Mercurial > repos > galaxyp > openms_peakpickerhires
annotate PeakPickerHiRes.xml @ 11:401f500aae50 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 21:35:28 +0000 |
| parents | 6b01678ec2fc |
| children |
| rev | line source |
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d34c1a10e713
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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1 <!--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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401f500aae50
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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2 <!--Proposed Tool Section: [Spectrum processing: Centroiding]--> |
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6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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3 <tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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401f500aae50
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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4 <description>Finds mass spectrometric peaks in profile mass spectra</description> |
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5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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5 <macros> |
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5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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6 <token name="@EXECUTABLE@">PeakPickerHiRes</token> |
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5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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7 <import>macros.xml</import> |
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5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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8 </macros> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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9 <expand macro="requirements"/> |
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5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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10 <expand macro="stdio"/> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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12 @EXT_FOO@ |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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13 #import re |
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5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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14 |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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15 ## Preprocessing |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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16 mkdir in && |
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401f500aae50
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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18 mkdir out && |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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19 |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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20 ## Main program call |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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21 |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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22 set -o pipefail && |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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23 @EXECUTABLE@ -write_ctd ./ && |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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24 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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25 @EXECUTABLE@ -ini @EXECUTABLE@.ctd |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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26 -in |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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27 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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28 -out |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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29 'out/output.${gxy2omsext("mzml")}' |
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5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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30 |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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31 ## Postprocessing |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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32 && mv 'out/output.${gxy2omsext("mzml")}' '$out' |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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34 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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35 #end if]]></command> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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36 <configfiles> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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37 <inputs name="args_json" data_style="paths"/> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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39 </configfiles> |
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5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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40 <inputs> |
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401f500aae50
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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41 <param argument="-in" type="data" format="mzml" label="input profile data file" help=" select mzml data sets(s)"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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42 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> |
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401f500aae50
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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43 <param name="signal_to_noise" argument="-algorithm:signal_to_noise" type="float" min="0.0" value="0.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help=""/> |
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401f500aae50
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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44 <param name="spacing_difference_gap" argument="-algorithm:spacing_difference_gap" type="float" min="0.0" value="4.0" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" help="'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms"/> |
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401f500aae50
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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45 <param name="spacing_difference" argument="-algorithm:spacing_difference" type="float" min="0.0" value="1.5" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" help="If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms"/> |
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401f500aae50
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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46 <param name="missing" argument="-algorithm:missing" type="integer" min="0" value="1" label="Maximum number of missing points allowed when extending a peak to the left or to the right" help="A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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47 <param name="ms_levels" argument="-algorithm:ms_levels" type="text" optional="true" value="" label="List of MS levels for which the peak picking is applied" help="If empty, auto mode is enabled, all peaks which aren't picked yet will get picked. Other scans are copied to the output without changes (space separated list, in order to allow for spaces in list items surround them by single quotes)"> |
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6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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48 <expand macro="list_integer_valsan" name="ms_levels"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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49 <validator type="expression" message="a space separated list of integer values in the range 1: is required"><![CDATA[len(value.split(' ')) == len([_ for _ in value.split(' ') if 1 <= int(_)]) |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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50 ]]></validator> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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51 </expand> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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52 </param> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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53 <param name="report_FWHM" argument="-algorithm:report_FWHM" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak" help=""/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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54 <param name="report_FWHM_unit" argument="-algorithm:report_FWHM_unit" type="select" label="Unit of FWHM" help="Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)"> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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55 <option value="relative" selected="true">relative</option> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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56 <option value="absolute">absolute</option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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57 <expand macro="list_string_san" name="report_FWHM_unit"/> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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58 </param> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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59 <section name="SignalToNoise" title="" help="" expanded="false"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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60 <param name="max_intensity" argument="-algorithm:SignalToNoise: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 be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/> |
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401f500aae50
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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61 <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoise: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=""/> |
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401f500aae50
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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62 <param name="auto_max_percentile" argument="-algorithm:SignalToNoise: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=""/> |
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401f500aae50
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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63 <param name="auto_mode" argument="-algorithm:SignalToNoise: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=""/> |
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401f500aae50
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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64 <param name="win_len" argument="-algorithm:SignalToNoise:win_len" type="float" min="1.0" value="200.0" label="window length in Thomson" help=""/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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65 <param name="bin_count" argument="-algorithm:SignalToNoise:bin_count" type="integer" min="3" value="30" label="number of bins for intensity values" help=""/> |
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66 <param name="min_required_elements" argument="-algorithm:SignalToNoise:min_required_elements" type="integer" min="1" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help=""/> |
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401f500aae50
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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67 <param name="noise_for_empty_window" argument="-algorithm:SignalToNoise:noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help=""/> |
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8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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68 <param name="write_log_messages" argument="-algorithm:SignalToNoise:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help=""/> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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69 </section> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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70 </section> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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71 <expand macro="adv_opts_macro"> |
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11
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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72 <param argument="-processOption" type="select" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help=""> |
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0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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73 <option value="inmemory" selected="true">inmemory</option> |
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5ae104d0da6e
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74 <option value="lowmemory">lowmemory</option> |
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10
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75 <expand macro="list_string_san" name="processOption"/> |
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0
5ae104d0da6e
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76 </param> |
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10
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77 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
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78 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> |
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10
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79 <expand macro="list_string_san" name="test"/> |
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8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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80 </param> |
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0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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81 </expand> |
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8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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82 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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83 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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84 </param> |
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0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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85 </inputs> |
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5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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86 <outputs> |
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8
146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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87 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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88 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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89 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
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146b59d2d3e5
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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90 </data> |
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0
5ae104d0da6e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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91 </outputs> |
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11
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92 <tests> |
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93 <!-- TOPP_PeakPickerHiRes_1 --> |
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94 <test expect_num_outputs="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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95 <section name="adv_opts"> |
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6b01678ec2fc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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96 <param name="processOption" value="inmemory"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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97 <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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98 <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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99 </section> |
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100 <param name="in" value="PeakPickerHiRes_input.mzML"/> |
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11
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101 <output name="out" value="PeakPickerHiRes_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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10
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102 <section name="algorithm"> |
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103 <param name="signal_to_noise" value="1.0"/> |
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104 <param name="spacing_difference_gap" value="4.0"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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105 <param name="spacing_difference" value="1.5"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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106 <param name="missing" value="1"/> |
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107 <param name="ms_levels" value="1"/> |
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108 <param name="report_FWHM" 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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109 <param name="report_FWHM_unit" value="relative"/> |
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110 <section name="SignalToNoise"> |
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111 <param name="max_intensity" value="-1"/> |
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112 <param name="auto_max_stdev_factor" value="3.0"/> |
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113 <param name="auto_max_percentile" value="95"/> |
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114 <param name="auto_mode" value="0"/> |
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115 <param name="win_len" value="200.0"/> |
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116 <param name="bin_count" value="30"/> |
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117 <param name="min_required_elements" value="10"/> |
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118 <param name="noise_for_empty_window" value="1e+20"/> |
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119 <param name="write_log_messages" value="true"/> |
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120 </section> |
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121 </section> |
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122 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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123 <output name="ctd_out" ftype="xml"> |
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124 <assert_contents> |
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125 <is_valid_xml/> |
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126 </assert_contents> |
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127 </output> |
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11
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128 <assert_stdout> |
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129 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
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130 </assert_stdout> |
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10
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131 </test> |
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132 <!-- TOPP_PeakPickerHiRes_2 --> |
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133 <test expect_num_outputs="2"> |
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134 <section name="adv_opts"> |
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135 <param name="processOption" value="inmemory"/> |
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136 <param name="force" value="false"/> |
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137 <param name="test" value="true"/> |
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138 </section> |
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139 <param name="in" value="PeakPickerHiRes_2_input.mzML"/> |
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140 <output name="out" value="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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141 <section name="algorithm"> |
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142 <param name="signal_to_noise" value="1.0"/> |
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143 <param name="spacing_difference_gap" value="4.0"/> |
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144 <param name="spacing_difference" value="1.5"/> |
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145 <param name="missing" value="1"/> |
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146 <param name="ms_levels" value="1"/> |
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147 <param name="report_FWHM" value="true"/> |
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148 <param name="report_FWHM_unit" value="relative"/> |
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149 <section name="SignalToNoise"> |
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150 <param name="max_intensity" value="-1"/> |
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151 <param name="auto_max_stdev_factor" value="3.0"/> |
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152 <param name="auto_max_percentile" value="95"/> |
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153 <param name="auto_mode" value="0"/> |
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154 <param name="win_len" value="200.0"/> |
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155 <param name="bin_count" value="30"/> |
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156 <param name="min_required_elements" value="10"/> |
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157 <param name="noise_for_empty_window" value="1e+20"/> |
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158 <param name="write_log_messages" value="true"/> |
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159 </section> |
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160 </section> |
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161 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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162 <output name="ctd_out" ftype="xml"> |
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163 <assert_contents> |
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164 <is_valid_xml/> |
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165 </assert_contents> |
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166 </output> |
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167 <assert_stdout> |
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168 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
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169 </assert_stdout> |
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170 </test> |
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171 <!-- TOPP_PeakPickerHiRes_3 --> |
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172 <test expect_num_outputs="2"> |
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173 <section name="adv_opts"> |
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174 <param name="processOption" value="lowmemory"/> |
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175 <param name="force" value="false"/> |
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176 <param name="test" value="true"/> |
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177 </section> |
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178 <param name="in" value="PeakPickerHiRes_input.mzML"/> |
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179 <output name="out" value="PeakPickerHiRes_output_lowMem.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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180 <section name="algorithm"> |
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181 <param name="signal_to_noise" value="1.0"/> |
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182 <param name="spacing_difference_gap" value="4.0"/> |
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183 <param name="spacing_difference" value="1.5"/> |
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184 <param name="missing" value="1"/> |
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185 <param name="ms_levels" value="1"/> |
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186 <param name="report_FWHM" value="true"/> |
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187 <param name="report_FWHM_unit" value="relative"/> |
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188 <section name="SignalToNoise"> |
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189 <param name="max_intensity" value="-1"/> |
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190 <param name="auto_max_stdev_factor" value="3.0"/> |
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191 <param name="auto_max_percentile" value="95"/> |
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192 <param name="auto_mode" value="0"/> |
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193 <param name="win_len" value="200.0"/> |
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194 <param name="bin_count" value="30"/> |
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195 <param name="min_required_elements" value="10"/> |
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196 <param name="noise_for_empty_window" value="1e+20"/> |
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197 <param name="write_log_messages" value="true"/> |
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198 </section> |
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199 </section> |
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200 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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201 <output name="ctd_out" ftype="xml"> |
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202 <assert_contents> |
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203 <is_valid_xml/> |
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204 </assert_contents> |
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205 </output> |
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206 <assert_stdout> |
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207 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
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208 </assert_stdout> |
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209 </test> |
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210 <!-- TOPP_PeakPickerHiRes_4 --> |
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211 <test expect_num_outputs="2"> |
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212 <section name="adv_opts"> |
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213 <param name="processOption" value="lowmemory"/> |
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214 <param name="force" value="false"/> |
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215 <param name="test" value="true"/> |
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216 </section> |
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217 <param name="in" value="PeakPickerHiRes_2_input.mzML"/> |
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218 <output name="out" value="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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219 <section name="algorithm"> |
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220 <param name="signal_to_noise" value="1.0"/> |
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221 <param name="spacing_difference_gap" value="4.0"/> |
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222 <param name="spacing_difference" value="1.5"/> |
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223 <param name="missing" value="1"/> |
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224 <param name="ms_levels" value="1"/> |
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225 <param name="report_FWHM" value="true"/> |
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226 <param name="report_FWHM_unit" value="relative"/> |
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227 <section name="SignalToNoise"> |
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228 <param name="max_intensity" value="-1"/> |
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229 <param name="auto_max_stdev_factor" value="3.0"/> |
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230 <param name="auto_max_percentile" value="95"/> |
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231 <param name="auto_mode" value="0"/> |
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232 <param name="win_len" value="200.0"/> |
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233 <param name="bin_count" value="30"/> |
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234 <param name="min_required_elements" value="10"/> |
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235 <param name="noise_for_empty_window" value="1e+20"/> |
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236 <param name="write_log_messages" value="true"/> |
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237 </section> |
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238 </section> |
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239 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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240 <output name="ctd_out" ftype="xml"> |
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241 <assert_contents> |
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242 <is_valid_xml/> |
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243 </assert_contents> |
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244 </output> |
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245 <assert_stdout> |
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246 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
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247 </assert_stdout> |
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248 </test> |
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249 <!-- TOPP_PeakPickerHiRes_5 --> |
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250 <test expect_num_outputs="2"> |
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251 <section name="adv_opts"> |
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252 <param name="processOption" value="inmemory"/> |
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253 <param name="force" value="false"/> |
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254 <param name="test" value="true"/> |
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255 </section> |
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256 <param name="in" value="PeakPickerHiRes_5_input.mzML"/> |
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257 <output name="out" value="PeakPickerHiRes_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> |
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258 <section name="algorithm"> |
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259 <param name="signal_to_noise" value="0.0"/> |
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260 <param name="spacing_difference_gap" value="4.0"/> |
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261 <param name="spacing_difference" value="1.5"/> |
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262 <param name="missing" value="1"/> |
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263 <param name="report_FWHM" value="false"/> |
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264 <param name="report_FWHM_unit" value="relative"/> |
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265 <section name="SignalToNoise"> |
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266 <param name="max_intensity" value="-1"/> |
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267 <param name="auto_max_stdev_factor" value="3.0"/> |
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268 <param name="auto_max_percentile" value="95"/> |
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269 <param name="auto_mode" value="0"/> |
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270 <param name="win_len" value="200.0"/> |
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271 <param name="bin_count" value="30"/> |
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272 <param name="min_required_elements" value="10"/> |
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273 <param name="noise_for_empty_window" value="1e+20"/> |
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274 <param name="write_log_messages" value="true"/> |
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275 </section> |
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276 </section> |
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277 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> |
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278 <output name="ctd_out" ftype="xml"> |
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279 <assert_contents> |
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280 <is_valid_xml/> |
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281 </assert_contents> |
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282 </output> |
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283 <assert_stdout> |
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284 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> |
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285 </assert_stdout> |
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286 </test> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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287 </tests> |
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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit e499c9124d3fd85a7fc47b95c206ce91a5e3678c-dirty"
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288 <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra. |
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289 |
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290 |
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291 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PeakPickerHiRes.html]]></help> |
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292 <expand macro="references"/> |
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293 </tool> |