Mercurial > repos > galaxyp > openms_tofcalibration
diff TOFCalibration.xml @ 11:90f459a4da0e draft
"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 |
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--- a/TOFCalibration.xml Wed Sep 23 14:58:29 2020 +0000 +++ b/TOFCalibration.xml Tue Oct 13 20:06:52 2020 +0000 @@ -55,8 +55,8 @@ <inputs> <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input peak or raw data file" help=" select mzml data sets(s)"/> <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)"/> - <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)"/> - <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)"/> + <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)"/> + <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)"/> <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=""/> <section name="algorithm" title="Algorithm section for peak picking" help="" expanded="false"> <section name="PeakPicker" title="" help="" expanded="false"> @@ -122,12 +122,12 @@ </section> </section> <expand macro="adv_opts_macro"> - <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> <expand macro="list_string_san"/> </param> </expand> - <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> + <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> @@ -144,6 +144,6 @@ <help><![CDATA[Applies time of flight calibration. -For more information, visit http://www.openms.de/documentation/TOPP_TOFCalibration.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_TOFCalibration.html]]></help> <expand macro="references"/> </tool>