Mercurial > repos > galaxyp > openms_idposteriorerrorprobability

annotate test-data/examples/TOPPAS/Ecoli_Identification.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="1.11.0" type="string" description="" required="false" advanced="false" />
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5 <ITEM name="num_vertices" value="8" type="int" description="" required="false" advanced="false" />
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6 <ITEM name="num_edges" value="8" 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; &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; p, li { white-space: pre-wrap; } &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; &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 simple identification workflow.&lt;/span&gt;&lt;/p&gt; &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;/p&gt; &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;This workflow requires OMSSA to be installed on your machine. The path to the OMSSA executable (&amp;quot;omssacl&amp;quot;) must be set in the parameters of the OMSSAAdapter node.&lt;/span&gt;&lt;/p&gt; &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;/p&gt; &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;Node #1 accepts mzML files containing MS2 spectra.&lt;/span&gt;&lt;/p&gt; &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;/p&gt; &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;Node #2 provides the database and is set to &amp;quot;recycling mode&amp;quot; to allow the database to be reused when there is more than one input file in node #1.&lt;/span&gt;&lt;/p&gt; &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;/p&gt; &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;OMSSAAdapter calls OMSSA which performs the actual search.&lt;/span&gt;&lt;/p&gt; &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;/p&gt; &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;PeptideIndexer annotates for each search result whether it is a target or a decoy hit.&lt;/span&gt;&lt;/p&gt; &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;/p&gt; &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;FalseDiscoveryRate computes q-values for the IDs.&lt;/span&gt;&lt;/p&gt; &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;/p&gt; &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;Finally, IDFilter selects only those IDs with a q-value of less than 0.01.&lt;/span&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;]]&gt;" 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"
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8 </NODE>
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9 <NODE name="vertices" description="">
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10 <NODE name="0" description="">
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11 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
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12 <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"
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13 <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false">
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14 <LISTITEM value="../ID/Ecoli_MS2_small.mzML"/>
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15 </ITEMLIST>
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16 <ITEM name="x_pos" value="-100" type="double" description="" required="false" advanced="false" />
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17 <ITEM name="y_pos" value="120" type="double" description="" required="false" advanced="false" />
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18 </NODE>
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19 <NODE name="3" description="">
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20 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
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21 <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
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22 <ITEM name="tool_name" value="PeptideIndexer" type="string" description="" required="false" advanced="false" />
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23 <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" />
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24 <ITEM name="x_pos" value="100" type="double" description="" required="false" advanced="false" />
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25 <ITEM name="y_pos" value="-40" type="double" description="" required="false" advanced="false" />
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26 <NODE name="parameters" description="">
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27 <ITEM name="in" value="" type="input-file" description="Input idXML file containing the identifications." required="true" advanced="false" supported_formats="*.idXML" />
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28 <ITEM name="fasta" value="" type="input-file" description="Input sequence database in FASTA format. Non-existing relative file-names are looked up via&apos;OpenMS.ini:id_db_dir&apos;" required="true" advanced="false" supported_formats="*.fasta" />
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29 <ITEM name="out" value="" type="output-file" description="Output idXML file." required="true" advanced="false" supported_formats="*.idXML" />
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30 <ITEM name="decoy_string" value="rev_" type="string" description="String that was appended (or prepended - see &apos;prefix&apos; flag below) to the accession of the protein database to indicate a decoy protein." required="false" advanced="false" />
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31 <ITEM name="missing_decoy_action" value="error" type="string" description="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): &apos;error&apos; (exit with error, no output), &apos;warn&apos; (exit with success, warning message)" required="false" advanced="false" restrictions="error,warn" />
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32 <ITEM name="write_protein_sequence" value="false" type="string" description="If set, the protein sequences are stored as well." required="false" advanced="false" restrictions="true,false" />
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33 <ITEM name="prefix" value="true" type="string" description="If set, the database has protein accessions with &apos;decoy_string&apos; as prefix." required="false" advanced="false" restrictions="true,false" />
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34 <ITEM name="keep_unreferenced_proteins" value="false" type="string" description="If set, protein hits which are not referenced by any peptide are kept." required="false" advanced="false" restrictions="true,false" />
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35 <ITEM name="allow_unmatched" value="false" type="string" description="If set, unmatched peptide sequences are allowed. By default (i.e. this flag is not set) the program terminates with error status on unmatched peptides." required="false" advanced="false" restrictions="true,false" />
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36 <ITEM name="full_tolerant_search" value="false" type="string" description="If set, all peptide sequences are matched using tolerant search. Thus potentially more proteins (containing ambiguous AA&apos;s) are associated. This is much slower!" required="false" advanced="false" restrictions="true,false" />
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37 <ITEM name="aaa_max" value="4" type="int" description="Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein DB with AAA&apos;s. AAA&apos;s are &apos;B&apos;, &apos;Z&apos;, and &apos;X&apos;" required="false" advanced="false" restrictions="0:" />
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38 <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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39 <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
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40 <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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41 <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
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42 <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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43 <NODE name="enzyme" description="The enzyme determines valid cleavage-sites and the cleavage specificity set by the user determines how these are enforced.">
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44 <ITEM name="name" value="Trypsin" type="string" description="Enzyme which determines valid cleavage sites, e.g., for trypsin it should (unless at protein terminus) end on K or R and the AA-before should also be K or R, and not followed by proline." required="false" advanced="false" restrictions="Trypsin" />
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45 <ITEM name="specificity" value="full" type="string" description="Specificity of the enzyme.#br# &apos;full&apos;: both internal cleavage-sites must match.#br# &apos;semi&apos;: one of two internal cleavage-sites must match.#br# &apos;none&apos;: allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here" required="false" advanced="false" restrictions="full,semi,none" />
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46 </NODE>
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47 </NODE>
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48 </NODE>
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49 <NODE name="4" description="">
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50 <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" />
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51 <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" />
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52 <ITEM name="tool_name" value="FalseDiscoveryRate" type="string" description="" required="false" advanced="false" />
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53 <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
54 <ITEM name="x_pos" value="300" 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
55 <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
56 <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
57 <ITEM name="in" value="" type="input-file" description="Identification input file which contains a search against a concatenated sequence database. Either specify &apos;-in&apos; alone or &apos;fwd_in&apos; together with &apos;rev_in&apos; as input." required="false" advanced="false" supported_formats="*.idXML" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
58 <ITEM name="fwd_in" value="" type="input-file" description="Identification input to estimate FDR, forward run." required="false" advanced="false" supported_formats="*.idXML" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
59 <ITEM name="rev_in" value="" type="input-file" description="Identification input to estimate FDR, decoy run." required="false" advanced="false" supported_formats="*.idXML" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
60 <ITEM name="out" value="" type="output-file" description="Identification output with annotated FDR" required="true" advanced="false" supported_formats="*.idXML" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
61 <ITEM name="proteins_only" value="false" type="string" description="If set, the FDR of the proteins only is calculated" 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
62 <ITEM name="peptides_only" value="false" type="string" description="If set, the FDR of the peptides only is calculated" 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
63 <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
64 <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
65 <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
66 <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" 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
67 <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
68 <NODE name="algorithm" description="Parameter section for the FDR calculation algorithm">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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69 <ITEM name="q_value" value="true" type="string" description="If &apos;true&apos;, the q-values will be calculated instead of the FDRs" 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
70 <ITEM name="use_all_hits" value="false" type="string" description="If &apos;true&apos; not only the first hit, but all are used (peptides 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
71 <ITEM name="split_charge_variants" value="false" type="string" description="If set to &apos;true&apos; charge variants are treated separately (for peptides of combined target/decoy searches 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
72 <ITEM name="treat_runs_separately" value="false" type="string" description="If set to &apos;true&apos; different search runs are treated separately (for peptides of combined target/decoy searches 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
73 <ITEM name="decoy_string" value="_rev" type="string" description="String which is appended at the accession of the protein to indicate that it is a decoy protein (for proteins only)." 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
74 <ITEM name="add_decoy_peptides" value="false" type="string" description="If set to true, decoy peptides will be written to output file, too. The q-value is set to the closest target score." 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
75 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
76 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
77 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
78 <NODE name="5" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
79 <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
80 <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
81 <ITEM name="tool_name" value="IDFilter" 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 <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
83 <ITEM name="x_pos" value="500" 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
84 <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
85 <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
86 <ITEM name="in" value="" type="input-file" description="input file " required="true" advanced="false" supported_formats="*.idXML" />
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="out" value="" type="output-file" description="output file " required="true" advanced="false" supported_formats="*.idXML" />
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="min_length" value="6" type="int" description="Keep only peptide hits with a length greater or equal this value. Value 0 will have no filter effect." required="false" advanced="false" restrictions="0:" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
89 <ITEM name="max_length" value="0" type="int" description="Keep only peptide hits with a length less or equal this value. Value 0 will have no filter effect. Value is overridden by min_length, i.e. if max_length &lt; min_length, max_length will be ignored." required="false" advanced="false" restrictions=":0" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
90 <ITEM name="min_charge" value="1" type="int" description="Keep only peptide hits for tandem spectra with charge greater or equal this value." required="false" advanced="false" restrictions="1:" />
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="var_mods" value="false" type="string" description="Keep only peptide hits with variable modifications (fixed modifications from SearchParameters will be ignored)." 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
92 <ITEM name="unique" value="false" type="string" description="If a peptide hit occurs more than once per PSM, only one instance is kept." 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
93 <ITEM name="unique_per_protein" value="false" type="string" description="Only peptides matching exactly one protein are kept. Remember that isoforms count as different proteins!" 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
94 <ITEM name="keep_unreferenced_protein_hits" value="false" type="string" description="Proteins not referenced by a peptide are retained in the idXML." 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
95 <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
96 <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
97 <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"
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parents:
diff changeset
98 <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" 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
99 <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"
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parents:
diff changeset
100 <NODE name="score" description="Filtering by peptide/protein score. To enable any of the filters below, just change their default value. All active filters will be applied in order.">
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="pep" value="0.01" type="double" description="The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc." 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:
diff changeset
102 <ITEM name="prot" value="0" type="double" description="The score which should be reached by a protein hit to be kept." 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 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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parents:
diff changeset
104 <NODE name="thresh" description="Filtering by significance threshold">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
105 <ITEM name="pep" value="0" type="double" description="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold." 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
106 <ITEM name="prot" value="0" type="double" description="Keep a protein hit only if its score is above this fraction of the protein significance threshold." 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
107 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
108 <NODE name="whitelist" description="Filtering by whitelisting (only instances also present in a whitelist file can pass)">
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="proteins" value="" type="input-file" description="filename of a FASTA file containing protein sequences.#br#All peptides that are not a substring of a sequence in this file are removed#br#All proteins whose accession is not present in this file are removed." required="false" advanced="false" supported_formats="*.fasta" />
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="by_seq_only" value="false" type="string" description="Match peptides with FASTA file by sequence instead of accession and disable protein filtering." 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
111 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
112 <NODE name="blacklist" description="Filtering by blacklisting (only instances not present in a blacklist file can pass)">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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113 <ITEM name="peptides" value="" type="input-file" description="Peptides having the same sequence as any peptide in this file will be filtered out#br#" required="false" advanced="false" supported_formats="*.idXML" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
114 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
115 <NODE name="rt" description="Filtering by RT predicted by &apos;RTPredict&apos;">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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116 <ITEM name="p_value" value="0" type="double" description="Retention time filtering by the p-value predicted by RTPredict." required="false" advanced="false" restrictions="0:1" />
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="p_value_1st_dim" value="0" type="double" description="Retention time filtering by the p-value predicted by RTPredict for first dimension." required="false" advanced="false" restrictions="0:1" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
118 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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119 <NODE name="mz" description="Filtering by mz">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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120 <ITEM name="error" value="-1" type="double" description="Filtering by deviation to theoretical mass (disabled for negative values)." 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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121 <ITEM name="unit" value="ppm" type="string" description="Absolute or relativ error." required="false" advanced="false" restrictions="Da,ppm" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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122 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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123 <NODE name="best" description="Filtering best hits per spectrum (for peptides) or from proteins">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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124 <ITEM name="n_peptide_hits" value="0" type="int" description="Keep only the &apos;n&apos; highest scoring peptide hits per spectrum (for n&gt;0)." required="false" advanced="false" restrictions="0:" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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125 <ITEM name="n_protein_hits" value="0" type="int" description="Keep only the &apos;n&apos; highest scoring protein hits (for n&gt;0)." required="false" advanced="false" restrictions="0:" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
126 <ITEM name="strict" value="false" type="string" description="Keep only the highest scoring peptide hit.#br#Similar to n_peptide_hits=1, but if there are two or more highest scoring hits, none are kept." 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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127 <ITEM name="n_to_m_peptide_hits" value=":" type="string" description="peptide hit rank range to extracts" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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128 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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129 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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130 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
131 <NODE name="1" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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132 <ITEM name="recycle_output" 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"
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133 <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"
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134 <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"
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135 <LISTITEM value="data/Identification/target_decoy_Ecoli_K12_TaxID_83333.proteomes.fasta"/>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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136 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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137 <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:
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138 <ITEM name="y_pos" value="-200" 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"
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139 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
140 <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
141 <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"
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142 <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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143 <ITEM name="tool_name" value="OMSSAAdapter" 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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144 <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"
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parents:
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145 <ITEM name="x_pos" value="-100" 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
146 <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"
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147 <NODE name="parameters" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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148 <ITEM name="in" value="" type="input-file" description="Input file " required="true" advanced="false" supported_formats="*.mzML" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
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149 <ITEM name="out" value="" type="output-file" description="Output file " required="true" advanced="false" supported_formats="*.idXML" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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150 <ITEM name="precursor_mass_tolerance" value="10" type="double" description="Precursor mass tolerance (Default: Dalton)" 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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151 <ITEM name="precursor_mass_tolerance_unit_ppm" value="true" type="string" description="If this flag is set, ppm is used as precursor mass tolerance unit" 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"
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parents:
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152 <ITEM name="fragment_mass_tolerance" value="0.5" type="double" description="Fragment mass error in Dalton" 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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153 <ITEM name="database" value="" type="input-file" description="NCBI formatted FASTA files. Only the .psq filename should be given, e.g. &apos;SwissProt.fasta.psq&apos;. If the filename does not end in &apos;.psq&apos; the suffix will be added automatically. Non-existing relative file-names are looked up via&apos;OpenMS.ini:id_db_dir&apos;" required="true" advanced="false" supported_formats="*.psq,*.fasta" />
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 <ITEM name="min_precursor_charge" value="2" type="int" description="Minimum precursor ion charge" 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
155 <ITEM name="max_precursor_charge" value="5" type="int" description="Maximum precursor ion charge" 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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156 <ITEMLIST name="fixed_modifications" type="string" description="Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. &apos;Carbamidomethyl (C)&apos; or &apos;Oxidation (M)&apos;" required="false" advanced="false" restrictions="15dB-biotin (C),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (E),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Ala-&gt;Asp (A),Ala-&gt;Glu (A),Ala-&gt;Gly (A),Ala-&gt;Pro (A),Ala-&gt;Ser (A),Ala-&gt;Thr (A),Ala-&gt;Val (A),Amidated (C-term),Amidine (K),Amidine (N-term),Amidino (C),Amino (Y),Ammonia-loss (N),Ammonia-loss (N-term C),Ammonium (C-term),Ammonium (D),Ammonium (E),Archaeol (C),Arg-&gt;Cys (R),Arg-&gt;Gln (R),Arg-&gt;GluSA (R),Arg-&gt;Gly (R),Arg-&gt;His (R),Arg-&gt;Ile (R),Arg-&gt;Lys (R),Arg-&gt;Met (R),Arg-&gt;Npo (R),Arg-&gt;Orn (R),Arg-&gt;Pro (R),Arg-&gt;Ser (R),Arg-&gt;Thr (R),Arg-&gt;Trp (R),Arg2PG (R),Argbiotinhydrazide (R),Asn-&gt;Asp (N),Asn-&gt;His (N),Asn-&gt;Ile (N),Asn-&gt;Lys (N),Asn-&gt;Ser (N),Asn-&gt;Thr (N),Asn-&gt;Tyr (N),Asp-&gt;Ala (D),Asp-&gt;Asn (D),Asp-&gt;Glu (D),Asp-&gt;Gly (D),Asp-&gt;His (D),Asp-&gt;Tyr (D),Asp-&gt;Val (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-PEO4-hydrazide (C-term),Biotin-maleimide (C),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromobimane (C),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_1 (K),CLIP_TRAQ_1 (N-term),CLIP_TRAQ_1 (Y),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),ChromoBiotin (K),CoenzymeA (C),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),CuSMo (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys-&gt;Arg (C),Cys-&gt;Dha (C),Cys-&gt;Gly (C),Cys-&gt;Oxoalanine (C),Cys-&gt;Phe (C),Cys-&gt;Ser (C),Cys-&gt;Trp (C),Cys-&gt;Tyr (C),Cys-&gt;ethylaminoAla (C),Cys-&gt;methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DNPS (C),DNPS (W),DTBP (K),DTBP (N),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),Dansyl (K),Dansyl (N-term),DeStreak (C),Deamidated (N),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),Dehydrated (D),Dehydrated (N-term C),Dehydrated (S),Dehydrated (T),Dehydrated (Y),Dehydro (C),Delta:H(1)O(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),Delta:H(2)C(3) (K),Delta:H(2)C(3)O(1) (K),Delta:H(2)C(3)O(1) (R),Delta:H(2)C(5) (K),Delta:H(4)C(2) (H),Delta:H(4)C(2) (K),Delta:H(4)C(2)O(-1)S(1) (S),Delta:H(4)C(3) (H),Delta:H(4)C(3) (K),Delta:H(4)C(3)O(1) (C),Delta:H(4)C(3)O(1) (H),Delta:H(4)C(3)O(1) (K),Delta:H(4)C(6) (K),Delta:H(5)C(2) (P),Delta:H(6)C(6)O(1) (K),Delta:H(8)C(6)O(2) (K),Delta:Hg(1) (C),Delta:S(-1)Se(1) (C),Delta:S(-1)Se(1) (M),Delta:Se(1) (C),Deoxy (D),Deoxy (S),Deoxy (T),Dethiomethyl (M),Diacylglycerol (C),Dibromo (Y),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Dihydroxyimidazolidine (R),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),EthylAmide (N),EthylAmide (Q),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),G-H1 (R),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),GalNAzBiotin (N),GalNAzBiotin (S),GalNAzBiotin (T),Galactosyl (K),GeranylGeranyl (C),Gln-&gt;Arg (Q),Gln-&gt;Glu (Q),Gln-&gt;His (Q),Gln-&gt;Leu (Q),Gln-&gt;Lys (Q),Gln-&gt;Pro (Q),Gln-&gt;pyro-Glu (N-term Q),Glu (E),Glu-&gt;Ala (E),Glu-&gt;Asp (E),Glu-&gt;Gln (E),Glu-&gt;Gly (E),Glu-&gt;Lys (E),Glu-&gt;Val (E),Glu-&gt;pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly-&gt;Ala (G),Gly-&gt;Arg (G),Gly-&gt;Asp (G),Gly-&gt;Cys (G),Gly-&gt;Glu (G),Gly-&gt;Ser (G),Gly-&gt;Trp (G),Gly-&gt;Val (G),Gly-loss+Amide (C-term G),GlyGly (C),GlyGly (K),GlyGly (S),GlyGly (T),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),HMVK (C),HNE (C),HNE (H),HNE (K),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His-&gt;Arg (H),His-&gt;Asn (H),His-&gt;Asp (H),His-&gt;Gln (H),His-&gt;Leu (H),His-&gt;Pro (H),His-&gt;Tyr (H),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Ile-&gt;Arg (I),Ile-&gt;Asn (I),Ile-&gt;Lys (I),Ile-&gt;Met (I),Ile-&gt;Phe (I),Ile-&gt;Ser (I),Ile-&gt;Thr (I),Ile-&gt;Val (I),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(4)15N(2)+GlyGly (K),Label:13C(5) (P),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GlyGly (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GlyGly (K),Label:13C(6)15N(4) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(3) (L),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GlyGly (K),Label:2H(9)13C(6)15N(2) (K),Leu-&gt;Arg (L),Leu-&gt;Gln (L),Leu-&gt;His (L),Leu-&gt;Met (L),Leu-&gt;MetOx (L),Leu-&gt;Phe (L),Leu-&gt;Pro (L),Leu-&gt;Ser (L),Leu-&gt;Trp (L),Leu-&gt;Val (L),LeuArgGlyGly (K),Lipoyl (K),Lys-&gt;Allysine (K),Lys-&gt;AminoadipicAcid (K),Lys-&gt;Arg (K),Lys-&gt;Asn (K),Lys-&gt;CamCys (K),Lys-&gt;Gln (K),Lys-&gt;Glu (K),Lys-&gt;Ile (K),Lys-&gt;Met (K),Lys-&gt;MetOx (K),Lys-&gt;Thr (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met-&gt;Aha (M),Met-&gt;Arg (M),Met-&gt;Hpg (M),Met-&gt;Hse (C-term M),Met-&gt;Hsl (C-term M),Met-&gt;Ile (M),Met-&gt;Leu (M),Met-&gt;Lys (M),Met-&gt;Thr (M),Met-&gt;Val (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (N),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Diethylphosphate (C),O-Diethylphosphate (H),O-Diethylphosphate (K),O-Diethylphosphate (S),O-Diethylphosphate (T),O-Diethylphosphate (Y),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Ethylphosphate (S),O-Ethylphosphate (T),O-Ethylphosphate (Y),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PGA1-biotin (C),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),PentylamineBiotin (Q),Phe-&gt;CamCys (F),Phe-&gt;Cys (F),Phe-&gt;Ile (F),Phe-&gt;Ser (F),Phe-&gt;Tyr (F),Phe-&gt;Val (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro-&gt;Ala (P),Pro-&gt;Arg (P),Pro-&gt;Gln (P),Pro-&gt;His (P),Pro-&gt;Leu (P),Pro-&gt;Pyrrolidinone (P),Pro-&gt;Pyrrolidone (P),Pro-&gt;Ser (P),Pro-&gt;Thr (P),Pro-&gt;pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Ser-&gt;Ala (S),Ser-&gt;Arg (S),Ser-&gt;Asn (S),Ser-&gt;Cys (S),Ser-&gt;Gly (S),Ser-&gt;Ile (S),Ser-&gt;Phe (S),Ser-&gt;Pro (S),Ser-&gt;Thr (S),Ser-&gt;Trp (S),Ser-&gt;Tyr (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (K),TMT (N-term),TMT2plex (K),TMT2plex (N-term),TMT6plex (K),TMT6plex (N-term),TNBS (K),TNBS (N-term),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr-&gt;Ala (T),Thr-&gt;Arg (T),Thr-&gt;Asn (T),Thr-&gt;Ile (T),Thr-&gt;Lys (T),Thr-&gt;Met (T),Thr-&gt;Pro (T),Thr-&gt;Ser (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trioxidation (C),Trp-&gt;Arg (W),Trp-&gt;Cys (W),Trp-&gt;Gly (W),Trp-&gt;Hydroxykynurenin (W),Trp-&gt;Kynurenin (W),Trp-&gt;Leu (W),Trp-&gt;Oxolactone (W),Trp-&gt;Ser (W),Tyr-&gt;Asn (Y),Tyr-&gt;Asp (Y),Tyr-&gt;Cys (Y),Tyr-&gt;Dha (Y),Tyr-&gt;His (Y),Tyr-&gt;Phe (Y),Tyr-&gt;Ser (Y),VFQQQTGG (K),VIEVYQEQTGG (K),Val-&gt;Ala (V),Val-&gt;Asp (V),Val-&gt;Glu (V),Val-&gt;Gly (V),Val-&gt;Ile (V),Val-&gt;Met (V),Val-&gt;Phe (V),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-s (K),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (S),dHex (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4) (N),dNIC (N-term),dichlorination (Y),ethylamino (S),ethylamino (T),glucosone (R),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),lapachenole (C),mTRAQ (K),mTRAQ (N-term),mTRAQ (Y),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),probiotinhydrazide (P),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
157 <LISTITEM value="Carbamidomethyl (C)"/>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
158 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
parents:
diff changeset
159 <ITEMLIST name="variable_modifications" type="string" description="Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. &apos;Carbamidomethyl (C)&apos; or &apos;Oxidation (M)&apos;" required="false" advanced="false" restrictions="15dB-biotin (C),2-succinyl (C),2HPG (R),3-deoxyglucosone (R),3sulfo (N-term),4-ONE (C),4-ONE (H),4-ONE (K),4-ONE+Delta:H(-2)O(-1) (C),4-ONE+Delta:H(-2)O(-1) (H),4-ONE+Delta:H(-2)O(-1) (K),4AcAllylGal (C),ADP-Ribosyl (C),ADP-Ribosyl (E),ADP-Ribosyl (N),ADP-Ribosyl (R),ADP-Ribosyl (S),AEBS (H),AEBS (K),AEBS (S),AEBS (Y),AEC-MAEC (S),AEC-MAEC (T),AEC-MAEC:2H(4) (S),AEC-MAEC:2H(4) (T),AROD (C),AccQTag (K),AccQTag (N-term),Acetyl (C),Acetyl (H),Acetyl (K),Acetyl (N-term),Acetyl (S),Acetyl (T),Acetyl (Y),Acetyl:2H(3) (K),Acetyl:2H(3) (N-term),Ala-&gt;Asp (A),Ala-&gt;Glu (A),Ala-&gt;Gly (A),Ala-&gt;Pro (A),Ala-&gt;Ser (A),Ala-&gt;Thr (A),Ala-&gt;Val (A),Amidated (C-term),Amidine (K),Amidine (N-term),Amidino (C),Amino (Y),Ammonia-loss (N),Ammonia-loss (N-term C),Ammonium (C-term),Ammonium (D),Ammonium (E),Archaeol (C),Arg-&gt;Cys (R),Arg-&gt;Gln (R),Arg-&gt;GluSA (R),Arg-&gt;Gly (R),Arg-&gt;His (R),Arg-&gt;Ile (R),Arg-&gt;Lys (R),Arg-&gt;Met (R),Arg-&gt;Npo (R),Arg-&gt;Orn (R),Arg-&gt;Pro (R),Arg-&gt;Ser (R),Arg-&gt;Thr (R),Arg-&gt;Trp (R),Arg2PG (R),Argbiotinhydrazide (R),Asn-&gt;Asp (N),Asn-&gt;His (N),Asn-&gt;Ile (N),Asn-&gt;Lys (N),Asn-&gt;Ser (N),Asn-&gt;Thr (N),Asn-&gt;Tyr (N),Asp-&gt;Ala (D),Asp-&gt;Asn (D),Asp-&gt;Glu (D),Asp-&gt;Gly (D),Asp-&gt;His (D),Asp-&gt;Tyr (D),Asp-&gt;Val (D),Atto495Maleimide (C),BADGE (C),BDMAPP (H),BDMAPP (K),BDMAPP (W),BDMAPP (Y),BHAc (K),BHT (C),BHT (H),BHT (K),BHTOH (C),BHTOH (H),BHTOH (K),BITC (C),BITC (K),BITC (N-term),BMOE (C),Bacillosamine (N),Benzoyl (K),Benzoyl (N-term),Biotin (K),Biotin (N-term),Biotin-HPDP (C),Biotin-PEG-PRA (M),Biotin-PEO-Amine (D),Biotin-PEO-Amine (E),Biotin-PEO4-hydrazide (C-term),Biotin-maleimide (C),Biotin-phenacyl (C),Biotin-phenacyl (H),Biotin-phenacyl (S),BisANS (K),Bodipy (C),Bromo (F),Bromo (H),Bromo (W),Bromobimane (C),C8-QAT (K),C8-QAT (N-term),CAF (N-term),CAMthiopropanoyl (K),CHDH (D),CLIP_TRAQ_1 (K),CLIP_TRAQ_1 (N-term),CLIP_TRAQ_1 (Y),CLIP_TRAQ_2 (K),CLIP_TRAQ_2 (N-term),CLIP_TRAQ_2 (Y),CLIP_TRAQ_3 (K),CLIP_TRAQ_3 (N-term),CLIP_TRAQ_3 (Y),CLIP_TRAQ_4 (K),CLIP_TRAQ_4 (N-term),CLIP_TRAQ_4 (Y),Can-FP-biotin (S),Can-FP-biotin (T),Can-FP-biotin (Y),Carbamidomethyl (C),Carbamidomethyl (D),Carbamidomethyl (E),Carbamidomethyl (H),Carbamidomethyl (K),Carbamidomethyl (N-term),CarbamidomethylDTT (C),Carbamyl (C),Carbamyl (K),Carbamyl (M),Carbamyl (N-term),Carbamyl (R),Carbamyl (S),Carbamyl (T),Carbamyl (Y),Carbofuran (S),Carboxy (D),Carboxy (E),Carboxy (K),Carboxy (W),Carboxyethyl (K),Carboxymethyl (C),Carboxymethyl (K),Carboxymethyl (N-term),Carboxymethyl (W),Carboxymethyl:13C(2) (C),CarboxymethylDTT (C),Cation:Ag (C-term),Cation:Ag (D),Cation:Ag (E),Cation:Ca[II] (C-term),Cation:Ca[II] (D),Cation:Ca[II] (E),Cation:Cu[I] (C-term),Cation:Cu[I] (D),Cation:Cu[I] (E),Cation:Fe[II] (C-term),Cation:Fe[II] (D),Cation:Fe[II] (E),Cation:K (C-term),Cation:K (D),Cation:K (E),Cation:Li (C-term),Cation:Li (D),Cation:Li (E),Cation:Mg[II] (C-term),Cation:Mg[II] (D),Cation:Mg[II] (E),Cation:Na (C-term),Cation:Na (D),Cation:Na (E),Cation:Ni[II] (C-term),Cation:Ni[II] (D),Cation:Ni[II] (E),Cation:Zn[II] (C-term),Cation:Zn[II] (D),Cation:Zn[II] (E),Chlorination (Y),Chlorpyrifos (S),Chlorpyrifos (T),Chlorpyrifos (Y),ChromoBiotin (K),CoenzymeA (C),Crotonaldehyde (C),Crotonaldehyde (H),Crotonaldehyde (K),CuSMo (C),Cy3b-maleimide (C),CyDye-Cy3 (C),CyDye-Cy5 (C),Cyano (C),Cys-&gt;Arg (C),Cys-&gt;Dha (C),Cys-&gt;Gly (C),Cys-&gt;Oxoalanine (C),Cys-&gt;Phe (C),Cys-&gt;Ser (C),Cys-&gt;Trp (C),Cys-&gt;Tyr (C),Cys-&gt;ethylaminoAla (C),Cys-&gt;methylaminoAla (C),Cysteinyl (C),Cytopiloyne (C),Cytopiloyne (K),Cytopiloyne (N-term),Cytopiloyne (P),Cytopiloyne (R),Cytopiloyne (S),Cytopiloyne (Y),Cytopiloyne+water (C),Cytopiloyne+water (K),Cytopiloyne+water (N-term),Cytopiloyne+water (R),Cytopiloyne+water (S),Cytopiloyne+water (T),Cytopiloyne+water (Y),DAET (S),DAET (T),DFDNB (K),DFDNB (N),DFDNB (Q),DFDNB (R),DHP (C),DNPS (C),DNPS (W),DTBP (K),DTBP (N),DTBP (Q),DTBP (R),DTT_C (C),DTT_C:2H(6) (C),DTT_ST (S),DTT_ST (T),DTT_ST:2H(6) (S),DTT_ST:2H(6) (T),Dansyl (K),Dansyl (N-term),DeStreak (C),Deamidated (N),Deamidated (Q),Deamidated (R),Deamidated:18O(1) (N),Deamidated:18O(1) (Q),Decanoyl (S),Decanoyl (T),Dehydrated (D),Dehydrated (N-term C),Dehydrated (S),Dehydrated (T),Dehydrated (Y),Dehydro (C),Delta:H(1)O(-1)18O(1) (N),Delta:H(2)C(2) (H),Delta:H(2)C(2) (K),Delta:H(2)C(3) (K),Delta:H(2)C(3)O(1) (K),Delta:H(2)C(3)O(1) (R),Delta:H(2)C(5) (K),Delta:H(4)C(2) (H),Delta:H(4)C(2) (K),Delta:H(4)C(2)O(-1)S(1) (S),Delta:H(4)C(3) (H),Delta:H(4)C(3) (K),Delta:H(4)C(3)O(1) (C),Delta:H(4)C(3)O(1) (H),Delta:H(4)C(3)O(1) (K),Delta:H(4)C(6) (K),Delta:H(5)C(2) (P),Delta:H(6)C(6)O(1) (K),Delta:H(8)C(6)O(2) (K),Delta:Hg(1) (C),Delta:S(-1)Se(1) (C),Delta:S(-1)Se(1) (M),Delta:Se(1) (C),Deoxy (D),Deoxy (S),Deoxy (T),Dethiomethyl (M),Diacylglycerol (C),Dibromo (Y),Didehydro (C-term K),Didehydro (S),Didehydro (T),Didehydro (Y),Didehydroretinylidene (K),Diethyl (K),Diethyl (N-term),Dihydroxyimidazolidine (R),Diiodo (Y),Diironsubcluster (C),Diisopropylphosphate (K),Diisopropylphosphate (S),Diisopropylphosphate (T),Diisopropylphosphate (Y),Dimethyl (K),Dimethyl (N),Dimethyl (N-term),Dimethyl (R),Dimethyl:2H(4) (K),Dimethyl:2H(4) (N-term),Dimethyl:2H(4)13C(2) (K),Dimethyl:2H(4)13C(2) (N-term),Dimethyl:2H(6)13C(2) (K),Dimethyl:2H(6)13C(2) (N-term),Dimethyl:2H(6)13C(2) (R),DimethylArsino (C),DimethylamineGMBS (C),DimethylpyrroleAdduct (K),Dioxidation (C),Dioxidation (F),Dioxidation (K),Dioxidation (M),Dioxidation (P),Dioxidation (R),Dioxidation (W),Dioxidation (Y),Diphthamide (H),Dipyrrolylmethanemethyl (C),DyLight-maleimide (C),EDT-iodoacetyl-PEO-biotin (S),EDT-iodoacetyl-PEO-biotin (T),EDT-maleimide-PEO-biotin (S),EDT-maleimide-PEO-biotin (T),EQAT (C),EQAT:2H(5) (C),EQIGG (K),ESP (K),ESP (N-term),ESP:2H(10) (K),ESP:2H(10) (N-term),Ethanedithiol (S),Ethanedithiol (T),Ethanolamine (C-term),Ethanolamine (D),Ethanolamine (E),Ethanolyl (C),Ethanolyl (K),Ethanolyl (R),Ethoxyformyl (H),Ethyl (C-term),Ethyl (D),Ethyl (E),Ethyl (K),Ethyl (N-term),EthylAmide (N),EthylAmide (Q),ExacTagAmine (K),ExacTagThiol (C),FAD (C),FAD (H),FAD (Y),FMN (S),FMN (T),FMNC (C),FMNH (C),FMNH (H),FNEM (C),FP-Biotin (K),FP-Biotin (S),FP-Biotin (T),FP-Biotin (Y),FTC (C),FTC (K),FTC (P),FTC (R),FTC (S),Farnesyl (C),Fluorescein (C),Fluoro (F),Fluoro (W),Fluoro (Y),Formyl (K),Formyl (N-term),Formyl (S),Formyl (T),G-H1 (R),GIST-Quat (K),GIST-Quat (N-term),GIST-Quat:2H(3) (K),GIST-Quat:2H(3) (N-term),GIST-Quat:2H(6) (K),GIST-Quat:2H(6) (N-term),GIST-Quat:2H(9) (K),GIST-Quat:2H(9) (N-term),GalNAzBiotin (N),GalNAzBiotin (S),GalNAzBiotin (T),Galactosyl (K),GeranylGeranyl (C),Gln-&gt;Arg (Q),Gln-&gt;Glu (Q),Gln-&gt;His (Q),Gln-&gt;Leu (Q),Gln-&gt;Lys (Q),Gln-&gt;Pro (Q),Gln-&gt;pyro-Glu (N-term Q),Glu (E),Glu-&gt;Ala (E),Glu-&gt;Asp (E),Glu-&gt;Gln (E),Glu-&gt;Gly (E),Glu-&gt;Lys (E),Glu-&gt;Val (E),Glu-&gt;pyro-Glu (N-term E),GluGlu (E),GluGluGlu (E),GluGluGluGlu (E),Glucosylgalactosyl (K),Glucuronyl (S),Glutathione (C),Gly-&gt;Ala (G),Gly-&gt;Arg (G),Gly-&gt;Asp (G),Gly-&gt;Cys (G),Gly-&gt;Glu (G),Gly-&gt;Ser (G),Gly-&gt;Trp (G),Gly-&gt;Val (G),Gly-loss+Amide (C-term G),GlyGly (C),GlyGly (K),GlyGly (S),GlyGly (T),Glycerophospho (S),GlycerylPE (E),Glycosyl (P),Guanidinyl (K),HMVK (C),HNE (C),HNE (H),HNE (K),HNE+Delta:H(2) (C),HNE+Delta:H(2) (H),HNE+Delta:H(2) (K),HNE-BAHAH (C),HNE-BAHAH (H),HNE-BAHAH (K),HNE-Delta:H(2)O (C),HNE-Delta:H(2)O (H),HNE-Delta:H(2)O (K),HPG (R),Heme (C),Heme (H),Hep (K),Hep (N),Hep (Q),Hep (R),Hep (S),Hep (T),Hex (C),Hex (K),Hex (N),Hex (N-term),Hex (R),Hex (T),Hex (W),Hex (Y),Hex(1)HexNAc(1)NeuAc(1) (N),Hex(1)HexNAc(1)NeuAc(1) (S),Hex(1)HexNAc(1)NeuAc(1) (T),Hex(1)HexNAc(1)NeuAc(2) (N),Hex(1)HexNAc(1)NeuAc(2) (S),Hex(1)HexNAc(1)NeuAc(2) (T),Hex(1)HexNAc(1)dHex(1) (N),Hex(1)HexNAc(2) (N),Hex(1)HexNAc(2)Pent(1) (N),Hex(1)HexNAc(2)dHex(1) (N),Hex(1)HexNAc(2)dHex(1)Pent(1) (N),Hex(1)HexNAc(2)dHex(2) (N),Hex(2) (K),Hex(2) (R),Hex(2)HexNAc(2) (N),Hex(2)HexNAc(2)Pent(1) (N),Hex(2)HexNAc(2)dHex(1) (N),Hex(3) (N),Hex(3)HexNAc(1)Pent(1) (N),Hex(3)HexNAc(2) (N),Hex(3)HexNAc(2)P(1) (N),Hex(3)HexNAc(4) (N),Hex(4)HexNAc(4) (N),Hex(5)HexNAc(2) (N),Hex(5)HexNAc(4) (N),Hex1HexNAc1 (S),Hex1HexNAc1 (T),HexN (K),HexN (N),HexN (T),HexN (W),HexNAc (N),HexNAc (S),HexNAc (T),HexNAc(1)dHex(1) (N),HexNAc(1)dHex(2) (N),HexNAc(2) (N),HexNAc(2)dHex(1) (N),HexNAc(2)dHex(2) (N),His-&gt;Arg (H),His-&gt;Asn (H),His-&gt;Asp (H),His-&gt;Gln (H),His-&gt;Leu (H),His-&gt;Pro (H),His-&gt;Tyr (H),Hydroxycinnamyl (C),Hydroxyfarnesyl (C),Hydroxyheme (E),Hydroxymethyl (N),HydroxymethylOP (K),Hydroxytrimethyl (K),Hypusine (K),IBTP (C),ICAT-C (C),ICAT-C:13C(9) (C),ICAT-D (C),ICAT-D:2H(8) (C),ICAT-G (C),ICAT-G:2H(8) (C),ICAT-H (C),ICAT-H:13C(6) (C),ICPL (K),ICPL (N-term),ICPL:13C(6) (K),ICPL:13C(6) (N-term),ICPL:13C(6)2H(4) (K),ICPL:13C(6)2H(4) (N-term),ICPL:2H(4) (K),ICPL:2H(4) (N-term),IDEnT (C),IED-Biotin (C),IGBP (C),IGBP:13C(2) (C),IMID (K),IMID:2H(4) (K),ISD_z+2_ion (N-term),Ile-&gt;Arg (I),Ile-&gt;Asn (I),Ile-&gt;Lys (I),Ile-&gt;Met (I),Ile-&gt;Phe (I),Ile-&gt;Ser (I),Ile-&gt;Thr (I),Ile-&gt;Val (I),Iminobiotin (K),Iminobiotin (N-term),Iodo (H),Iodo (Y),IodoU-AMP (F),IodoU-AMP (W),IodoU-AMP (Y),Isopropylphospho (S),Isopropylphospho (T),Isopropylphospho (Y),LG-Hlactam-K (K),LG-Hlactam-R (R),LG-anhydrolactam (K),LG-anhydrolactam (N-term),LG-anhyropyrrole (K),LG-anhyropyrrole (N-term),LG-lactam-K (K),LG-lactam-R (R),LG-pyrrole (K),LG-pyrrole (N-term),Label:13C(1)2H(3) (M),Label:13C(1)2H(3)+Oxidation (M),Label:13C(4)15N(2)+GlyGly (K),Label:13C(5) (P),Label:13C(5)15N(1) (M),Label:13C(5)15N(1) (P),Label:13C(5)15N(1) (V),Label:13C(6) (I),Label:13C(6) (K),Label:13C(6) (L),Label:13C(6) (R),Label:13C(6)+Acetyl (K),Label:13C(6)+Dimethyl (K),Label:13C(6)+GlyGly (K),Label:13C(6)15N(1) (I),Label:13C(6)15N(1) (L),Label:13C(6)15N(2) (K),Label:13C(6)15N(2)+Acetyl (K),Label:13C(6)15N(2)+Dimethyl (K),Label:13C(6)15N(2)+GlyGly (K),Label:13C(6)15N(4) (R),Label:13C(8)15N(2) (R),Label:13C(9) (F),Label:13C(9) (Y),Label:13C(9)+Phospho (Y),Label:13C(9)15N(1) (F),Label:15N(1) (A),Label:15N(1) (C),Label:15N(1) (D),Label:15N(1) (E),Label:15N(1) (F),Label:15N(1) (G),Label:15N(1) (I),Label:15N(1) (L),Label:15N(1) (M),Label:15N(1) (P),Label:15N(1) (S),Label:15N(1) (T),Label:15N(1) (V),Label:15N(1) (Y),Label:15N(2) (K),Label:15N(2) (N),Label:15N(2) (Q),Label:15N(2) (W),Label:15N(2)2H(9) (K),Label:15N(3) (H),Label:15N(4) (R),Label:18O(1) (C-term),Label:18O(1) (S),Label:18O(1) (T),Label:18O(1) (Y),Label:18O(2) (C-term),Label:2H(3) (L),Label:2H(4) (F),Label:2H(4) (K),Label:2H(4) (Y),Label:2H(4)+Acetyl (K),Label:2H(4)+GlyGly (K),Label:2H(9)13C(6)15N(2) (K),Leu-&gt;Arg (L),Leu-&gt;Gln (L),Leu-&gt;His (L),Leu-&gt;Met (L),Leu-&gt;MetOx (L),Leu-&gt;Phe (L),Leu-&gt;Pro (L),Leu-&gt;Ser (L),Leu-&gt;Trp (L),Leu-&gt;Val (L),LeuArgGlyGly (K),Lipoyl (K),Lys-&gt;Allysine (K),Lys-&gt;AminoadipicAcid (K),Lys-&gt;Arg (K),Lys-&gt;Asn (K),Lys-&gt;CamCys (K),Lys-&gt;Gln (K),Lys-&gt;Glu (K),Lys-&gt;Ile (K),Lys-&gt;Met (K),Lys-&gt;MetOx (K),Lys-&gt;Thr (K),Lysbiotinhydrazide (K),MDCC (C),MG-H1 (R),MTSL (C),Maleimide-PEO2-Biotin (C),Malonyl (C),Malonyl (S),Menadione (C),Menadione (K),Menadione-HQ (C),Menadione-HQ (K),MercaptoEthanol (S),MercaptoEthanol (T),Met-&gt;Aha (M),Met-&gt;Arg (M),Met-&gt;Hpg (M),Met-&gt;Hse (C-term M),Met-&gt;Hsl (C-term M),Met-&gt;Ile (M),Met-&gt;Leu (M),Met-&gt;Lys (M),Met-&gt;Thr (M),Met-&gt;Val (M),Methyl (C),Methyl (C-term),Methyl (D),Methyl (E),Methyl (H),Methyl (I),Methyl (K),Methyl (L),Methyl (N),Methyl (N-term),Methyl (Q),Methyl (R),Methyl (S),Methyl (T),Methyl+Acetyl:2H(3) (K),Methyl+Deamidated (N),Methyl+Deamidated (Q),Methyl-PEO12-Maleimide (C),Methyl:2H(2) (K),Methyl:2H(3) (C-term),Methyl:2H(3) (D),Methyl:2H(3) (E),Methyl:2H(3)13C(1) (R),Methylamine (S),Methylamine (T),Methylmalonylation (S),Methylphosphonate (S),Methylphosphonate (T),Methylphosphonate (Y),Methylpyrroline (K),Methylthio (C),Methylthio (D),Methylthio (N),Molybdopterin (C),MolybdopterinGD (C),MolybdopterinGD (D),MolybdopterinGD+Delta:S(-1)Se(1) (C),Myristoyl (C),Myristoyl (K),Myristoyl (N-term G),NA-LNO2 (C),NA-LNO2 (H),NA-OA-NO2 (C),NA-OA-NO2 (H),NBS (W),NBS:13C(6) (W),NDA (K),NDA (N-term),NEIAA (C),NEIAA (Y),NEIAA:2H(5) (C),NEIAA:2H(5) (Y),NEM:2H(5) (C),NHS-LC-Biotin (K),NHS-LC-Biotin (N-term),NIC (N-term),NIPCAM (C),NO_SMX_SEMD (C),NO_SMX_SIMD (C),NO_SMX_SMCT (C),Nethylmaleimide (C),Nethylmaleimide+water (C),Nethylmaleimide+water (K),Nitro (W),Nitro (Y),Nitrosyl (C),Nmethylmaleimide (C),Nmethylmaleimide (K),Nmethylmaleimide+water (C),O-Diethylphosphate (C),O-Diethylphosphate (H),O-Diethylphosphate (K),O-Diethylphosphate (S),O-Diethylphosphate (T),O-Diethylphosphate (Y),O-Dimethylphosphate (S),O-Dimethylphosphate (T),O-Dimethylphosphate (Y),O-Ethylphosphate (S),O-Ethylphosphate (T),O-Ethylphosphate (Y),O-Isopropylmethylphosphonate (S),O-Isopropylmethylphosphonate (T),O-Isopropylmethylphosphonate (Y),O-Methylphosphate (S),O-Methylphosphate (T),O-Methylphosphate (Y),O-pinacolylmethylphosphonate (H),O-pinacolylmethylphosphonate (K),O-pinacolylmethylphosphonate (S),O-pinacolylmethylphosphonate (T),O-pinacolylmethylphosphonate (Y),Octanoyl (S),Octanoyl (T),OxArgBiotin (R),OxArgBiotinRed (R),OxLysBiotin (K),OxLysBiotinRed (K),OxProBiotin (P),OxProBiotinRed (P),Oxidation (C),Oxidation (C-term G),Oxidation (D),Oxidation (F),Oxidation (H),Oxidation (K),Oxidation (M),Oxidation (N),Oxidation (P),Oxidation (R),Oxidation (W),Oxidation (Y),PEITC (C),PEITC (K),PEITC (N-term),PEO-Iodoacetyl-LC-Biotin (C),PET (S),PET (T),PGA1-biotin (C),Palmitoleyl (C),Palmitoleyl (S),Palmitoleyl (T),Palmitoyl (C),Palmitoyl (K),Palmitoyl (S),Palmitoyl (T),Pentylamine (Q),PentylamineBiotin (Q),Phe-&gt;CamCys (F),Phe-&gt;Cys (F),Phe-&gt;Ile (F),Phe-&gt;Ser (F),Phe-&gt;Tyr (F),Phe-&gt;Val (F),Phenylisocyanate (N-term),Phenylisocyanate:2H(5) (N-term),Phospho (C),Phospho (D),Phospho (H),Phospho (R),Phospho (S),Phospho (T),Phospho (Y),PhosphoHex (S),PhosphoHexNAc (S),PhosphoUridine (H),PhosphoUridine (Y),Phosphoadenosine (H),Phosphoadenosine (K),Phosphoadenosine (T),Phosphoadenosine (Y),Phosphoguanosine (H),Phosphoguanosine (K),Phosphopantetheine (S),Phosphopropargyl (S),Phosphopropargyl (T),Phosphopropargyl (Y),PhosphoribosyldephosphoCoA (S),Phycocyanobilin (C),Phycoerythrobilin (C),Phytochromobilin (C),Piperidine (K),Piperidine (N-term),Pro-&gt;Ala (P),Pro-&gt;Arg (P),Pro-&gt;Gln (P),Pro-&gt;His (P),Pro-&gt;Leu (P),Pro-&gt;Pyrrolidinone (P),Pro-&gt;Pyrrolidone (P),Pro-&gt;Ser (P),Pro-&gt;Thr (P),Pro-&gt;pyro-Glu (P),Propargylamine (C-term),Propargylamine (D),Propargylamine (E),Propionamide (C),Propionamide:2H(3) (C),Propionyl (K),Propionyl (N-term),Propionyl (S),Propionyl:13C(3) (K),Propionyl:13C(3) (N-term),PropylNAGthiazoline (C),Puromycin (C-term),PyMIC (N-term),PyridoxalPhosphate (K),Pyridylacetyl (K),Pyridylacetyl (N-term),Pyridylethyl (C),Pyro-carbamidomethyl (N-term C),PyruvicAcidIminyl (K),QAT (C),QAT:2H(3) (C),QEQTGG (K),QQQTGG (K),Quinone (W),Quinone (Y),RNPXlink1 (C),RNPXlink2 (F),RNPXlink2 (K),RNPXlink2 (L),RNPXlink3 (C),RNPXlink3 (F),RNPXlink4 (C),RNPXlink5 (F),RNPXlink5 (Y),Retinylidene (K),SMA (K),SMA (N-term),SMCC-maleimide (C),SPITC (K),SPITC (N-term),SPITC:13C(6) (K),SPITC:13C(6) (N-term),SUMO2135 (K),SUMO3549 (K),Ser-&gt;Ala (S),Ser-&gt;Arg (S),Ser-&gt;Asn (S),Ser-&gt;Cys (S),Ser-&gt;Gly (S),Ser-&gt;Ile (S),Ser-&gt;Phe (S),Ser-&gt;Pro (S),Ser-&gt;Thr (S),Ser-&gt;Trp (S),Ser-&gt;Tyr (S),Succinyl (K),Succinyl (N-term),Succinyl:13C(4) (K),Succinyl:13C(4) (N-term),Succinyl:2H(4) (K),Succinyl:2H(4) (N-term),SulfanilicAcid (C-term),SulfanilicAcid (D),SulfanilicAcid (E),SulfanilicAcid:13C(6) (C-term),SulfanilicAcid:13C(6) (D),SulfanilicAcid:13C(6) (E),Sulfide (C),Sulfide (D),Sulfo (C),Sulfo (S),Sulfo (T),Sulfo (Y),Sulfo-NHS-LC-LC-Biotin (K),Sulfo-NHS-LC-LC-Biotin (N-term),SulfoGMBS (C),TMAB (K),TMAB (N-term),TMAB:2H(9) (K),TMAB:2H(9) (N-term),TMPP-Ac (N-term),TMT (K),TMT (N-term),TMT2plex (K),TMT2plex (N-term),TMT6plex (K),TMT6plex (N-term),TNBS (K),TNBS (N-term),Thioacyl (K),Thioacyl (N-term),Thiophos-S-S-biotin (S),Thiophos-S-S-biotin (T),Thiophos-S-S-biotin (Y),Thiophospho (S),Thiophospho (T),Thiophospho (Y),Thr-&gt;Ala (T),Thr-&gt;Arg (T),Thr-&gt;Asn (T),Thr-&gt;Ile (T),Thr-&gt;Lys (T),Thr-&gt;Met (T),Thr-&gt;Pro (T),Thr-&gt;Ser (T),Thrbiotinhydrazide (T),Thyroxine (Y),Triiodo (Y),Triiodothyronine (Y),Trimethyl (K),Trimethyl (R),Trioxidation (C),Trp-&gt;Arg (W),Trp-&gt;Cys (W),Trp-&gt;Gly (W),Trp-&gt;Hydroxykynurenin (W),Trp-&gt;Kynurenin (W),Trp-&gt;Leu (W),Trp-&gt;Oxolactone (W),Trp-&gt;Ser (W),Tyr-&gt;Asn (Y),Tyr-&gt;Asp (Y),Tyr-&gt;Cys (Y),Tyr-&gt;Dha (Y),Tyr-&gt;His (Y),Tyr-&gt;Phe (Y),Tyr-&gt;Ser (Y),VFQQQTGG (K),VIEVYQEQTGG (K),Val-&gt;Ala (V),Val-&gt;Asp (V),Val-&gt;Glu (V),Val-&gt;Gly (V),Val-&gt;Ile (V),Val-&gt;Met (V),Val-&gt;Phe (V),Xlink:B10621 (C),Xlink:DMP (K),Xlink:DMP-s (K),Xlink:SSD (K),ZGB (K),ZGB (N-term),a-type-ion (C-term),cGMP (C),cGMP (S),cGMP+RMP-loss (C),cGMP+RMP-loss (S),cysTMT (C),cysTMT6plex (C),dHex (S),dHex (T),dHex(1)Hex(3)HexNAc(4) (N),dHex(1)Hex(4)HexNAc(4) (N),dHex(1)Hex(5)HexNAc(4) (N),dNIC (N-term),dichlorination (Y),ethylamino (S),ethylamino (T),glucosone (R),iTRAQ4plex (K),iTRAQ4plex (N-term),iTRAQ4plex (Y),iTRAQ4plex114 (K),iTRAQ4plex114 (N-term),iTRAQ4plex114 (Y),iTRAQ4plex115 (K),iTRAQ4plex115 (N-term),iTRAQ4plex115 (Y),iTRAQ8plex (K),iTRAQ8plex (N-term),iTRAQ8plex (Y),iTRAQ8plex:13C(6)15N(2) (K),iTRAQ8plex:13C(6)15N(2) (N-term),iTRAQ8plex:13C(6)15N(2) (Y),lapachenole (C),mTRAQ (K),mTRAQ (N-term),mTRAQ (Y),mTRAQ:13C(3)15N(1) (K),mTRAQ:13C(3)15N(1) (N-term),mTRAQ:13C(3)15N(1) (Y),maleimide (C),maleimide (K),maleimide3 (C),maleimide3 (K),maleimide5 (C),maleimide5 (K),probiotinhydrazide (P),pyrophospho (S),pyrophospho (T),sulfo+amino (Y),thioacylPA (K),trifluoro (L)">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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160 <LISTITEM value="Oxidation (M)"/>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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161 </ITEMLIST>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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162 <ITEM name="omssa_executable" value="omssacl" type="input-file" description="The &apos;omssacl&apos; executable of the OMSSA installation" required="true" advanced="false" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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163 <ITEM name="pc" value="1" type="int" description="The number of pseudocounts to add to each precursor mass bin" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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164 <ITEM name="hs" value="4" type="int" description="the minimum number of m/z values a spectrum must have to be searched" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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165 <ITEM name="tez" value="1" type="int" description="scaling of precursor mass tolerance with charge (0 = none, 1= linear)" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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166 <ITEM name="tom" value="0" type="int" description="product ion search type, with 0 = monoisotopic, 1 = average, 2 = monoisotopic N15, 3 = exact" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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167 <ITEM name="tem" value="0" type="int" description="precursor ion search type, with 0 = monoisotopic, 1 = average, 2 = monoisotopic N15, 3 = exact" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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168 <ITEM name="tex" value="1446.94" type="double" description="threshold in Da above which the mass of a neutron should be added in an exact mass search" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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169 <ITEM name="zt" value="3" type="int" description="minimum precursor charge to start considering multiply charged products" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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170 <ITEM name="z1" value="0.95" type="double" description="the fraction of peaks below the precursor used to determine if the spectrum is charge +1" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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171 <ITEM name="zc" value="1" type="int" description="should charge +1 be determined algorithmically (1=yes)" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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172 <ITEM name="zcc" value="2" type="int" description="how should precursor charges be determined? (1=believe the input file,2=use the specified range)" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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173 <ITEM name="zoh" value="2" type="int" description="set the maximum product charge to search" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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174 <ITEM name="v" value="1" type="int" description="number of missed cleavages allowed" 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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175 <ITEM name="e" value="0" type="int" description="id number of enzyme to use (0 (i.e. trypsin) is the default, 17 would be no enzyme (i.e. unspecific digestion), for more please refer to omssacl -help)." 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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176 <ITEM name="no" value="4" type="int" description="minimum size of peptides for no-enzyme and semi-tryptic searches" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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177 <ITEM name="nox" value="40" type="int" description="maximum size of peptides for no-enzyme and semi-tryptic searches" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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178 <ITEM name="i" value="1,4" type="string" description="comma delimited list of id numbers of ions to search" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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179 <ITEM name="sp" value="100" type="int" description="number of product ions to search" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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180 <ITEM name="sb1" value="1" type="int" description="should first forward (e.g. b1) product ions be searched (1 = no, 0 = yes)" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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181 <ITEM name="sct" value="0" type="int" description="should c terminus ions (e.g. y1) be searched (1 = no, 0 = yes)" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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182 <ITEM name="x" value="0" type="string" description="comma delimited list of NCBI taxonomy ids to search (0 = all. This is the default)" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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183 <ITEM name="hm" value="2" type="int" description="the minimum number of m/z matches a sequence library peptide must have for the hit to the peptide to be recorded" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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184 <ITEM name="ht" value="6" type="int" description="number of m/z values corresponding to the most intense peaks that must include one match to the theoretical peptide" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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185 <ITEM name="hl" value="1" type="int" description="maximum number of hits retained for one spectrum. Note: even when set to 1 OMSSA may report multiple hits with different charge states" 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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186 <ITEM name="he" value="100000" type="double" description="the maximum e-value allowed in the hit list. If you set this parameter too small (e.g., he=1), this will effectively introduce FDR filtering. Thus, allowing a less stringent FDR during post-processing will nevertheless return the (better) FDR introduced here, since mediocre hits are not even reported." 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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187 <ITEM name="mm" value="128" type="int" description="the maximum number of mass ladders to generate per database peptide" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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188 <ITEM name="mnm" value="false" type="string" description="n-term methionine should not be cleaved" 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"
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189 <ITEM name="is" value="0" type="double" description="evalue threshold to include a sequence in the iterative search, 0 = all" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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190 <ITEM name="ir" value="0" type="double" description="evalue threshold to replace a hit, 0 = only if better" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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191 <ITEM name="ii" value="0" type="double" description="evalue threshold to iteratively search a spectrum again, 0 = always" required="false" advanced="true" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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192 <ITEM name="log" value="" 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"
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193 <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"
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194 <ITEM name="threads" value="12" 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"
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195 <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" 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"
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196 <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"
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197 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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198 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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199 <NODE name="6" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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200 <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"
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201 <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"
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202 <ITEM name="tool_name" value="FileInfo" 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"
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203 <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"
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parents:
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204 <ITEM name="x_pos" value="500" 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"
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diff changeset
205 <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"
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diff changeset
206 <NODE name="parameters" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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207 <ITEM name="in" value="" type="input-file" description="input file " required="true" advanced="false" supported_formats="*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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208 <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,idXML,pepXML,fid" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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209 <ITEM name="out" value="" type="output-file" description="Optional output file. If left out, the output is written to the command line." required="false" advanced="false" supported_formats="*.txt" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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210 <ITEM name="out_tsv" value="" type="output-file" description="Second optional output file. Tab separated flat text file." required="false" advanced="true" supported_formats="*.csv" />
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
211 <ITEM name="m" value="false" type="string" description="Show meta information about the whole experiment" 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
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diff changeset
212 <ITEM name="p" value="false" type="string" description="Shows data processing information" 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"
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213 <ITEM name="s" value="false" type="string" description="Computes a five-number statistics of intensities, qualities, and widths" 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
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diff changeset
214 <ITEM name="d" value="false" type="string" description="Show detailed listing of all spectra and chromatograms (peak files 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
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215 <ITEM name="c" value="false" type="string" description="Check for corrupt data in the file (peak files 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
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216 <ITEM name="v" value="false" type="string" description="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" 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
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217 <ITEM name="log" value="" 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
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218 <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
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219 <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
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220 <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" 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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221 <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
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diff changeset
222 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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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
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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
225 <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
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diff changeset
226 <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
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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
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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diff changeset
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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diff changeset
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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galaxyp
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diff changeset
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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
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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
242 </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
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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
244 <NODE name="source/target" description="">
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
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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
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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
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galaxyp
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diff changeset
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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
249 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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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
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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
252 </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
253 </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
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
255 <NODE name="source/target" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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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
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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
260 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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galaxyp
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diff changeset
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
263 </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
264 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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diff changeset
266 <NODE name="source/target" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
268 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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galaxyp
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
271 </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
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273 <ITEM name="" value="fasta" 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"
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diff changeset
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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
275 </NODE>
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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diff changeset
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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
277 <NODE name="source/target" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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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="source_out_param" description="">
6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
galaxyp
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6daaa75ccb99 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
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318 </NODE>
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319 </NODE>
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320 </NODE>
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