diff MapAlignerTreeGuided.xml @ 2:25c08f95cdf4 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

--- a/MapAlignerTreeGuided.xml	Thu Sep 24 12:12:52 2020 +0000
+++ b/MapAlignerTreeGuided.xml	Tue Oct 13 20:39:15 2020 +0000
@@ -57,7 +57,7 @@
 #end if]]></command>
   <configfiles>
     <inputs name="args_json" data_style="paths"/>
-    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+    <configfile name="hardcoded_json"><![CDATA[{"copy_data": "false", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
     <param name="in" argument="-in" type="data" format="featurexml" multiple="true" optional="false" label="Input files to align (all must have the same file type)" help=" select featurexml data sets(s)"/>
@@ -154,14 +154,14 @@
       </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="false">
-      <option value="out_FLAG">out (When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to)</option>
-      <option value="trafo_out_FLAG">trafo_out (When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to)</option>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="out_FLAG">out (Output files (same file type as 'in'))</option>
+      <option value="trafo_out_FLAG">trafo_out (Transformation output files)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -188,6 +188,6 @@
   <help><![CDATA[Tree guided correction of retention time distortions between maps.
 
 
-For more information, visit http://www.openms.de/documentation/TOPP_MapAlignerTreeGuided.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MapAlignerTreeGuided.html]]></help>
   <expand macro="references"/>
 </tool>