Mercurial > repos > galaxyp > openms_mrmtransitiongrouppicker
diff MRMTransitionGroupPicker.xml @ 0:2c8729a286ea draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 12:38:23 -0500 |
| parents | |
| children | 289009115eb2 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MRMTransitionGroupPicker.xml Wed Mar 01 12:38:23 2017 -0500 @@ -0,0 +1,147 @@ +<?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: [Utilities]--> +<tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="2.1.0"> + <macros> + <token name="@EXECUTABLE@">MRMTransitionGroupPicker</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>MRMTransitionGroupPicker + +#if $param_in: + -in $param_in +#end if +#if $param_tr: + -tr $param_tr +#end if +#if $param_out: + -out $param_out +#end if +#if $param_algorithm_stop_after_feature: + -algorithm:stop_after_feature $param_algorithm_stop_after_feature +#end if +#if $param_algorithm_stop_after_intensity_ratio: + -algorithm:stop_after_intensity_ratio $param_algorithm_stop_after_intensity_ratio +#end if +#if $param_algorithm_PeakPickerMRM_sgolay_frame_length: + -algorithm:PeakPickerMRM:sgolay_frame_length $param_algorithm_PeakPickerMRM_sgolay_frame_length +#end if +#if $param_algorithm_PeakPickerMRM_sgolay_polynomial_order: + -algorithm:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_PeakPickerMRM_sgolay_polynomial_order +#end if +#if $param_algorithm_PeakPickerMRM_gauss_width: + -algorithm:PeakPickerMRM:gauss_width $param_algorithm_PeakPickerMRM_gauss_width +#end if +#if $param_algorithm_PeakPickerMRM_use_gauss: + -algorithm:PeakPickerMRM:use_gauss $param_algorithm_PeakPickerMRM_use_gauss +#end if +#if $param_algorithm_PeakPickerMRM_peak_width: + -algorithm:PeakPickerMRM:peak_width $param_algorithm_PeakPickerMRM_peak_width +#end if +#if $param_algorithm_PeakPickerMRM_signal_to_noise: + -algorithm:PeakPickerMRM:signal_to_noise $param_algorithm_PeakPickerMRM_signal_to_noise +#end if +#if $param_algorithm_PeakPickerMRM_sn_win_len: + -algorithm:PeakPickerMRM:sn_win_len $param_algorithm_PeakPickerMRM_sn_win_len +#end if +#if $param_algorithm_PeakPickerMRM_sn_bin_count: + -algorithm:PeakPickerMRM:sn_bin_count $param_algorithm_PeakPickerMRM_sn_bin_count +#end if +#if $param_algorithm_PeakPickerMRM_write_sn_log_messages: + -algorithm:PeakPickerMRM:write_sn_log_messages $param_algorithm_PeakPickerMRM_write_sn_log_messages +#end if +#if $param_algorithm_PeakPickerMRM_remove_overlapping_peaks: + -algorithm:PeakPickerMRM:remove_overlapping_peaks +#end if +#if $param_algorithm_PeakPickerMRM_method: + -algorithm:PeakPickerMRM:method $param_algorithm_PeakPickerMRM_method +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_min_peak_width: + -algorithm:min_peak_width $adv_opts.param_algorithm_min_peak_width +#end if + #if $adv_opts.param_algorithm_background_subtraction: + -algorithm:background_subtraction $adv_opts.param_algorithm_background_subtraction +#end if + #if $adv_opts.param_algorithm_recalculate_peaks: + -algorithm:recalculate_peaks "$adv_opts.param_algorithm_recalculate_peaks" +#end if + #if $adv_opts.param_algorithm_recalculate_peaks_max_z: + -algorithm:recalculate_peaks_max_z $adv_opts.param_algorithm_recalculate_peaks_max_z +#end if + #if $adv_opts.param_algorithm_minimal_quality: + -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality +#end if + #if $adv_opts.param_algorithm_compute_peak_quality: + -algorithm:compute_peak_quality "$adv_opts.param_algorithm_compute_peak_quality" +#end if +#end if +</command> + <inputs> + <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/> + <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/> + <param name="param_algorithm_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help="(-stop_after_feature) "/> + <param name="param_algorithm_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio) "/> + <param name="param_algorithm_PeakPickerMRM_sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="(-sgolay_frame_length) <br>This number has to be uneven. If it is not, 1 will be added"/> + <param name="param_algorithm_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/> + <param name="param_algorithm_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/> + <param name="param_algorithm_PeakPickerMRM_use_gauss" display="radio" type="select" optional="False" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) "> + <option value="false">false</option> + <option value="true" selected="true">true</option> + </param> + <param name="param_algorithm_PeakPickerMRM_peak_width" type="float" value="40.0" label="Force a certain minimal peak_width on the data (" help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/> + <param name="param_algorithm_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (" help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured"/> + <param name="param_algorithm_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/> + <param name="param_algorithm_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/> + <param name="param_algorithm_PeakPickerMRM_write_sn_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" help="(-write_sn_log_messages) "> + <option value="true" selected="true">true</option> + <option value="false">false</option> + </param> + <param name="param_algorithm_PeakPickerMRM_remove_overlapping_peaks" display="radio" type="boolean" truevalue="-algorithm:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/> + <param name="param_algorithm_PeakPickerMRM_method" display="radio" type="select" optional="False" value="legacy" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" help="(-method) "> + <option value="legacy" selected="true">legacy</option> + <option value="corrected">corrected</option> + <option value="crawdad">crawdad</option> + </param> + <expand macro="advanced_options"> + <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_min_peak_width" type="float" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/> + <param name="param_algorithm_background_subtraction" display="radio" type="select" optional="False" value="none" label="Try to apply a background subtraction to the peak (experimental)" help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that"> + <option value="none" selected="true">none</option> + <option value="smoothed">smoothed</option> + <option value="original">original</option> + </param> + <param name="param_algorithm_recalculate_peaks" type="text" size="30" value="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_algorithm_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/> + <param name="param_algorithm_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/> + <param name="param_algorithm_compute_peak_quality" type="text" size="30" value="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </expand> + </inputs> + <outputs> + <data name="param_out" format="featurexml"/> + </outputs> + <help>None + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_MRMTransitionGroupPicker.html</help> +</tool>