Mercurial > repos > galaxyp > openms_peakpickerwavelet
annotate PeakPickerWavelet.xml @ 13:2077efa205de draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:16:26 +0000 |
| parents | 341af0b11af9 |
| children | bf0b36140329 |
| rev | line source |
|---|---|
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4ee66bd832d9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?> |
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5
409cec15d717
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
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4ee66bd832d9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> |
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13
2077efa205de
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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4 <tool id="PeakPickerWavelet" name="PeakPickerWavelet" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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4ee66bd832d9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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5 <description>Finds mass spectrometric peaks in profile mass spectra.</description> |
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4ee66bd832d9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <macros> |
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4ee66bd832d9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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7 <token name="@EXECUTABLE@">PeakPickerWavelet</token> |
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4ee66bd832d9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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8 <import>macros.xml</import> |
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4ee66bd832d9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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9 </macros> |
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9
bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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10 <expand macro="requirements"/> |
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4ee66bd832d9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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11 <expand macro="stdio"/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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13 @EXT_FOO@ |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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14 #import re |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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15 |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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16 ## Preprocessing |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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17 mkdir in && |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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19 mkdir out && |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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20 |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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21 ## Main program call |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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22 |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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23 set -o pipefail && |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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24 @EXECUTABLE@ -write_ctd ./ && |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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25 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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26 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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27 -in |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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28 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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29 -out |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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30 'out/output.${gxy2omsext("mzml")}' |
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4ee66bd832d9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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31 |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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32 ## Postprocessing |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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33 && mv 'out/output.${gxy2omsext("mzml")}' '$out' |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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34 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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35 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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36 #end if]]></command> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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37 <configfiles> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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38 <inputs name="args_json" data_style="paths"/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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40 </configfiles> |
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4ee66bd832d9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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41 <inputs> |
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2077efa205de
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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42 <param argument="-in" type="data" format="mzml" optional="false" label="input profile data file" help=" select mzml data sets(s)"/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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43 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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44 <param name="signal_to_noise" argument="-algorithm:signal_to_noise" type="float" optional="true" min="0.0" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help=""/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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45 <param name="centroid_percentage" argument="-algorithm:centroid_percentage" type="float" optional="true" 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"/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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46 <param name="peak_width" argument="-algorithm:peak_width" type="float" optional="true" min="0.0" value="0.15" label="Approximate fwhm of the peaks" help=""/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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47 <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"/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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48 <param name="fwhm_lower_bound_factor" argument="-algorithm:fwhm_lower_bound_factor" type="float" optional="true" 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"/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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49 <param name="fwhm_upper_bound_factor" argument="-algorithm:fwhm_upper_bound_factor" type="float" optional="true" 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"/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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50 <section name="optimization" title="" help="" expanded="false"> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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51 <param name="iterations" argument="-algorithm:optimization:iterations" type="integer" optional="true" min="1" value="400" label="maximal number of iterations for the fitting step" help=""/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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52 <section name="penalties" title="" help="" expanded="false"> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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53 <param name="position" argument="-algorithm:optimization:penalties:position" type="float" optional="true" 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=""/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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54 <param name="left_width" argument="-algorithm:optimization:penalties:left_width" type="float" optional="true" 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=""/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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55 <param name="right_width" argument="-algorithm:optimization:penalties:right_width" type="float" optional="true" 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=""/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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56 <param name="height" argument="-algorithm:optimization:penalties:height" type="float" optional="true" 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=""/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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57 </section> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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58 <section name="2d" title="" help="" expanded="false"> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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59 <param name="tolerance_mz" argument="-algorithm:optimization:2d:tolerance_mz" type="float" optional="true" min="0.0" value="2.2" label="mz tolerance for cluster construction" help=""/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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60 <param name="max_peak_distance" argument="-algorithm:optimization:2d:max_peak_distance" type="float" optional="true" min="0.0" value="1.2" label="maximal peak distance in mz in a cluste" help=""/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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61 </section> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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62 </section> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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63 <section name="thresholds" title="" help="" expanded="false"> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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64 <param name="peak_bound" argument="-algorithm:thresholds:peak_bound" type="float" optional="true" min="0.0" value="10.0" label="Minimal peak intensity" help=""/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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65 <param name="peak_bound_ms2_level" argument="-algorithm:thresholds:peak_bound_ms2_level" type="float" optional="true" min="0.0" value="10.0" label="Minimal peak intensity for MS/MS peaks" help=""/> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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66 <param name="correlation" argument="-algorithm:thresholds:correlation" type="float" optional="true" 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"/> |
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67 <param name="noise_level" argument="-algorithm:thresholds:noise_level" type="float" optional="true" min="0.0" value="0.1" label="noise level for the search of the peak endpoints" help=""/> |
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68 <param name="search_radius" argument="-algorithm:thresholds:search_radius" type="integer" optional="true" 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=""/> |
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69 </section> |
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70 <section name="wavelet_transform" title="" help="" expanded="false"> |
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71 <param name="spacing" argument="-algorithm:wavelet_transform:spacing" type="float" optional="true" 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"/> |
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72 </section> |
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73 <section name="deconvolution" title="" help="" expanded="false"> |
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74 <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=""/> |
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75 <param name="asym_threshold" argument="-algorithm:deconvolution:asym_threshold" type="float" optional="true" 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=""/> |
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76 <param name="left_width" argument="-algorithm:deconvolution:left_width" type="float" optional="true" 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=""/> |
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77 <param name="right_width" argument="-algorithm:deconvolution:right_width" type="float" optional="true" 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=""/> |
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78 <param name="scaling" argument="-algorithm:deconvolution:scaling" type="float" optional="true" 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"/> |
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79 <section name="fitting" title="" help="" expanded="false"> |
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80 <param name="fwhm_threshold" argument="-algorithm:deconvolution:fitting:fwhm_threshold" type="float" optional="true" 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=""/> |
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81 <param name="eps_abs" argument="-algorithm:deconvolution:fitting:eps_abs" type="float" optional="true" min="0.0" value="9.999999747378752e-06" label="if the absolute error gets smaller than this value the fitting is stopped" help=""/> |
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82 <param name="eps_rel" argument="-algorithm:deconvolution:fitting:eps_rel" type="float" optional="true" min="0.0" value="9.999999747378752e-06" label="if the relative error gets smaller than this value the fitting is stopped" help=""/> |
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83 <param name="max_iteration" argument="-algorithm:deconvolution:fitting:max_iteration" type="integer" optional="true" min="1" value="10" label="maximal number of iterations for the fitting step" help=""/> |
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84 <section name="penalties" title="" help="" expanded="false"> |
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85 <param name="position" argument="-algorithm:deconvolution:fitting:penalties:position" type="float" optional="true" 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=""/> |
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86 <param name="height" argument="-algorithm:deconvolution:fitting:penalties:height" type="float" optional="true" 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=""/> |
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87 <param name="left_width" argument="-algorithm:deconvolution:fitting:penalties:left_width" type="float" optional="true" 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=""/> |
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88 <param name="right_width" argument="-algorithm:deconvolution:fitting:penalties:right_width" type="float" optional="true" 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=""/> |
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89 </section> |
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90 </section> |
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91 </section> |
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92 <section name="SignalToNoiseEstimationParameter" title="" help="" expanded="false"> |
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93 <param name="max_intensity" argument="-algorithm:SignalToNoiseEstimationParameter:max_intensity" type="integer" optional="true" 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)"/> |
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94 <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoiseEstimationParameter:auto_max_stdev_factor" type="float" optional="true" 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=""/> |
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95 <param name="auto_max_percentile" argument="-algorithm:SignalToNoiseEstimationParameter:auto_max_percentile" type="integer" optional="true" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/> |
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96 <param name="auto_mode" argument="-algorithm:SignalToNoiseEstimationParameter:auto_mode" type="integer" optional="true" 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=""/> |
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97 <param name="win_len" argument="-algorithm:SignalToNoiseEstimationParameter:win_len" type="float" optional="true" min="1.0" value="200.0" label="window length in Thomson" help=""/> |
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98 <param name="bin_count" argument="-algorithm:SignalToNoiseEstimationParameter:bin_count" type="integer" optional="true" min="3" value="30" label="number of bins for intensity values" help=""/> |
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99 <param name="stdev_mp" argument="-algorithm:SignalToNoiseEstimationParameter:stdev_mp" type="float" optional="true" min="0.01" max="999.0" value="3.0" label="multiplier for stdev" help=""/> |
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100 <param name="min_required_elements" argument="-algorithm:SignalToNoiseEstimationParameter:min_required_elements" type="integer" optional="true" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/> |
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101 <param name="noise_for_empty_window" argument="-algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/> |
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102 </section> |
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103 </section> |
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104 <expand macro="adv_opts_macro"> |
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105 <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!"/> |
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106 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
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107 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
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108 <expand macro="list_string_san" name="test"/> |
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9
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109 </param> |
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0
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110 </expand> |
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11
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111 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
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9
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112 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
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113 </param> |
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0
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114 </inputs> |
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115 <outputs> |
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9
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116 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
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117 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
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118 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
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119 </data> |
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0
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120 </outputs> |
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121 <tests><!-- TOPP_PeakPickerWavelet_1 --> |
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122 <test expect_num_outputs="2"> |
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123 <section name="adv_opts"> |
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124 <param name="write_peak_meta_data" value="true"/> |
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125 <param name="force" value="false"/> |
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126 <param name="test" value="true"/> |
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127 </section> |
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128 <param name="in" value="PeakPickerWavelet_input.mzML"/> |
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129 <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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130 <section name="algorithm"> |
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131 <param name="signal_to_noise" value="3.0"/> |
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132 <param name="centroid_percentage" value="0.6"/> |
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133 <param name="peak_width" value="0.2"/> |
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134 <param name="estimate_peak_width" value="false"/> |
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135 <param name="fwhm_lower_bound_factor" value="0.5"/> |
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136 <param name="fwhm_upper_bound_factor" value="20.0"/> |
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137 <section name="optimization"> |
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138 <param name="iterations" value="400"/> |
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139 <section name="penalties"> |
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140 <param name="position" value="0.0"/> |
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141 <param name="left_width" value="1.0"/> |
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142 <param name="right_width" value="1.0"/> |
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143 <param name="height" value="1.0"/> |
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144 </section> |
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145 <section name="2d"> |
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146 <param name="tolerance_mz" value="2.2"/> |
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147 <param name="max_peak_distance" value="1.2"/> |
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148 </section> |
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149 </section> |
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150 <section name="thresholds"> |
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151 <param name="peak_bound" value="100.0"/> |
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152 <param name="peak_bound_ms2_level" value="10.0"/> |
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153 <param name="correlation" value="0.5"/> |
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154 <param name="noise_level" value="0.1"/> |
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155 <param name="search_radius" value="3"/> |
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156 </section> |
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157 <section name="wavelet_transform"> |
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158 <param name="spacing" value="0.001"/> |
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159 </section> |
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160 <section name="deconvolution"> |
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161 <param name="deconvolution" value="false"/> |
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162 <param name="asym_threshold" value="0.3"/> |
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163 <param name="left_width" value="2.0"/> |
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164 <param name="right_width" value="2.0"/> |
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165 <param name="scaling" value="0.12"/> |
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166 <section name="fitting"> |
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167 <param name="fwhm_threshold" value="0.7"/> |
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168 <param name="eps_abs" value="9.999999747378752e-06"/> |
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169 <param name="eps_rel" value="9.999999747378752e-06"/> |
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170 <param name="max_iteration" value="10"/> |
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171 <section name="penalties"> |
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172 <param name="position" value="0.0"/> |
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173 <param name="height" value="1.0"/> |
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174 <param name="left_width" value="0.0"/> |
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175 <param name="right_width" value="0.0"/> |
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176 </section> |
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177 </section> |
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178 </section> |
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179 <section name="SignalToNoiseEstimationParameter"> |
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180 <param name="max_intensity" value="-1"/> |
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181 <param name="auto_max_stdev_factor" value="3.0"/> |
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182 <param name="auto_max_percentile" value="95"/> |
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183 <param name="auto_mode" value="0"/> |
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184 <param name="win_len" value="200.0"/> |
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185 <param name="bin_count" value="30"/> |
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186 <param name="stdev_mp" value="3.0"/> |
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187 <param name="min_required_elements" value="10"/> |
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188 <param name="noise_for_empty_window" value="1e+20"/> |
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189 </section> |
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190 </section> |
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191 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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192 <output name="ctd_out" ftype="xml"> |
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193 <assert_contents> |
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194 <is_valid_xml/> |
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195 </assert_contents> |
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196 </output> |
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197 </test> |
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198 <!-- TOPP_PeakPickerWavelet_2 --> |
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199 <test expect_num_outputs="2"> |
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200 <section name="adv_opts"> |
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201 <param name="write_peak_meta_data" value="true"/> |
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202 <param name="force" value="false"/> |
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203 <param name="test" value="true"/> |
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204 </section> |
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205 <param name="in" value="PeakPickerWavelet_deconv_input.mzML"/> |
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206 <output name="out" file="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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207 <section name="algorithm"> |
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208 <param name="signal_to_noise" value="2.0"/> |
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209 <param name="centroid_percentage" value="0.8"/> |
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210 <param name="peak_width" value="0.15"/> |
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211 <param name="estimate_peak_width" value="false"/> |
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212 <param name="fwhm_lower_bound_factor" value="1.0"/> |
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213 <param name="fwhm_upper_bound_factor" value="20.0"/> |
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214 <section name="optimization"> |
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215 <param name="iterations" value="400"/> |
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216 <section name="penalties"> |
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217 <param name="position" value="0.0"/> |
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218 <param name="left_width" value="1.0"/> |
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219 <param name="right_width" value="1.0"/> |
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220 <param name="height" value="1.0"/> |
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221 </section> |
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222 <section name="2d"> |
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223 <param name="tolerance_mz" value="2.2"/> |
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224 <param name="max_peak_distance" value="1.2"/> |
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225 </section> |
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226 </section> |
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227 <section name="thresholds"> |
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228 <param name="peak_bound" value="200.0"/> |
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229 <param name="peak_bound_ms2_level" value="50.0"/> |
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230 <param name="correlation" value="0.5"/> |
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231 <param name="noise_level" value="0.1"/> |
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232 <param name="search_radius" value="3"/> |
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233 </section> |
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234 <section name="wavelet_transform"> |
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235 <param name="spacing" value="0.001"/> |
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236 </section> |
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237 <section name="deconvolution"> |
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238 <param name="deconvolution" value="true"/> |
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239 <param name="asym_threshold" value="0.3"/> |
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240 <param name="left_width" value="2.0"/> |
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241 <param name="right_width" value="2.0"/> |
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242 <param name="scaling" value="0.1"/> |
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243 <section name="fitting"> |
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244 <param name="fwhm_threshold" value="0.7"/> |
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245 <param name="eps_abs" value="1e-05"/> |
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246 <param name="eps_rel" value="1e-05"/> |
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247 <param name="max_iteration" value="100"/> |
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248 <section name="penalties"> |
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249 <param name="position" value="1.0"/> |
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250 <param name="height" value="1.0"/> |
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251 <param name="left_width" value="0.0"/> |
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252 <param name="right_width" value="0.0"/> |
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253 </section> |
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254 </section> |
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255 </section> |
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256 <section name="SignalToNoiseEstimationParameter"> |
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257 <param name="max_intensity" value="-1"/> |
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258 <param name="auto_max_stdev_factor" value="3.0"/> |
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259 <param name="auto_max_percentile" value="95"/> |
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260 <param name="auto_mode" value="0"/> |
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261 <param name="win_len" value="200.0"/> |
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262 <param name="bin_count" value="30"/> |
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263 <param name="stdev_mp" value="3.0"/> |
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264 <param name="min_required_elements" value="10"/> |
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265 <param name="noise_for_empty_window" value="1e+20"/> |
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266 </section> |
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267 </section> |
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268 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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269 <output name="ctd_out" ftype="xml"> |
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270 <assert_contents> |
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271 <is_valid_xml/> |
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272 </assert_contents> |
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273 </output> |
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274 </test> |
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275 <!-- TOPP_PeakPickerWavelet_4 --> |
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276 <test expect_num_outputs="2"> |
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277 <section name="adv_opts"> |
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278 <param name="write_peak_meta_data" value="true"/> |
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279 <param name="force" value="false"/> |
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280 <param name="test" value="true"/> |
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281 </section> |
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282 <param name="in" value="PeakPickerWavelet_input.mzML"/> |
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283 <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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284 <section name="algorithm"> |
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285 <param name="signal_to_noise" value="3.0"/> |
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286 <param name="centroid_percentage" value="0.6"/> |
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287 <param name="peak_width" value="0.2"/> |
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288 <param name="estimate_peak_width" value="false"/> |
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289 <param name="fwhm_lower_bound_factor" value="0.5"/> |
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290 <param name="fwhm_upper_bound_factor" value="20.0"/> |
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291 <section name="optimization"> |
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292 <param name="iterations" value="400"/> |
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293 <section name="penalties"> |
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294 <param name="position" value="0.0"/> |
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295 <param name="left_width" value="1.0"/> |
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296 <param name="right_width" value="1.0"/> |
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297 <param name="height" value="1.0"/> |
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298 </section> |
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299 <section name="2d"> |
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300 <param name="tolerance_mz" value="2.2"/> |
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301 <param name="max_peak_distance" value="1.2"/> |
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302 </section> |
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303 </section> |
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304 <section name="thresholds"> |
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305 <param name="peak_bound" value="100.0"/> |
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306 <param name="peak_bound_ms2_level" value="10.0"/> |
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307 <param name="correlation" value="0.5"/> |
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308 <param name="noise_level" value="0.1"/> |
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309 <param name="search_radius" value="3"/> |
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310 </section> |
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311 <section name="wavelet_transform"> |
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312 <param name="spacing" value="0.001"/> |
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313 </section> |
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314 <section name="deconvolution"> |
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315 <param name="deconvolution" value="false"/> |
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316 <param name="asym_threshold" value="0.3"/> |
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317 <param name="left_width" value="2.0"/> |
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318 <param name="right_width" value="2.0"/> |
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319 <param name="scaling" value="0.12"/> |
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320 <section name="fitting"> |
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321 <param name="fwhm_threshold" value="0.7"/> |
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322 <param name="eps_abs" value="9.999999747378752e-06"/> |
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323 <param name="eps_rel" value="9.999999747378752e-06"/> |
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324 <param name="max_iteration" value="10"/> |
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325 <section name="penalties"> |
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326 <param name="position" value="0.0"/> |
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327 <param name="height" value="1.0"/> |
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328 <param name="left_width" value="0.0"/> |
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329 <param name="right_width" value="0.0"/> |
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330 </section> |
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331 </section> |
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332 </section> |
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333 <section name="SignalToNoiseEstimationParameter"> |
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334 <param name="max_intensity" value="-1"/> |
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335 <param name="auto_max_stdev_factor" value="3.0"/> |
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336 <param name="auto_max_percentile" value="95"/> |
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337 <param name="auto_mode" value="0"/> |
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338 <param name="win_len" value="200.0"/> |
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339 <param name="bin_count" value="30"/> |
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340 <param name="stdev_mp" value="3.0"/> |
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341 <param name="min_required_elements" value="10"/> |
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342 <param name="noise_for_empty_window" value="1e+20"/> |
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343 </section> |
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344 </section> |
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345 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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346 <output name="ctd_out" ftype="xml"> |
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347 <assert_contents> |
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348 <is_valid_xml/> |
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349 </assert_contents> |
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350 </output> |
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351 </test> |
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352 <!-- TOPP_PeakPickerWavelet_5 --> |
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353 <test expect_num_outputs="2"> |
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354 <section name="adv_opts"> |
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355 <param name="write_peak_meta_data" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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356 <param name="force" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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357 <param name="test" value="true"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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358 </section> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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359 <param name="in" value="PeakPickerWavelet_input.mzML"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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360 <output name="out" file="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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361 <section name="algorithm"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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362 <param name="signal_to_noise" value="3.0"/> |
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2077efa205de
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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363 <param name="centroid_percentage" value="0.6"/> |
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2077efa205de
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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364 <param name="peak_width" value="0.2"/> |
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2077efa205de
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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365 <param name="estimate_peak_width" value="false"/> |
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2077efa205de
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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366 <param name="fwhm_lower_bound_factor" value="0.5"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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367 <param name="fwhm_upper_bound_factor" value="20.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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368 <section name="optimization"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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369 <param name="iterations" value="400"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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370 <section name="penalties"> |
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371 <param name="position" value="0.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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372 <param name="left_width" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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373 <param name="right_width" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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374 <param name="height" value="1.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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375 </section> |
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376 <section name="2d"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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377 <param name="tolerance_mz" value="2.2"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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378 <param name="max_peak_distance" value="1.2"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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379 </section> |
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380 </section> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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381 <section name="thresholds"> |
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382 <param name="peak_bound" value="100.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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383 <param name="peak_bound_ms2_level" value="10.0"/> |
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384 <param name="correlation" value="0.5"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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385 <param name="noise_level" value="0.1"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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386 <param name="search_radius" value="3"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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387 </section> |
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388 <section name="wavelet_transform"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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389 <param name="spacing" value="0.001"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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390 </section> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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391 <section name="deconvolution"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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392 <param name="deconvolution" value="false"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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393 <param name="asym_threshold" value="0.3"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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394 <param name="left_width" value="2.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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395 <param name="right_width" value="2.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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396 <param name="scaling" value="0.12"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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397 <section name="fitting"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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398 <param name="fwhm_threshold" value="0.7"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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399 <param name="eps_abs" value="9.999999747378752e-06"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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400 <param name="eps_rel" value="9.999999747378752e-06"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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401 <param name="max_iteration" value="10"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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402 <section name="penalties"> |
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2077efa205de
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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403 <param name="position" value="0.0"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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404 <param name="height" value="1.0"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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405 <param name="left_width" value="0.0"/> |
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2077efa205de
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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406 <param name="right_width" value="0.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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407 </section> |
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408 </section> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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409 </section> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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410 <section name="SignalToNoiseEstimationParameter"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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411 <param name="max_intensity" value="-1"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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412 <param name="auto_max_stdev_factor" value="3.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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413 <param name="auto_max_percentile" value="95"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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414 <param name="auto_mode" value="0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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415 <param name="win_len" value="200.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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416 <param name="bin_count" value="30"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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417 <param name="stdev_mp" value="3.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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418 <param name="min_required_elements" value="10"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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419 <param name="noise_for_empty_window" value="1e+20"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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420 </section> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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421 </section> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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422 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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423 <output name="ctd_out" ftype="xml"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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424 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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425 <is_valid_xml/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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426 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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427 </output> |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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428 </test> |
|
9
bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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429 </tests> |
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bf3353f27d33
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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430 <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
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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433 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PeakPickerWavelet.html]]></help> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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434 <expand macro="references"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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435 </tool> |