm_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help="(-signal_to_noise) "/> + <repeat name="rep_param_algorithm_ms_levels" min="0" max="1" title="param_algorithm_ms_levels"> + <param name="param_algorithm_ms_levels" type="text" min="1" optional="True" size="30" value="1 2" label="List of MS levels for which the peak picking is applied" help="(-ms_levels) Other scans are copied to the output without changes"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param name="param_algorithm_report_FWHM" display="radio" type="boolean" truevalue="-algorithm:report_FWHM" falsevalue="" checked="false" optional="True" label="Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak" help="(-report_FWHM) "/> + <param name="param_algorithm_report_FWHM_unit" display="radio" type="select" optional="False" value="relative(ppm)" label="Unit of FWHM. Either absolute in the unit of input," help="(-report_FWHM_unit) e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)"> + <option value="absolute">absolute</option> + <option value="relative(ppm)" selected="true">relative(ppm)</option> + </param> + <param name="param_algorithm_SignalToNoise_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/> + <param name="param_algorithm_SignalToNoise_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/> + <param name="param_algorithm_SignalToNoise_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements) "/> + <param name="param_algorithm_SignalToNoise_write_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help="(-write_log_messages) "> + <option value="true" selected="true">true</option> + <option value="false">false</option> + </param> + <expand macro="advanced_options"> + <param name="param_processOption" display="radio" type="select" optional="False" value="inmemory" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="(-processOption) "> + <option value="inmemory" selected="true">inmemory</option> + <option value="lowmemory">lowmemory</option> + </param> + <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <param name="param_algorithm_spacing_difference_gap" type="float" min="0.0" optional="True" value="4.0" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" help="(-spacing_difference_gap) 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms"/> + <param name="param_algorithm_spacing_difference" type="float" min="0.0" optional="True" value="1.5" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" help="(-spacing_difference) If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms"/> + <param name="param_algorithm_missing" type="integer" min="0" optional="True" value="1" label="Maximum number of missing points allowed when extending a peak to the left or to the right" help="(-missing) A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms"/> + <param name="param_algorithm_SignalToNoise_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction" help="(-max_intensity) By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/> + <param name="param_algorithm_SignalToNoise_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor) "/> + <param name="param_algorithm_SignalToNoise_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile) "/> + <param name="param_algorithm_SignalToNoise_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" help="(-auto_mode) "/> + <param name="param_algorithm_SignalToNoise_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window) "/> + </expand> + </inputs> + <outputs> + <data name="param_out" format="mzml"/> + </outputs> + <help>Finds mass spectrometric peaks in profile mass spectra. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html</help> +</tool>