diff MascotAdapter.xml @ 11:57fb2083a8cb draft

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

--- a/MascotAdapter.xml	Thu Sep 24 12:28:14 2020 +0000
+++ b/MascotAdapter.xml	Tue Oct 13 20:36:02 2020 +0000
@@ -29,10 +29,10 @@
 -in
 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
 -out
-'out/output.${gxy2omsext("idxml")}'
+'out/output.${out_type}'
 
 ## Postprocessing
-&& mv 'out/output.${gxy2omsext("idxml")}' '$out'
+&& mv 'out/output.${out_type}' '$out'
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
@@ -41,9 +41,12 @@
     <configfile name="hardcoded_json"><![CDATA[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="txt" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select txt data sets(s)"/>
-    <param name="mascot_in" argument="-mascot_in" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if this flag is set the MascotAdapter will read in mzData and write Mascot generic format" help=""/>
-    <param name="mascot_out" argument="-mascot_out" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if this flag is set the MascotAdapter will read in a Mascot results file (.mascotXML) and write idXML" help=""/>
+    <param name="in" argument="-in" type="data" format="mascotxml,mzdata" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/>
+    <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="output file type (for TOPPAS)" help="">
+      <option value="idXML">idxml</option>
+      <option value="mgf">mgf</option>
+      <expand macro="list_string_san"/>
+    </param>
     <param name="instrument" argument="-instrument" type="text" optional="true" value="Default" label="the instrument that was used to measure the spectra" help="">
       <expand macro="list_string_san"/>
     </param>
@@ -176,17 +179,22 @@
       <expand macro="list_string_san"/>
     </param>
     <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>
   <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
+    <data name="out" label="${tool.name} on ${on_string}: out">
+      <change_format>
+        <when input="out_type" value="idXML" format="idxml"/>
+        <when input="out_type" value="mgf" format="mgf"/>
+      </change_format>
+    </data>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
@@ -198,6 +206,6 @@
   <help><![CDATA[Annotates MS/MS spectra using Mascot.
 
 
-For more information, visit http://www.openms.de/documentation/TOPP_MascotAdapter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MascotAdapter.html]]></help>
   <expand macro="references"/>
 </tool>