diff IDFileConverter.xml @ 12:eb48359e371b draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

--- a/IDFileConverter.xml	Mon Feb 12 08:55:44 2018 -0500
+++ b/IDFileConverter.xml	Wed May 15 06:44:45 2019 -0400
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [ID Processing]-->
-<tool id="IDFileConverter" name="IDFileConverter" version="2.2.0">
+<tool id="IDFileConverter" name="IDFileConverter" version="2.3.0">
   <description>Converts identification engine file formats.</description>
   <macros>
     <token name="@EXECUTABLE@">IDFileConverter</token>
@@ -10,19 +10,19 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command><![CDATA[
+ <command detect_errors="aggressive"><![CDATA[
 
-## check input file type
-#set $in_type = $param_in.ext
+   ## check input file type
+   #set $in_type = $param_in.ext
 
-## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
-ln -s '$param_in' 'param_in.${in_type}' &&
+   ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
+   ln -s '$param_in' 'param_in.${in_type}' &&
 
-IDFileConverter
+   IDFileConverter
 
-#if $param_in:
-  -in 'param_in.${in_type}'
-#end if
+   #if $param_in:
+     -in 'param_in.${in_type}'
+   #end if
 #if $param_out:
   -out $param_out
 #end if
@@ -61,6 +61,9 @@
     #if $adv_opts.param_no_spectra_data_override:
   -no_spectra_data_override
 #end if
+    #if $adv_opts.param_add_ionmatch_annotation:
+  -add_ionmatch_annotation $adv_opts.param_add_ionmatch_annotation
+#end if
     #if $adv_opts.param_force:
   -force
 #end if
@@ -101,6 +104,7 @@
         </sanitizer>
       </param>
       <param name="param_no_spectra_data_override" display="radio" type="boolean" truevalue="-no_spectra_data_override" falsevalue="" checked="false" optional="True" label="[+mz_file only] Setting this flag will avoid overriding 'spectra_data' in ProteinIdentifications if mz_file is given and 'spectrum_reference's are added/updated" help="(-no_spectra_data_override) Use only if you are sure it is absolutely the same mz_file as used for identification"/>
+      <param name="param_add_ionmatch_annotation" type="float" value="0.0" label="[+mz_file only] Will annotate the contained identifications with their matches in the given mz_file" help="(-add_ionmatch_annotation) Will take quite some while. Match tolerance is .4"/>
       <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
     </expand>
   </inputs>
@@ -110,5 +114,5 @@
   <help>Converts identification engine file formats.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_IDFileConverter.html</help>
 </tool>