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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FileMerger" name="FileMerger" version="1.12.0">
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3 <description>Merges several MS files into one file.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">FileMerger</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>FileMerger
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11
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12 -in ${param_in}
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13 -in_type ${param_in_type}
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14 -out ${param_out}
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15 ${param_annotate_file_origin}
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16 -threads \${GALAXY_SLOTS:-24}
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17 ${param_rt_auto}
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18 -raw:rt_custom ${param_rt_custom}
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19 ${param_rt_filename}
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20 -raw:ms_level ${param_ms_level}
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21 ${param_user_ms_level}
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22 </command>
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23 <inputs>
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24 <param name="param_in" type="data" format="mzXML,mzML,mgf,featureXML,consensusXML" optional="False" size="20" label="Input files separated by blank" help="(-in)"/>
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25 <param name="param_in_type" type="select" optional="True" label="Input file type (default: determined from file extension or content)" help="(-in_type)">
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26 <option value="mzData">mzData</option>
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27 <option value="mzXML">mzXML</option>
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28 <option value="mzML">mzML</option>
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29 <option value="dta">dta</option>
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30 <option value="dta2d">dta2d</option>
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31 <option value="mgf">mgf</option>
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32 <option value="featureXML">featureXML</option>
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33 <option value="consensusXML">consensusXML</option>
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34 <option value="fid">fid</option>
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35 <option value="traML">traML</option>
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36 </param>
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37 <param name="param_annotate_file_origin" type="boolean" truevalue="-annotate_file_origin true" falsevalue="-annotate_file_origin false" checked="false" optional="True" label="Store the original filename in each feature using meta value "file_origin" (for featureXML and consensusXML only)." help="(-annotate_file_origin)"/>
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38 <param name="param_rt_auto" type="boolean" truevalue="-raw:rt_auto true" falsevalue="-raw:rt_auto false" checked="false" optional="True" label="Assign retention times automatically (integers starting at 1)" help="(-rt_auto)"/>
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39 <param name="param_rt_custom" type="text" size="20" value="0" label="List of custom retention times that are assigned to the files. The number of given retention times must be equal to the number of given input file." help="(-rt_custom)"/>
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40 <param name="param_rt_filename" type="boolean" truevalue="-raw:rt_filename true" falsevalue="-raw:rt_filename false" checked="false" optional="True" label="If this flag is set FileMerger tries to guess the rt of the file name.#br#This option is useful for merging DTA file, which should contain the string#br#'rt' directly followed by a floating point number:#br#i.e. my_spectrum_rt2795.15.dta" help="(-rt_filename)"/>
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41 <param name="param_ms_level" type="integer" value="2" label="This option is useful for use with DTA files which does not contain MS level information. The given level is assigned to the spectra." help="(-ms_level)"/>
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42 <param name="param_user_ms_level" type="boolean" truevalue="-raw:user_ms_level true" falsevalue="-raw:user_ms_level false" checked="false" optional="True" label="If this flag is set, the MS level given above is used" help="(-user_ms_level)"/>
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43 </inputs>
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44 <outputs>
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45 <data name="param_out" label="Output file" format="consensusXML">
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46 <change_format>
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47 <when input="param_out_type" value="mzML" format="mzML"/>
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48 <when input="param_out_type" value="featureXML" format="featureXML"/>
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49 </change_format>
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50 </data>
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51 </outputs>
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52 <help>**What it does**
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53
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54 Merges several MS files into one file.
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55
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56
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57 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html
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58
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59 @REFERENCES@
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60 </help>
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61 </tool>
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