Mercurial > repos > galaxyp > openms_idposteriorerrorprobability

comparison test-data/examples/TOPPAS/merger_tutorial.toppas @ 18:6daaa75ccb99 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
author galaxyp
date Sun, 13 Dec 2020 15:03:50 +0000
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17:6f6c1cb968a0 18:6daaa75ccb99
1 <?xml version="1.0" encoding="ISO-8859-1"?>
2 <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
3 <NODE name="info" description="">
4 <ITEM name="version" value="2.0.1" type="string" description="" required="false" advanced="false" />
5 <ITEM name="num_vertices" value="16" type="int" description="" required="false" advanced="false" />
6 <ITEM name="num_edges" value="15" type="int" description="" required="false" advanced="false" />
7 <ITEM name="description" value="&lt;![CDATA[&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
8 &lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
9 p, li { white-space: pre-wrap; }
10 &lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:&apos;Arial&apos;; font-size:12pt; font-weight:400; font-style:normal;&quot;&gt;
11 &lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt; &lt;/p&gt;
12 &lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; color:#000000;&quot;&gt;A dummy workflow demonstrating how merger and collector nodes work.&lt;/span&gt;&lt;/p&gt;
13 &lt;p style=&quot;-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; color:#000000;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
14 &lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; color:#000000;&quot;&gt;In order to track what is happening, just run the pipeline. When the execution has finished, have a look at all input and output files (e.g., select &amp;quot;Open files in TOPPView&amp;quot; in the context menu of the input/output nodes). The input files are named rt_1.mzML, rt_2.mzML, ... and each contains a single spectrum with RT as indicated by the filename, so you can easily see which files have been merged together.&lt;/span&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;]]&gt;" type="string" description="" required="false" advanced="false" />
15 </NODE>
16 <NODE name="vertices" description="">
17 <NODE name="0" description="">
18 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
19 <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" />
20 <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false">
21 <LISTITEM value="data/merger_tutorial/rt_1.mzML"/>
22 <LISTITEM value="data/merger_tutorial/rt_2.mzML"/>
23 <LISTITEM value="data/merger_tutorial/rt_3.mzML"/>
24 </ITEMLIST>
25 <ITEM name="x_pos" value="-480" type="double" description="" required="false" advanced="false" />
26 <ITEM name="y_pos" value="-260" type="double" description="" required="false" advanced="false" />
27 </NODE>
28 <NODE name="8" description="">
29 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
30 <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
31 <ITEM name="tool_name" value="FileMerger" type="string" description="" required="false" advanced="false" />
32 <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
33 <ITEM name="x_pos" value="-160" type="double" description="" required="false" advanced="false" />
34 <ITEM name="y_pos" value="60" type="double" description="" required="false" advanced="false" />
35 <NODE name="parameters" description="">
36 <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">
37 </ITEMLIST>
38 <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" />
39 <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML,*.traML" />
40 <ITEM name="annotate_file_origin" value="false" type="string" description="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)." required="false" advanced="false" restrictions="true,false" />
41 <ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
42 <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
43 <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" />
44 <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" />
45 <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
46 <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
47 <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)">
48 <ITEM name="gap" value="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" />
49 <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">
50 </ITEMLIST>
51 </NODE>
52 <NODE name="raw" description="Options for raw data input/output (primarily for DTA files)">
53 <ITEM name="rt_auto" value="false" type="string" description="Assign retention times automatically (integers starting at 1)" required="false" advanced="false" restrictions="true,false" />
54 <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">
55 </ITEMLIST>
56 <ITEM name="rt_filename" value="false" type="string" 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" restrictions="true,false" />
57 <ITEM name="ms_level" value="1" 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" />
58 </NODE>
59 </NODE>
60 </NODE>
61 <NODE name="5" description="">
62 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
63 <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" />
64 <ITEM name="x_pos" value="-320" type="double" description="" required="false" advanced="false" />
65 <ITEM name="y_pos" value="60" type="double" description="" required="false" advanced="false" />
66 <ITEM name="round_based" value="true" type="string" description="" required="false" advanced="false" />
67 </NODE>
68 <NODE name="1" description="">
69 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
70 <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" />
71 <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false">
72 <LISTITEM value="data/merger_tutorial/rt_4.mzML"/>
73 <LISTITEM value="data/merger_tutorial/rt_5.mzML"/>
74 <LISTITEM value="data/merger_tutorial/rt_6.mzML"/>
75 </ITEMLIST>
76 <ITEM name="x_pos" value="-480" type="double" description="" required="false" advanced="false" />
77 <ITEM name="y_pos" value="-140" type="double" description="" required="false" advanced="false" />
78 </NODE>
79 <NODE name="2" description="">
80 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
81 <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" />
82 <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false">
83 <LISTITEM value="data/merger_tutorial/rt_10.mzML"/>
84 <LISTITEM value="data/merger_tutorial/rt_11.mzML"/>
85 <LISTITEM value="data/merger_tutorial/rt_12.mzML"/>
86 </ITEMLIST>
87 <ITEM name="x_pos" value="-480" type="double" description="" required="false" advanced="false" />
88 <ITEM name="y_pos" value="60" type="double" description="" required="false" advanced="false" />
89 </NODE>
90 <NODE name="9" description="">
91 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
92 <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" />
93 <ITEM name="x_pos" value="0" type="double" description="" required="false" advanced="false" />
94 <ITEM name="y_pos" value="-40" type="double" description="" required="false" advanced="false" />
95 <ITEM name="round_based" value="true" type="string" description="" required="false" advanced="false" />
96 </NODE>
97 <NODE name="10" description="">
98 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
99 <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
100 <ITEM name="tool_name" value="FileMerger" type="string" description="" required="false" advanced="false" />
101 <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
102 <ITEM name="x_pos" value="160" type="double" description="" required="false" advanced="false" />
103 <ITEM name="y_pos" value="-40" type="double" description="" required="false" advanced="false" />
104 <NODE name="parameters" description="">
105 <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">
106 </ITEMLIST>
107 <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" />
108 <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML,*.traML" />
109 <ITEM name="annotate_file_origin" value="false" type="string" description="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)." required="false" advanced="false" restrictions="true,false" />
110 <ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
111 <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
112 <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" />
113 <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" />
114 <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
115 <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
116 <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)">
117 <ITEM name="gap" value="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" />
118 <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">
119 </ITEMLIST>
120 </NODE>
121 <NODE name="raw" description="Options for raw data input/output (primarily for DTA files)">
122 <ITEM name="rt_auto" value="false" type="string" description="Assign retention times automatically (integers starting at 1)" required="false" advanced="false" restrictions="true,false" />
123 <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">
124 </ITEMLIST>
125 <ITEM name="rt_filename" value="false" type="string" 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" restrictions="true,false" />
126 <ITEM name="ms_level" value="1" 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" />
127 </NODE>
128 </NODE>
129 </NODE>
130 <NODE name="11" description="">
131 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
132 <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" />
133 <ITEM name="x_pos" value="320" type="double" description="" required="false" advanced="false" />
134 <ITEM name="y_pos" value="-40" type="double" description="" required="false" advanced="false" />
135 <ITEM name="round_based" value="false" type="string" description="" required="false" advanced="false" />
136 </NODE>
137 <NODE name="15" description="">
138 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
139 <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" />
140 <ITEM name="x_pos" value="480" type="double" description="" required="false" advanced="false" />
141 <ITEM name="y_pos" value="120" type="double" description="" required="false" advanced="false" />
142 <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" />
143 </NODE>
144 <NODE name="3" description="">
145 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
146 <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" />
147 <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false">
148 <LISTITEM value="data/merger_tutorial/rt_7.mzML"/>
149 <LISTITEM value="data/merger_tutorial/rt_8.mzML"/>
150 <LISTITEM value="data/merger_tutorial/rt_9.mzML"/>
151 </ITEMLIST>
152 <ITEM name="x_pos" value="-480" type="double" description="" required="false" advanced="false" />
153 <ITEM name="y_pos" value="180" type="double" description="" required="false" advanced="false" />
154 </NODE>
155 <NODE name="6" description="">
156 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
157 <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
158 <ITEM name="tool_name" value="FileMerger" type="string" description="" required="false" advanced="false" />
159 <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
160 <ITEM name="x_pos" value="-160" type="double" description="" required="false" advanced="false" />
161 <ITEM name="y_pos" value="-140" type="double" description="" required="false" advanced="false" />
162 <NODE name="parameters" description="">
163 <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">
164 </ITEMLIST>
165 <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" />
166 <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML,*.traML" />
167 <ITEM name="annotate_file_origin" value="false" type="string" description="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)." required="false" advanced="false" restrictions="true,false" />
168 <ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
169 <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
170 <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" />
171 <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" />
172 <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
173 <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
174 <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)">
175 <ITEM name="gap" value="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" />
176 <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">
177 </ITEMLIST>
178 </NODE>
179 <NODE name="raw" description="Options for raw data input/output (primarily for DTA files)">
180 <ITEM name="rt_auto" value="false" type="string" description="Assign retention times automatically (integers starting at 1)" required="false" advanced="false" restrictions="true,false" />
181 <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">
182 </ITEMLIST>
183 <ITEM name="rt_filename" value="false" type="string" 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" restrictions="true,false" />
184 <ITEM name="ms_level" value="1" 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" />
185 </NODE>
186 </NODE>
187 </NODE>
188 <NODE name="12" description="">
189 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
190 <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" />
191 <ITEM name="x_pos" value="160" type="double" description="" required="false" advanced="false" />
192 <ITEM name="y_pos" value="120" type="double" description="" required="false" advanced="false" />
193 <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" />
194 </NODE>
195 <NODE name="13" description="">
196 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
197 <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
198 <ITEM name="tool_name" value="FileMerger" type="string" description="" required="false" advanced="false" />
199 <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
200 <ITEM name="x_pos" value="480" type="double" description="" required="false" advanced="false" />
201 <ITEM name="y_pos" value="-40" type="double" description="" required="false" advanced="false" />
202 <NODE name="parameters" description="">
203 <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">
204 </ITEMLIST>
205 <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" />
206 <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML,*.traML" />
207 <ITEM name="annotate_file_origin" value="false" type="string" description="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)." required="false" advanced="false" restrictions="true,false" />
208 <ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
209 <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
210 <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" />
211 <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" />
212 <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
213 <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
214 <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)">
215 <ITEM name="gap" value="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" />
216 <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">
217 </ITEMLIST>
218 </NODE>
219 <NODE name="raw" description="Options for raw data input/output (primarily for DTA files)">
220 <ITEM name="rt_auto" value="false" type="string" description="Assign retention times automatically (integers starting at 1)" required="false" advanced="false" restrictions="true,false" />
221 <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">
222 </ITEMLIST>
223 <ITEM name="rt_filename" value="false" type="string" 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" restrictions="true,false" />
224 <ITEM name="ms_level" value="1" 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" />
225 </NODE>
226 </NODE>
227 </NODE>
228 <NODE name="7" description="">
229 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
230 <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" />
231 <ITEM name="x_pos" value="-160" type="double" description="" required="false" advanced="false" />
232 <ITEM name="y_pos" value="-260" type="double" description="" required="false" advanced="false" />
233 <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" />
234 </NODE>
235 <NODE name="14" description="">
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