Mercurial > repos > galaxyp > openms_idposteriorerrorprobability

annotate 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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18
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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1 <?xml version="1.0" encoding="ISO-8859-1"?>
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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">
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3 <NODE name="info" description="">
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4 <ITEM name="version" value="2.0.1" type="string" description="" required="false" advanced="false" />
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5 <ITEM name="num_vertices" value="16" type="int" description="" required="false" advanced="false" />
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6 <ITEM name="num_edges" value="15" type="int" description="" required="false" advanced="false" />
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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;
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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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;
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9 p, li { white-space: pre-wrap; }
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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;
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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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;
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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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;
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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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;
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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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" />
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15 </NODE>
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16 <NODE name="vertices" description="">
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17 <NODE name="0" description="">
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18 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
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19 <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" />
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20 <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false">
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21 <LISTITEM value="data/merger_tutorial/rt_1.mzML"/>
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22 <LISTITEM value="data/merger_tutorial/rt_2.mzML"/>
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23 <LISTITEM value="data/merger_tutorial/rt_3.mzML"/>
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24 </ITEMLIST>
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25 <ITEM name="x_pos" value="-480" type="double" description="" required="false" advanced="false" />
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26 <ITEM name="y_pos" value="-260" type="double" description="" required="false" advanced="false" />
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27 </NODE>
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28 <NODE name="8" description="">
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29 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
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30 <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
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31 <ITEM name="tool_name" value="FileMerger" type="string" description="" required="false" advanced="false" />
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32 <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
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33 <ITEM name="x_pos" value="-160" type="double" description="" required="false" advanced="false" />
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34 <ITEM name="y_pos" value="60" type="double" description="" required="false" advanced="false" />
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35 <NODE name="parameters" description="">
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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">
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37 </ITEMLIST>
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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" />
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39 <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML,*.traML" />
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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" />
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41 <ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
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42 <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
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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" />
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44 <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" />
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45 <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
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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" />
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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)">
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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" />
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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">
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50 </ITEMLIST>
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51 </NODE>
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52 <NODE name="raw" description="Options for raw data input/output (primarily for DTA files)">
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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" />
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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">
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55 </ITEMLIST>
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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" />
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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" />
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58 </NODE>
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59 </NODE>
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60 </NODE>
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61 <NODE name="5" description="">
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62 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
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63 <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" />
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64 <ITEM name="x_pos" value="-320" type="double" description="" required="false" advanced="false" />
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65 <ITEM name="y_pos" value="60" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
66 <ITEM name="round_based" value="true" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
67 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
68 <NODE name="1" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
69 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
70 <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
71 <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
72 <LISTITEM value="data/merger_tutorial/rt_4.mzML"/>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
73 <LISTITEM value="data/merger_tutorial/rt_5.mzML"/>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
74 <LISTITEM value="data/merger_tutorial/rt_6.mzML"/>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
75 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
76 <ITEM name="x_pos" value="-480" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
77 <ITEM name="y_pos" value="-140" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
78 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
79 <NODE name="2" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
80 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
81 <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
82 <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
83 <LISTITEM value="data/merger_tutorial/rt_10.mzML"/>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
84 <LISTITEM value="data/merger_tutorial/rt_11.mzML"/>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
85 <LISTITEM value="data/merger_tutorial/rt_12.mzML"/>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
86 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
87 <ITEM name="x_pos" value="-480" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
88 <ITEM name="y_pos" value="60" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
89 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
90 <NODE name="9" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
91 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
92 <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
93 <ITEM name="x_pos" value="0" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
94 <ITEM name="y_pos" value="-40" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
95 <ITEM name="round_based" value="true" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
96 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
97 <NODE name="10" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
98 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
99 <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
100 <ITEM name="tool_name" value="FileMerger" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
101 <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
102 <ITEM name="x_pos" value="160" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
103 <ITEM name="y_pos" value="-40" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
104 <NODE name="parameters" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
106 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
108 <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML,*.traML" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
110 <ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
111 <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
113 <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
114 <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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)">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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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">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
119 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
120 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
121 <NODE name="raw" description="Options for raw data input/output (primarily for DTA files)">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
124 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
127 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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diff changeset
128 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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diff changeset
129 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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130 <NODE name="11" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
131 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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132 <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
133 <ITEM name="x_pos" value="320" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
134 <ITEM name="y_pos" value="-40" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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135 <ITEM name="round_based" value="false" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
136 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
137 <NODE name="15" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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138 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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139 <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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140 <ITEM name="x_pos" value="480" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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141 <ITEM name="y_pos" value="120" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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142 <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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143 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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144 <NODE name="3" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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145 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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146 <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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147 <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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148 <LISTITEM value="data/merger_tutorial/rt_7.mzML"/>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
149 <LISTITEM value="data/merger_tutorial/rt_8.mzML"/>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
150 <LISTITEM value="data/merger_tutorial/rt_9.mzML"/>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
151 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
152 <ITEM name="x_pos" value="-480" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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153 <ITEM name="y_pos" value="180" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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154 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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155 <NODE name="6" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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156 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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157 <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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158 <ITEM name="tool_name" value="FileMerger" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
159 <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
160 <ITEM name="x_pos" value="-160" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
161 <ITEM name="y_pos" value="-140" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
162 <NODE name="parameters" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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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">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
164 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
166 <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML,*.traML" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
168 <ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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169 <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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171 <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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172 <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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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)">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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parents:
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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">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
177 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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diff changeset
178 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
179 <NODE name="raw" description="Options for raw data input/output (primarily for DTA files)">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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parents:
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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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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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">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
182 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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diff changeset
185 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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186 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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diff changeset
187 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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188 <NODE name="12" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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189 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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190 <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
191 <ITEM name="x_pos" value="160" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
192 <ITEM name="y_pos" value="120" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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193 <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
194 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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195 <NODE name="13" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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196 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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197 <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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198 <ITEM name="tool_name" value="FileMerger" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
199 <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
200 <ITEM name="x_pos" value="480" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
201 <ITEM name="y_pos" value="-40" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
202 <NODE name="parameters" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
204 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
206 <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML,*.traML" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
208 <ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
209 <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
211 <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
212 <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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)">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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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">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
217 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
218 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
219 <NODE name="raw" description="Options for raw data input/output (primarily for DTA files)">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
222 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
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" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
225 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
226 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
227 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
228 <NODE name="7" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
229 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
230 <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
231 <ITEM name="x_pos" value="-160" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
232 <ITEM name="y_pos" value="-260" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
233 <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
234 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
235 <NODE name="14" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
236 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
237 <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
238 <ITEM name="x_pos" value="-160" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
239 <ITEM name="y_pos" value="180" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
240 <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
241 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
242 <NODE name="4" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
243 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
244 <ITEM name="toppas_type" value="merger" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
245 <ITEM name="x_pos" value="-320" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
246 <ITEM name="y_pos" value="-140" type="double" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
247 <ITEM name="round_based" value="true" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
248 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
249 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
250 <NODE name="edges" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
251 <NODE name="0" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
252 <NODE name="source/target" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
253 <ITEM name="" value="8/9" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
254 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
255 <NODE name="source_out_param" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
256 <ITEM name="" value="out" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
257 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
258 <NODE name="target_in_param" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
259 <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
260 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
261 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
262 <NODE name="1" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
263 <NODE name="source/target" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
264 <ITEM name="" value="10/11" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
265 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
266 <NODE name="source_out_param" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
267 <ITEM name="" value="out" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
268 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
269 <NODE name="target_in_param" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
270 <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
271 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
272 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
273 <NODE name="2" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
274 <NODE name="source/target" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
275 <ITEM name="" value="3/5" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
276 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
277 <NODE name="source_out_param" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
278 <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
279 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
280 <NODE name="target_in_param" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
281 <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
282 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
283 </NODE>
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diff changeset
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diff changeset
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417 </PARAMETERS>