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1 <tool name="IsoFix" id="isofix1" version="0.0.1">
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2 <description>Identifies in-source decay peptides and corrects protein assignments</description>
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3 <!--
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4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
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5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
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6 //////////////////////////
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7 -->
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8 <command interpreter="java -jar ">
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9 IsoFix.jar
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10 -identificationsFile $identificationsFile
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11 -outputFile $outputFile
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12 -format apml
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13 -rtTol $rtTol
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14 -logFile $logFile
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15 #if $useOriginalProteinSequences.useOriginalProteinSequencesFile == True
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16 -fastaFile $useOriginalProteinSequences.fastaFile
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17 #end if
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18 </command>
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19
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20 <inputs>
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21
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22 <param name="identificationsFile" type="data" format="apml" label="MS/MS identifications file" />
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23
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24 <param name="rtTol" type="integer" size="10" value="15" label="Retention time tolerance (seconds) " />
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25
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26 <param name="createLogFile" type="boolean" checked="true" label="Generate log file" help="Lists the in-source decay peptides found"/>
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27
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28 <conditional name="useOriginalProteinSequences">
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29 <param name="useOriginalProteinSequencesFile" type="boolean"
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30 truevalue="Yes" falsevalue="No" checked="true"
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31 label="Use original protein sequences for detecting peptide source relations"
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32 help="This can reduce redundancy in final set by correctly identifying which peptides derive from bigger peptides that are also identified"/>
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33 <when value="Yes">
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34 <param name="fastaFile" type="data" format="fasta" label="Protein sequences (fasta file)"/>
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35 </when>
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6
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36 <when value="No">
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37 </when>
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38 </conditional>
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39
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40 </inputs>
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41 <outputs>
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42 <data name="outputFile" format="apml" label="${identificationsFile.metadata.base_name} - ${tool.name} on ${on_string}: APML" metadata_source="identificationsFile"></data>
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43 <data name="logFile" format="txt" label="${tool.name} on ${on_string} - LOG file">
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44 <!-- If the expression is false, the file is not created -->
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45 <filter>( createLogFile == True )</filter>
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46 </data>
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47 </outputs>
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48 <tests>
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49 </tests>
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50 <help>
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51
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52 .. class:: infomark
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53
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54 This tool identifies in-source decay peptides and corrects protein assignments.
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55
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56 -----
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57
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58 **Output example**
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59
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60 This tools returns the given input file but then with corrected protein assignments and
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61 in-source decay peptides identified (by a small modification in their sequence string).
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62 E.g. if peptide TYNSIMK is found to be an in-source decay of HETTYNSIMK, then
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63 its sequence is changed to HET}TYNSIMK (so the decayed part + "}" + own sequence).
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64 E.g. decay from both sides: YNSI, HETTYNSIMK = HET}TYNSI{MK
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65
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66
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67 </help>
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68 </tool>
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