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
line wrap: on
line diff
--- 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>