--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ctd/FileMerger.ctd	Sun Dec 13 15:03:50 2020 +0000
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool ctdVersion="1.7" version="2.6.0-pre-exported-20201001" name="FileMerger" docurl="http://www.openms.de/documentation/TOPP_FileMerger.html" category="File Handling" >
+<description><![CDATA[Merges several MS files into one file.]]></description>
+<manual><![CDATA[Merges several MS files into one file.]]></manual>
+<citations>
+  <citation doi="10.1038/nmeth.3959" url="" />
+</citations>
+<PARAMETERS version="1.7.0" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_7_0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <NODE name="FileMerger" description="Merges several MS files into one file.">
+    <ITEM name="version" value="2.6.0-pre-exported-20201001" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
+    <NODE name="1" description="Instance &apos;1&apos; section for &apos;FileMerger&apos;">
+      <ITEMLIST name="in" type="input-file" description="Input files separated by blank" required="true" advanced="false" supported_formats="*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.fid,*.traML,*.fasta">
+      </ITEMLIST>
+      <ITEM name="in_type" value="" type="string" description="Input file type (default: determined from file extension or content)" required="false" advanced="false" restrictions="mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,fid,traML,fasta" />
+      <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML,*.traML,*.fasta" />
+      <ITEM name="annotate_file_origin" value="false" type="bool" description="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)." required="false" advanced="false" />
+      <ITEM name="append_method" value="append_rows" type="string" description="Append consensusMaps rowise or colwise. (Please use colwise for the MSstatsConverter)" required="false" advanced="false" restrictions="append_rows,append_cols" />
+      <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
+      <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
+      <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
+      <ITEM name="no_progress" value="false" type="bool" description="Disables progress logging to command line" required="false" advanced="true" />
+      <ITEM name="force" value="false" type="bool" description="Overrides tool-specific checks" required="false" advanced="true" />
+      <ITEM name="test" value="false" type="bool" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" />
+      <NODE name="rt_concat" description="Options for concatenating files in the retention time (RT) dimension. The RT ranges of inputs are adjusted so they don&apos;t overlap in the merged file (traML input not supported)">
+        <ITEM name="gap" value="0.0" type="double" description="The amount of gap (in seconds) to insert between the RT ranges of different input files. RT concatenation is enabled if a value &gt; 0 is set." required="false" advanced="false" />
+        <ITEMLIST name="trafo_out" type="output-file" description="Output of retention time transformations that were applied to the input files to produce non-overlapping RT ranges. If used, one output file per input file is required." required="false" advanced="false" supported_formats="*.trafoXML">
+        </ITEMLIST>
+      </NODE>
+      <NODE name="raw" description="Options for raw data input/output (primarily for DTA files)">
+        <ITEM name="rt_auto" value="false" type="bool" description="Assign retention times automatically (integers starting at 1)" required="false" advanced="false" />
+        <ITEMLIST name="rt_custom" type="double" description="List of custom retention times that are assigned to the files. The number of given retention times must be equal to the number of input files." required="false" advanced="false">
+        </ITEMLIST>
+        <ITEM name="rt_filename" value="false" type="bool" description="Try to guess the retention time of a file based on the filename. This option is useful for merging DTA files, where filenames should contain the string &apos;rt&apos; directly followed by a floating point number, e.g. &apos;my_spectrum_rt2795.15.dta&apos;" required="false" advanced="false" />
+        <ITEM name="ms_level" value="0" type="int" description="If 1 or higher, this number is assigned to spectra as the MS level. This option is useful for DTA files which do not contain MS level information." required="false" advanced="false" />
+      </NODE>
+    </NODE>
+  </NODE>
+</PARAMETERS>
+</tool>