Mercurial > repos > bgruening > openms
diff PeakPickerHiRes.xml @ 4:6ead64a594bd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
| author | bgruening |
|---|---|
| date | Wed, 27 Jan 2016 10:06:49 -0500 |
| parents | 3d84209d3178 |
| children |
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--- a/PeakPickerHiRes.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/PeakPickerHiRes.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,62 +1,126 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="1.12.0"> - <description>Finds mass spectrometric peaks in profile mass spectra.</description> - <macros> - <token name="@EXECUTABLE@">PeakPickerHiRes</token> - <import>macros.xml</import> - </macros> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>PeakPickerHiRes +<?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="2.0.0"> + <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 +-threads \${GALAXY_SLOTS:-24} +#if $param_algorithm_signal_to_noise: + -algorithm:signal_to_noise $param_algorithm_signal_to_noise +#end if --in ${param_in} --out ${param_out} --processOption inmemory --threads \${GALAXY_SLOTS:-24} --algorithm:signal_to_noise ${param_signal_to_noise} --algorithm:ms_levels ${param_ms_levels} --algorithm:SignalToNoise:win_len ${param_win_len} --algorithm:SignalToNoise:bin_count ${param_bin_count} --algorithm:SignalToNoise:min_required_elements ${param_min_required_elements} +#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_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 +#end if #if $adv_opts.adv_opts_selector=='advanced': - -algorithm:spacing_difference_gap ${adv_opts.param_spacing_difference_gap} - -algorithm:spacing_difference ${adv_opts.param_spacing_difference} - -algorithm:missing ${adv_opts.param_missing} - -algorithm:SignalToNoise:max_intensity ${adv_opts.param_max_intensity} - -algorithm:SignalToNoise:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor} - -algorithm:SignalToNoise:auto_max_percentile ${adv_opts.param_auto_max_percentile} - -algorithm:SignalToNoise:auto_mode ${adv_opts.param_auto_mode} - -algorithm:SignalToNoise:noise_for_empty_window ${adv_opts.param_noise_for_empty_window} + #if $adv_opts.param_processOption: + -processOption + #if " " in str($adv_opts.param_processOption): + "$adv_opts.param_processOption" + #else + $adv_opts.param_processOption + #end if +#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_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)"/> - <param name="param_ms_levels" type="text" min="1" optional="True" size="20" value="1 2" label="List of MS levels for which the peak picking is applied. Other scans are copied to the output without changes." help="(-ms_levels)"/> - <param name="param_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len)"/> - <param name="param_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count)"/> - <param name="param_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)"/> - <expand macro="advanced_options"> - <param name="param_spacing_difference_gap" type="float" min="0.0" optional="True" value="4.0" label="Maximum allowed m/z distance between data points in multiples of the minimal difference, above which a data point no longer belongs to the peak." help="(-spacing_difference_gap)"/> - <param name="param_spacing_difference" type="float" min="0.0" optional="True" value="1.5" label="Maximum allowed distance between peaks in multiples of the minimal difference. A higher value is implies a less stringent peak definition since individual signals within the peaks are allowed to further apart. E.g. if the value is set to 1.5 and in a peak the minimal spacing between peaks is 10 mDa, then only signals at most 15 mDa apart will be added to the peak." help="(-spacing_difference)"/> - <param name="param_missing" type="integer" min="0" optional="True" value="1" label="Maximum number of missing points." help="(-missing)"/> - <param name="param_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction. 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." help="(-max_intensity)"/> - <param name="param_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_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_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_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" label="output peak file " format="mzML"/> - </outputs> - <help>**What it does** - -Finds mass spectrometric peaks in profile mass spectra. + <inputs> + <param format="mzml" help="(-in) " label="input profile data file" name="param_in" optional="False" type="data"/> + <param help="(-signal_to_noise) " label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" min="0.0" name="param_algorithm_signal_to_noise" optional="True" type="float" value="1.0"/> + <repeat max="1" min="0" name="rep_param_algorithm_ms_levels" title="param_algorithm_ms_levels"> + <param help="(-ms_levels) Other scans are copied to the output without changes" label="List of MS levels for which the peak picking is applied" min="1" name="param_algorithm_ms_levels" optional="True" size="30" type="text" value="1 2"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param help="(-win_len) " label="window length in Thomson" min="1.0" name="param_algorithm_SignalToNoise_win_len" optional="True" type="float" value="200.0"/> + <param help="(-bin_count) " label="number of bins for intensity values" min="3" name="param_algorithm_SignalToNoise_bin_count" optional="True" type="integer" value="30"/> + <param help="(-min_required_elements) " label="minimum number of elements required in a window (otherwise it is considered sparse)" min="1" name="param_algorithm_SignalToNoise_min_required_elements" optional="True" type="integer" value="10"/> + <param checked="true" falsevalue="" help="(-write_log_messages) " label="Write out log messages in case of sparse windows or median in rightmost histogram bin" name="param_algorithm_SignalToNoise_write_log_messages" optional="True" truevalue="-algorithm:SignalToNoise:write_log_messages" type="boolean"/> + <expand macro="advanced_options"> + <param help="(-processOption) " 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" name="param_processOption" optional="True" type="select" value="inmemory"> + <option value="inmemory">inmemory</option> + <option value="lowmemory">lowmemory</option> + </param> + <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> + <param 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" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" min="0.0" name="param_algorithm_spacing_difference_gap" optional="True" type="float" value="4.0"/> + <param 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" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" min="0.0" name="param_algorithm_spacing_difference" optional="True" type="float" value="1.5"/> + <param 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" label="Maximum number of missing points allowed when extending a peak to the left or to the right" min="0" name="param_algorithm_missing" optional="True" type="integer" value="1"/> + <param 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" label="maximal intensity considered for histogram construction" min="-1" name="param_algorithm_SignalToNoise_max_intensity" optional="True" type="integer" value="-1"/> + <param help="(-auto_max_stdev_factor) " label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" max="999.0" min="0.0" name="param_algorithm_SignalToNoise_auto_max_stdev_factor" optional="True" type="float" value="3.0"/> + <param help="(-auto_max_percentile) " label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" max="100" min="0" name="param_algorithm_SignalToNoise_auto_max_percentile" optional="True" type="integer" value="95"/> + <param help="(-auto_mode) " label="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" max="1" min="-1" name="param_algorithm_SignalToNoise_auto_mode" optional="True" type="integer" value="0"/> + <param help="(-noise_for_empty_window) " label="noise value used for sparse windows" name="param_algorithm_SignalToNoise_noise_for_empty_window" type="float" value="1e+20"/> + </expand> + </inputs> + <outputs> + <data format="mzml" name="param_out"/> + </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 - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html</help> + </tool>