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1 <tool id="CufflinksGTFToBed" name="CufflinksGTFToBed" version="1.0">
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2 <description>CufflinksGTFToBed can convert a result GTF file of Cufflinks into a bed file.</description>
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3 <requirements>
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4 <requirement type="package" version="1.0">TEiso_Tools</requirement>
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5 </requirements>
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6 <version_command>
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7 CufflinksGTFToBed.py --version
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8 </version_command>
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9 <command interpreter="python">
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10 CufflinksGTFToBed_Wrapper.py -i $inputFile -o $outputFile
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11 </command>
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12 <inputs>
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13 <param name="inputFile" type="data" format="gtf" label="indicate a transcript GTF file of cufflinks."/>
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14 </inputs>
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15 <outputs>
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16 <data name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
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17 </outputs>
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18 <help><![CDATA[
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19
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20
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21
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22 **CufflinksGTFToBed_wrapper converts a result GTF file of Cufflinks into a bed file.**
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23
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24 **what it does :**
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25
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26 Converts a GTF file of transcripts into a bed file. In input file, there are all the information of the transcript and their exon. CufflinksGTFToBed takes only the transcripts to convert into a bed file.
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27
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28 It can take: Chromosome, Start, End, strand, Isoform ID, Gene ID, value of FPKM
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29
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30 -----
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31
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32 **example :**
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33
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34
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35 Transcript input file: ::
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36
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37 2L cufflinks transcript 10487 18076 372 - . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "1.3627628649"; frac "0.197041"; conf_lo "0.805777"; conf_hi "1.919748"; cov "1.706083";
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38
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39
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40
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41
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42 ----
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43
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44 output format: ::
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45
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46 2L 10487 18076 CUFF.1.1 CUFF.1 - 1.363
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47
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48
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49 ]]>
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50 </help>
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51 </tool>
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