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1 <tool id="iprscanToExcel" name="Export iprscan output to Excel" version="1.0">
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2 <description>Export iprscan output to Excel</description>
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3 <command>
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4 #if $input.select == '1':
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5 java -jar ${GALAXY_ROOT_DIR}/tools/iprscan/iprscanToExcel_v20.jar -xml $xmlfile -excel $output
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6 #else if $input.select == '2':
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7 java -jar ${GALAXY_ROOT_DIR}/tools/iprscan/iprscanToExcel_v20.jar -raw $rawfile -excel $output
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8 #else:
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9 java -jar ${GALAXY_ROOT_DIR}/tools/iprscan/iprscanToExcel_v20.jar -xml $input1 -raw $input2 -excel $output
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10 #end if
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11 </command>
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12 <inputs>
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13 <conditional name="input">
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14 <param name="select" type="select" label="Mode">
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15 <option value="1">convert XML file to Excel to get the iprscan summary tables for each protein</option>
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16 <option value="2">convert raw file to Excel to get all the iprscan results in one table</option>
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17 <option value="3" selected="true">convert both XML and raw file to Excel</option>
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18 </param>
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19 <when value="1">
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20 <param name="xmlfile" type="data" format="xml" label="Select the desired XML file from history" />
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21 </when>
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22 <when value="2">
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23 <param name="rawfile" type="data" format="raw" label="Select the desired raw data file from history" />
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24 </when>
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25 <when value="3">
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26 <param name="input1" type="data" format="xml" label="Select the desired XML file from history" />
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27 <param name="input2" type="data" format="raw" label="Select the desired raw data file from history" />
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28 </when>
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29 </conditional>
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30
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31 </inputs>
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32 <outputs>
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33 <data format="xlsx" name="output"></data>
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34 </outputs>
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35 <requirements>
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36 </requirements>
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37 <help>
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38 **What it does**
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39
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40 iprscanToExcel converts raw and/or xml output files from the interproscan program to Excel format (xlsx), which is more user-friendly and convenient than e.g. xml. Three modes of operation are available: convert both XML and raw iprscan output files to Excel, convert only the xml output file to Excel or convert only the raw file to Excel.
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41
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42 The xml output file of the interproscan program contains the source data for the Excel tabsheet "summary tables". Those summary tables give for each protein family information concerning the detailed matches, the parent, the child_list, where they are found_in, the GO-terms, ...
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43
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44 The raw output file of the interproscan program contains the source data for the Excel tabsheet "iprscan results", containing an overview table with proteinID, protein crc64, protein length, match dbname, classification id, classification description, start, end, score, status, date, interproID, interpro name, (title, GO number, description)n. The columns can be sorted and filtered via the filters present in the headers of the columns.
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45
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46 The program requires the availability of raw and/or xml files in the Galaxy history. The files can be generated via the application "Interproscan functional predictions" (under the header Sequence Annotation).
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47
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48 **Author and affiliation**
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49
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50 Katrien Bernaerts and Domantas Motiejunas, 10/06/2012
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51
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52 Corresponding author: domantas dot motiejunas at cropdesign dot com
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53
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54
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55
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56 Affiliation: CropDesign N.V., a BASF Plant Science Company - Technologiepark 3, 9052 Zwijnaarde - Belgium
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57
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58 **Terms of use**
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59
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60 iprscanToExcel - Copyright (C) 2012 CropDesign N.V. - this software may be used, copied and redistributed, with or without modification freely, without advance permission, provided that the above Copyright statement is reproduced with each copy.
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61 THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE (INCLUDING NEGLIGENCE OR OTHERWISE).
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62
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63 (R)Excel is a registered trademark of Microsoft Corporation in the United States and/or other countries
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64
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65 </help>
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66 </tool>
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