diff SpectraSTSearchAdapter.xml @ 10:27ddea86fe90 draft

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

--- a/SpectraSTSearchAdapter.xml	Thu Sep 24 12:12:19 2020 +0000
+++ b/SpectraSTSearchAdapter.xml	Tue Oct 13 19:50:42 2020 +0000
@@ -73,12 +73,11 @@
     <configfile name="hardcoded_json"><![CDATA[{"executable": "spectrast", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="spectra_files" argument="-spectra_files" type="data" format="dta,msp,mzdata,mzml,mzxml" multiple="true" optional="false" label="File names(s) of spectra to be searched" help=" select dta,msp,mzdata,mzml,mzxml data sets(s)"/>
+    <param name="spectra_files" argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="true" optional="false" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/>
     <param name="output_files_type" type="select" optional="false" label="File type of output output_files (Output files. Make sure to specify one output file for each input file)">
       <option value="txt">txt</option>
       <option value="tsv">tabular (tsv)</option>
       <option value="pep.xml">pepxml (pep.xml)</option>
-      <option value="xml">xml</option>
       <option value="pepXML">pepxml</option>
       <option value="html">html</option>
     </param>
@@ -95,12 +94,12 @@
       <param name="use_isotopically_averaged_mass" argument="-use_isotopically_averaged_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use isotopically averaged mass instead of monoisotopic mass" help=""/>
       <param name="use_all_charge_states" argument="-use_all_charge_states" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Search library spectra of all charge states" help="i.e., ignore specified charge state (if any) of the query spectrum"/>
       <param name="user_mod_file" argument="-user_mod_file" type="data" format="txt" optional="true" label="Specify name of user-defined modifications file" help="Default is &quot;spectrast.usermods&quot; select txt data sets(s)"/>
-      <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>
@@ -119,6 +118,6 @@
   <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable
 
 
-For more information, visit http://www.openms.de/documentation/UTILS_SpectraSTSearchAdapter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SpectraSTSearchAdapter.html]]></help>
   <expand macro="references"/>
 </tool>