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1 <tool id="reorient_coordinates" name="Reorient Coordinates" version="0.1.0">
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2 <description>Switches Start and End if needed</description>
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3
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4 <command interpreter="perl">reorient_coordinates.pl $input_file $output_file</command>
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5
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6 <inputs>
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7 <param name="input_file" type="data" format="tabular" label="3-column tabular file with columns 2 and 3 indicating genomic positions"/>
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8 </inputs>
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9
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10 <outputs>
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11 <data name="output_file" format="tabular" />
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12 </outputs>
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13
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14 <!-- TODO implement tests: namely generate test data and put it in place
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15 <tests>
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16 <test>
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17 <param name="input_file" value="test_transcript_count.bam" />
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18 <param name="coherent" value="1" />
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19 <output name="output_file" file="test_transcript_count.tab" />
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20 </test>
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21 </tests>
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22 -->
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23 <help>
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24
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25 Switches positions in a tabular file to guarantee that the 2nd colum is always less or the same as the 3rd column.
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26
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27 E.g.
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28 datafile:
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29 entry1 100 200
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30 entry2 200 200
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31 entry3 300 200
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32
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33 Output:
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34 entry1 100 200
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35 entry2 200 200
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36 entry3 200 300
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37
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38 ------
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39
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40 **Citation**
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41
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42 This tools and Galaxy wrapper was developed by the IGC Bioinformatics unit (author: Daniel Sobral dsobral@igc.gulbenkian.pt)
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43
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44 </help>
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45
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46 </tool> |
