Mercurial > repos > galaxyp > openms_internalcalibration

diff InternalCalibration.xml @ 11:6c58aa0ed5c1 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 20:00:38 +0000
parents cca2b6c3ae61
children f49a58e03ada
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--- a/InternalCalibration.xml	Thu Sep 24 09:56:27 2020 +0000
+++ b/InternalCalibration.xml	Tue Oct 13 20:00:38 2020 +0000
@@ -150,17 +150,17 @@
       <param name="MAD" argument="-goodness:MAD" type="float" optional="true" value="2.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" help=""/>
     </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">
-      <option value="lock_out_FLAG">lock_out (Plot image of pre- and post calibration errors)</option>
-      <option value="lock_fail_out_FLAG">lock_fail_out (Plot image of pre- and post calibration errors)</option>
-      <option value="models_FLAG">models (Plot image of pre- and post calibration errors)</option>
-      <option value="models_plot_FLAG">models_plot (Plot image of pre- and post calibration errors)</option>
-      <option value="residuals_FLAG">residuals (Plot image of pre- and post calibration errors)</option>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="lock_out_FLAG">lock_out (Optional output file containing peaks from 'in' which were matched to reference m/z values)</option>
+      <option value="lock_fail_out_FLAG">lock_fail_out (Optional output file containing lock masses which were NOT found or accepted(!) in data from 'in')</option>
+      <option value="models_FLAG">models (Table of model parameters for each spectrum)</option>
+      <option value="models_plot_FLAG">models_plot (Plot image of model parameters for each spectrum)</option>
+      <option value="residuals_FLAG">residuals (Table of pre- and post calibration errors)</option>
       <option value="residuals_plot_FLAG">residuals_plot (Plot image of pre- and post calibration errors)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
@@ -196,6 +196,6 @@
   <help><![CDATA[Applies an internal mass recalibration.
 
 
-For more information, visit http://www.openms.de/documentation/TOPP_InternalCalibration.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_InternalCalibration.html]]></help>
   <expand macro="references"/>
 </tool>