openms_peakpickerwavelet: PeakPickerWavelet.xml annotate

annotate PeakPickerWavelet.xml @ 14:bf0b36140329 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

author	galaxyp
date	Fri, 14 Jun 2024 21:37:22 +0000
parents	2077efa205de
children

rev	line source
5 409cec15d717 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b galaxyp parents: 1 diff changeset	1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	2 <!--Proposed Tool Section: [Spectrum processing: Centroiding]-->
13 2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	3 <tool id="PeakPickerWavelet" name="PeakPickerWavelet" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	4 <description>Finds mass spectrometric peaks in profile mass spectra</description>
0 4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	5 <macros>
4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	6 <token name="@EXECUTABLE@">PeakPickerWavelet</token>
4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	7 <import>macros.xml</import>
4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	8 </macros>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	9 <expand macro="requirements"/>
0 4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	10 <expand macro="stdio"/>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	12 @EXT_FOO@
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	13 #import re
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	14
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	15 ## Preprocessing
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	16 mkdir in &&
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	18 mkdir out &&
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	19
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	20 ## Main program call
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	21
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	22 set -o pipefail &&
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	23 @EXECUTABLE@ -write_ctd ./ &&
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	24 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	25 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	26 -in
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	27 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	28 -out
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	29 'out/output.${gxy2omsext("mzml")}'
0 4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	30
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	31 ## Postprocessing
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	32 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	34 && mv '@EXECUTABLE@.ctd' '$ctd_out'
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	35 #end if]]></command>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	36 <configfiles>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	37 <inputs name="args_json" data_style="paths"/>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	39 </configfiles>
0 4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	40 <inputs>
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	41 <param argument="-in" type="data" format="mzml" label="input profile data file" help=" select mzml data sets(s)"/>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	42 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	43 <param name="signal_to_noise" argument="-algorithm:signal_to_noise" type="float" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	44 <param name="centroid_percentage" argument="-algorithm:centroid_percentage" type="float" min="0.0" max="1.0" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="If it is 1 the centroid position corresponds to the position of the highest intensity"/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	45 <param name="peak_width" argument="-algorithm:peak_width" type="float" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	46 <param name="estimate_peak_width" argument="-algorithm:estimate_peak_width" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Flag if the average peak width shall be estimated" help="Attention: when this flag is set, the peak_width is ignored"/>
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	47 <param name="fwhm_lower_bound_factor" argument="-algorithm:fwhm_lower_bound_factor" type="float" min="0.0" value="0.7" label="Factor that calculates the minimal fwhm value from the peak_width" help="All peaks with width smaller than fwhm_bound_factor * peak_width are discarded"/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	48 <param name="fwhm_upper_bound_factor" argument="-algorithm:fwhm_upper_bound_factor" type="float" min="0.0" value="20.0" label="Factor that calculates the maximal fwhm value from the peak_width" help="All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded"/>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	49 <section name="optimization" title="" help="" expanded="false">
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	50 <param name="iterations" argument="-algorithm:optimization:iterations" type="integer" min="1" value="400" label="maximal number of iterations for the fitting step" help=""/>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	51 <section name="penalties" title="" help="" expanded="false">
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	52 <param name="position" argument="-algorithm:optimization:penalties:position" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	53 <param name="left_width" argument="-algorithm:optimization:penalties:left_width" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	54 <param name="right_width" argument="-algorithm:optimization:penalties:right_width" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	55 <param name="height" argument="-algorithm:optimization:penalties:height" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized" help=""/>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	56 </section>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	57 <section name="2d" title="" help="" expanded="false">
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	58 <param name="tolerance_mz" argument="-algorithm:optimization:2d:tolerance_mz" type="float" min="0.0" value="2.2" label="mz tolerance for cluster construction" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	59 <param name="max_peak_distance" argument="-algorithm:optimization:2d:max_peak_distance" type="float" min="0.0" value="1.2" label="maximal peak distance in mz in a cluste" help=""/>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	60 </section>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	61 </section>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	62 <section name="thresholds" title="" help="" expanded="false">
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	63 <param name="peak_bound" argument="-algorithm:thresholds:peak_bound" type="float" min="0.0" value="10.0" label="Minimal peak intensity" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	64 <param name="peak_bound_ms2_level" argument="-algorithm:thresholds:peak_bound_ms2_level" type="float" min="0.0" value="10.0" label="Minimal peak intensity for MS/MS peaks" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	65 <param name="correlation" argument="-algorithm:thresholds:correlation" type="float" min="0.0" max="1.0" value="0.5" label="minimal correlation of a peak and the raw signal" help="If a peak has a lower correlation it is skipped"/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	66 <param name="noise_level" argument="-algorithm:thresholds:noise_level" type="float" min="0.0" value="0.1" label="noise level for the search of the peak endpoints" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	67 <param name="search_radius" argument="-algorithm:thresholds:search_radius" type="integer" min="0" value="3" label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" help=""/>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	68 </section>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	69 <section name="wavelet_transform" title="" help="" expanded="false">
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	70 <param name="spacing" argument="-algorithm:wavelet_transform:spacing" type="float" min="0.0" value="0.001" label="Spacing of the CWT" help="Note that the accuracy of the picked peak's centroid position depends in the Raw data spacing, i.e., 50% of raw peak distance at most"/>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	71 </section>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	72 <section name="deconvolution" title="" help="" expanded="false">
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	73 <param name="deconvolution" argument="-algorithm:deconvolution:deconvolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If you want heavily overlapping peaks to be separated set this value to "true"" help=""/>
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	74 <param name="asym_threshold" argument="-algorithm:deconvolution:asym_threshold" type="float" min="0.0" value="0.3" label="If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	75 <param name="left_width" argument="-algorithm:deconvolution:left_width" type="float" min="0.0" value="2.0" label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	76 <param name="right_width" argument="-algorithm:deconvolution:right_width" type="float" min="0.0" value="2.0" label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	77 <param name="scaling" argument="-algorithm:deconvolution:scaling" type="float" min="0.0" value="0.12" label="Initial scaling of the cwt used in the separation of heavily overlapping peaks" help="The initial value is used for charge 1, for higher charges it is adapted to scaling/charge"/>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	78 <section name="fitting" title="" help="" expanded="false">
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	79 <param name="fwhm_threshold" argument="-algorithm:deconvolution:fitting:fwhm_threshold" type="float" min="0.0" value="0.7" label="If the FWHM of a peak is higher than 'fwhm_thresholds' it is assumed that it consists of more than one peak and the deconvolution procedure is started" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	80 <param name="eps_abs" argument="-algorithm:deconvolution:fitting:eps_abs" type="float" min="0.0" value="9.999999747378752e-06" label="if the absolute error gets smaller than this value the fitting is stopped" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	81 <param name="eps_rel" argument="-algorithm:deconvolution:fitting:eps_rel" type="float" min="0.0" value="9.999999747378752e-06" label="if the relative error gets smaller than this value the fitting is stopped" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	82 <param name="max_iteration" argument="-algorithm:deconvolution:fitting:max_iteration" type="integer" min="1" value="10" label="maximal number of iterations for the fitting step" help=""/>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	83 <section name="penalties" title="" help="" expanded="false">
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	84 <param name="position" argument="-algorithm:deconvolution:fitting:penalties:position" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	85 <param name="height" argument="-algorithm:deconvolution:fitting:penalties:height" type="float" min="0.0" value="1.0" label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	86 <param name="left_width" argument="-algorithm:deconvolution:fitting:penalties:left_width" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	87 <param name="right_width" argument="-algorithm:deconvolution:fitting:penalties:right_width" type="float" min="0.0" value="0.0" label="penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized" help=""/>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	88 </section>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	89 </section>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	90 </section>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	91 <section name="SignalToNoiseEstimationParameter" title="" help="" expanded="false">
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	92 <param name="max_intensity" argument="-algorithm:SignalToNoiseEstimationParameter:max_intensity" type="integer" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="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 not be added to the histogram. 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)"/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	93 <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoiseEstimationParameter:auto_max_stdev_factor" type="float" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	94 <param name="auto_max_percentile" argument="-algorithm:SignalToNoiseEstimationParameter:auto_max_percentile" type="integer" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	95 <param name="auto_mode" argument="-algorithm:SignalToNoiseEstimationParameter:auto_mode" type="integer" min="-1" max="1" 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=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	96 <param name="win_len" argument="-algorithm:SignalToNoiseEstimationParameter:win_len" type="float" min="1.0" value="200.0" label="window length in Thomson" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	97 <param name="bin_count" argument="-algorithm:SignalToNoiseEstimationParameter:bin_count" type="integer" min="3" value="30" label="number of bins for intensity values" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	98 <param name="stdev_mp" argument="-algorithm:SignalToNoiseEstimationParameter:stdev_mp" type="float" min="0.01" max="999.0" value="3.0" label="multiplier for stdev" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	99 <param name="min_required_elements" argument="-algorithm:SignalToNoiseEstimationParameter:min_required_elements" type="integer" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	100 <param name="noise_for_empty_window" argument="-algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help=""/>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	101 </section>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	102 </section>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	103 <expand macro="adv_opts_macro">
13 2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	104 <param argument="-write_peak_meta_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write additional information about the picked peaks (maximal intensity, left and right area...) into the mzML-file" help="Attention: this can blow up files, since seven arrays are stored per spectrum!"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	105 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	106 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
13 2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	107 <expand macro="list_string_san" name="test"/>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	108 </param>
0 4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	109 </expand>
11 341af0b11af9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c" galaxyp parents: 9 diff changeset	110 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	111 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	112 </param>
0 4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	113 </inputs>
4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	114 <outputs>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	115 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	116 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	117 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	118 </data>
0 4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	119 </outputs>
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	120 <tests>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	121 <!-- TOPP_PeakPickerWavelet_1 -->
13 2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	122 <test expect_num_outputs="2">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	123 <section name="adv_opts">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	124 <param name="write_peak_meta_data" value="true"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	125 <param name="force" value="false"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	126 <param name="test" value="true"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	127 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	128 <param name="in" value="PeakPickerWavelet_input.mzML"/>
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	129 <output name="out" value="PeakPickerWavelet_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13 2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	130 <section name="algorithm">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	131 <param name="signal_to_noise" value="3.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	132 <param name="centroid_percentage" value="0.6"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	133 <param name="peak_width" value="0.2"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	134 <param name="estimate_peak_width" value="false"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	135 <param name="fwhm_lower_bound_factor" value="0.5"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	136 <param name="fwhm_upper_bound_factor" value="20.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	137 <section name="optimization">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	138 <param name="iterations" value="400"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	139 <section name="penalties">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	140 <param name="position" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	141 <param name="left_width" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	142 <param name="right_width" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	143 <param name="height" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	144 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	145 <section name="2d">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	146 <param name="tolerance_mz" value="2.2"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	147 <param name="max_peak_distance" value="1.2"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	148 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	149 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	150 <section name="thresholds">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	151 <param name="peak_bound" value="100.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	152 <param name="peak_bound_ms2_level" value="10.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	153 <param name="correlation" value="0.5"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	154 <param name="noise_level" value="0.1"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	155 <param name="search_radius" value="3"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	156 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	157 <section name="wavelet_transform">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	158 <param name="spacing" value="0.001"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	159 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	160 <section name="deconvolution">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	161 <param name="deconvolution" value="false"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	162 <param name="asym_threshold" value="0.3"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	163 <param name="left_width" value="2.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	164 <param name="right_width" value="2.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	165 <param name="scaling" value="0.12"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	166 <section name="fitting">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	167 <param name="fwhm_threshold" value="0.7"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	168 <param name="eps_abs" value="9.999999747378752e-06"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	169 <param name="eps_rel" value="9.999999747378752e-06"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	170 <param name="max_iteration" value="10"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	171 <section name="penalties">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	172 <param name="position" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	173 <param name="height" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	174 <param name="left_width" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	175 <param name="right_width" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	176 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	177 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	178 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	179 <section name="SignalToNoiseEstimationParameter">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	180 <param name="max_intensity" value="-1"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	181 <param name="auto_max_stdev_factor" value="3.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	182 <param name="auto_max_percentile" value="95"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	183 <param name="auto_mode" value="0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	184 <param name="win_len" value="200.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	185 <param name="bin_count" value="30"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	186 <param name="stdev_mp" value="3.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	187 <param name="min_required_elements" value="10"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	188 <param name="noise_for_empty_window" value="1e+20"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	189 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	190 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	191 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	192 <output name="ctd_out" ftype="xml">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	193 <assert_contents>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	194 <is_valid_xml/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	195 </assert_contents>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	196 </output>
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	197 <assert_stdout>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	198 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	199 </assert_stdout>
13 2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	200 </test>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	201 <!-- TOPP_PeakPickerWavelet_2 -->
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	202 <test expect_num_outputs="2">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	203 <section name="adv_opts">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	204 <param name="write_peak_meta_data" value="true"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	205 <param name="force" value="false"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	206 <param name="test" value="true"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	207 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	208 <param name="in" value="PeakPickerWavelet_deconv_input.mzML"/>
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	209 <output name="out" value="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13 2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	210 <section name="algorithm">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	211 <param name="signal_to_noise" value="2.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	212 <param name="centroid_percentage" value="0.8"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	213 <param name="peak_width" value="0.15"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	214 <param name="estimate_peak_width" value="false"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	215 <param name="fwhm_lower_bound_factor" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	216 <param name="fwhm_upper_bound_factor" value="20.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	217 <section name="optimization">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	218 <param name="iterations" value="400"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	219 <section name="penalties">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	220 <param name="position" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	221 <param name="left_width" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	222 <param name="right_width" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	223 <param name="height" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	224 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	225 <section name="2d">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	226 <param name="tolerance_mz" value="2.2"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	227 <param name="max_peak_distance" value="1.2"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	228 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	229 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	230 <section name="thresholds">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	231 <param name="peak_bound" value="200.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	232 <param name="peak_bound_ms2_level" value="50.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	233 <param name="correlation" value="0.5"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	234 <param name="noise_level" value="0.1"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	235 <param name="search_radius" value="3"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	236 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	237 <section name="wavelet_transform">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	238 <param name="spacing" value="0.001"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	239 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	240 <section name="deconvolution">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	241 <param name="deconvolution" value="true"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	242 <param name="asym_threshold" value="0.3"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	243 <param name="left_width" value="2.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	244 <param name="right_width" value="2.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	245 <param name="scaling" value="0.1"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	246 <section name="fitting">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	247 <param name="fwhm_threshold" value="0.7"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	248 <param name="eps_abs" value="1e-05"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	249 <param name="eps_rel" value="1e-05"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	250 <param name="max_iteration" value="100"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	251 <section name="penalties">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	252 <param name="position" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	253 <param name="height" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	254 <param name="left_width" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	255 <param name="right_width" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	256 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	257 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	258 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	259 <section name="SignalToNoiseEstimationParameter">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	260 <param name="max_intensity" value="-1"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	261 <param name="auto_max_stdev_factor" value="3.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	262 <param name="auto_max_percentile" value="95"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	263 <param name="auto_mode" value="0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	264 <param name="win_len" value="200.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	265 <param name="bin_count" value="30"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	266 <param name="stdev_mp" value="3.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	267 <param name="min_required_elements" value="10"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	268 <param name="noise_for_empty_window" value="1e+20"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	269 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	270 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	271 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	272 <output name="ctd_out" ftype="xml">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	273 <assert_contents>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	274 <is_valid_xml/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	275 </assert_contents>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	276 </output>
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	277 <assert_stdout>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	278 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	279 </assert_stdout>
13 2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	280 </test>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	281 <!-- TOPP_PeakPickerWavelet_4 -->
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	282 <test expect_num_outputs="2">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	283 <section name="adv_opts">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	284 <param name="write_peak_meta_data" value="true"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	285 <param name="force" value="false"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	286 <param name="test" value="true"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	287 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	288 <param name="in" value="PeakPickerWavelet_input.mzML"/>
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	289 <output name="out" value="PeakPickerWavelet_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13 2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	290 <section name="algorithm">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	291 <param name="signal_to_noise" value="3.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	292 <param name="centroid_percentage" value="0.6"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	293 <param name="peak_width" value="0.2"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	294 <param name="estimate_peak_width" value="false"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	295 <param name="fwhm_lower_bound_factor" value="0.5"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	296 <param name="fwhm_upper_bound_factor" value="20.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	297 <section name="optimization">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	298 <param name="iterations" value="400"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	299 <section name="penalties">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	300 <param name="position" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	301 <param name="left_width" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	302 <param name="right_width" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	303 <param name="height" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	304 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	305 <section name="2d">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	306 <param name="tolerance_mz" value="2.2"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	307 <param name="max_peak_distance" value="1.2"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	308 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	309 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	310 <section name="thresholds">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	311 <param name="peak_bound" value="100.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	312 <param name="peak_bound_ms2_level" value="10.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	313 <param name="correlation" value="0.5"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	314 <param name="noise_level" value="0.1"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	315 <param name="search_radius" value="3"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	316 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	317 <section name="wavelet_transform">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	318 <param name="spacing" value="0.001"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	319 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	320 <section name="deconvolution">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	321 <param name="deconvolution" value="false"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	322 <param name="asym_threshold" value="0.3"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	323 <param name="left_width" value="2.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	324 <param name="right_width" value="2.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	325 <param name="scaling" value="0.12"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	326 <section name="fitting">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	327 <param name="fwhm_threshold" value="0.7"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	328 <param name="eps_abs" value="9.999999747378752e-06"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	329 <param name="eps_rel" value="9.999999747378752e-06"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	330 <param name="max_iteration" value="10"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	331 <section name="penalties">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	332 <param name="position" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	333 <param name="height" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	334 <param name="left_width" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	335 <param name="right_width" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	336 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	337 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	338 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	339 <section name="SignalToNoiseEstimationParameter">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	340 <param name="max_intensity" value="-1"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	341 <param name="auto_max_stdev_factor" value="3.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	342 <param name="auto_max_percentile" value="95"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	343 <param name="auto_mode" value="0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	344 <param name="win_len" value="200.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	345 <param name="bin_count" value="30"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	346 <param name="stdev_mp" value="3.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	347 <param name="min_required_elements" value="10"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	348 <param name="noise_for_empty_window" value="1e+20"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	349 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	350 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	351 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	352 <output name="ctd_out" ftype="xml">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	353 <assert_contents>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	354 <is_valid_xml/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	355 </assert_contents>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	356 </output>
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	357 <assert_stdout>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	358 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	359 </assert_stdout>
13 2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	360 </test>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	361 <!-- TOPP_PeakPickerWavelet_5 -->
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	362 <test expect_num_outputs="2">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	363 <section name="adv_opts">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	364 <param name="write_peak_meta_data" value="false"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	365 <param name="force" value="false"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	366 <param name="test" value="true"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	367 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	368 <param name="in" value="PeakPickerWavelet_input.mzML"/>
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	369 <output name="out" value="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
13 2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	370 <section name="algorithm">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	371 <param name="signal_to_noise" value="3.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	372 <param name="centroid_percentage" value="0.6"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	373 <param name="peak_width" value="0.2"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	374 <param name="estimate_peak_width" value="false"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	375 <param name="fwhm_lower_bound_factor" value="0.5"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	376 <param name="fwhm_upper_bound_factor" value="20.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	377 <section name="optimization">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	378 <param name="iterations" value="400"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	379 <section name="penalties">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	380 <param name="position" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	381 <param name="left_width" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	382 <param name="right_width" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	383 <param name="height" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	384 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	385 <section name="2d">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	386 <param name="tolerance_mz" value="2.2"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	387 <param name="max_peak_distance" value="1.2"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	388 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	389 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	390 <section name="thresholds">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	391 <param name="peak_bound" value="100.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	392 <param name="peak_bound_ms2_level" value="10.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	393 <param name="correlation" value="0.5"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	394 <param name="noise_level" value="0.1"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	395 <param name="search_radius" value="3"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	396 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	397 <section name="wavelet_transform">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	398 <param name="spacing" value="0.001"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	399 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	400 <section name="deconvolution">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	401 <param name="deconvolution" value="false"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	402 <param name="asym_threshold" value="0.3"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	403 <param name="left_width" value="2.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	404 <param name="right_width" value="2.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	405 <param name="scaling" value="0.12"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	406 <section name="fitting">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	407 <param name="fwhm_threshold" value="0.7"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	408 <param name="eps_abs" value="9.999999747378752e-06"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	409 <param name="eps_rel" value="9.999999747378752e-06"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	410 <param name="max_iteration" value="10"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	411 <section name="penalties">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	412 <param name="position" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	413 <param name="height" value="1.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	414 <param name="left_width" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	415 <param name="right_width" value="0.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	416 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	417 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	418 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	419 <section name="SignalToNoiseEstimationParameter">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	420 <param name="max_intensity" value="-1"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	421 <param name="auto_max_stdev_factor" value="3.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	422 <param name="auto_max_percentile" value="95"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	423 <param name="auto_mode" value="0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	424 <param name="win_len" value="200.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	425 <param name="bin_count" value="30"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	426 <param name="stdev_mp" value="3.0"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	427 <param name="min_required_elements" value="10"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	428 <param name="noise_for_empty_window" value="1e+20"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	429 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	430 </section>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	431 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	432 <output name="ctd_out" ftype="xml">
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	433 <assert_contents>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	434 <is_valid_xml/>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	435 </assert_contents>
2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	436 </output>
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	437 <assert_stdout>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	438 <has_text_matching expression="@EXECUTABLE@ took .* $wall$, .* $CPU$, .* $system$, .* $user$(; Peak Memory Usage: 32 MB)?."/>
bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	439 </assert_stdout>
13 2077efa205de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3 galaxyp parents: 11 diff changeset	440 </test>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	441 </tests>
bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	442 <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra.
0 4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	443
4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	444
14 bf0b36140329 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906 galaxyp parents: 13 diff changeset	445 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PeakPickerWavelet.html]]></help>
9 bf3353f27d33 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315" galaxyp parents: 7 diff changeset	446 <expand macro="references"/>
0 4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 galaxyp parents: diff changeset	447 </tool>

Mercurial > repos > galaxyp > openms_peakpickerwavelet

annotate PeakPickerWavelet.xml @ 14:bf0b36140329 draft default tip