Mercurial > repos > galaxyp > openms_tofcalibration

comparison TOFCalibration.xml @ 11:90f459a4da0e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:06:52 +0000
parents 40a101cabd0e
children 9f0e189d093c
comparison
equal deleted inserted replaced
10:58bdbab5cc5e 11:90f459a4da0e
53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
54 </configfiles> 54 </configfiles>
55 <inputs> 55 <inputs>
56 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input peak or raw data file" help=" select mzml data sets(s)"/> 56 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input peak or raw data file" help=" select mzml data sets(s)"/>
57 <param name="ext_calibrants" argument="-ext_calibrants" type="data" format="mzml" optional="false" label="input file containing the external calibrant spectra (peak or raw data)" help=" select mzml data sets(s)"/> 57 <param name="ext_calibrants" argument="-ext_calibrants" type="data" format="mzml" optional="false" label="input file containing the external calibrant spectra (peak or raw data)" help=" select mzml data sets(s)"/>
58 <param name="ref_masses" argument="-ref_masses" type="data" format="txt" optional="false" label="input file containing reference masses of the external calibrant spectra (one per line)" help=" select txt data sets(s)"/> 58 <param name="ref_masses" argument="-ref_masses" type="data" format="tabular,txt" optional="false" label="input file containing reference masses of the external calibrant spectra (one per line)" help=" select tabular,txt data sets(s)"/>
59 <param name="tof_const" argument="-tof_const" type="data" format="csv" optional="false" label="File containing TOF conversion constants" help="These can be either two or three constants. per set, depending on the conversion type. Either one set for all calibrant spectra . (tab separated), or one for each spectrum.. For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line) select csv data sets(s)"/> 59 <param name="tof_const" argument="-tof_const" type="data" format="tabular" optional="false" label="File containing TOF conversion constants" help="These can be either two or three constants. per set, depending on the conversion type. Either one set for all calibrant spectra . (tab separated), or one for each spectrum.. For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line) select tabular data sets(s)"/>
60 <param name="peak_data" argument="-peak_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)" help=""/> 60 <param name="peak_data" argument="-peak_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)" help=""/>
61 <section name="algorithm" title="Algorithm section for peak picking" help="" expanded="false"> 61 <section name="algorithm" title="Algorithm section for peak picking" help="" expanded="false">
62 <section name="PeakPicker" title="" help="" expanded="false"> 62 <section name="PeakPicker" title="" help="" expanded="false">
63 <param name="signal_to_noise" argument="-algorithm:PeakPicker: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=""/> 63 <param name="signal_to_noise" argument="-algorithm:PeakPicker: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=""/>
64 <param name="centroid_percentage" argument="-algorithm:PeakPicker: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"/> 64 <param name="centroid_percentage" argument="-algorithm:PeakPicker: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"/>
120 <param name="noise_for_empty_window" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/> 120 <param name="noise_for_empty_window" argument="-algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/>
121 </section> 121 </section>
122 </section> 122 </section>
123 </section> 123 </section>
124 <expand macro="adv_opts_macro"> 124 <expand macro="adv_opts_macro">
125 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 125 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
126 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 126 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
127 <expand macro="list_string_san"/> 127 <expand macro="list_string_san"/>
128 </param> 128 </param>
129 </expand> 129 </expand>
130 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 130 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
131 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 131 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
132 </param> 132 </param>
133 </inputs> 133 </inputs>
134 <outputs> 134 <outputs>
135 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 135 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
142 <expand macro="manutest_TOFCalibration"/> 142 <expand macro="manutest_TOFCalibration"/>
143 </tests> 143 </tests>
144 <help><![CDATA[Applies time of flight calibration. 144 <help><![CDATA[Applies time of flight calibration.
145 145
146 146
147 For more information, visit http://www.openms.de/documentation/TOPP_TOFCalibration.html]]></help> 147 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_TOFCalibration.html]]></help>
148 <expand macro="references"/> 148 <expand macro="references"/>
149 </tool> 149 </tool>