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1 <tool id="GFFToBed" name="GFFToBed" version="1.0">
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2 <description>GFFToBed 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 GFFToBed.py --version
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8 </version_command>
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9 <command interpreter="python">
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10 GFFToBedWrapper_Wrapper.py -i $inputFile -o $outputFile
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11 </command>
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12 <inputs>
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13 <param name="inputFile" type="data" format="gff" label="indicate a transcript GTF file of cufflinks."/>
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14 </inputs>
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15 <outputs>
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16 <data name="outputFile" format="bed" label="${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 **GFFToBed_wrapper converts a result GTF file of Cufflinks into a bed file.**
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21
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22
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23 **what it does :**
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24
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25 converts a result GTF file of Cufflinks into a bed file.
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26
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27 It can take: Chromosome, Start, End, ID, Target, strand
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28
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29 -----
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30
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31 **input format :**
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32
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33 .. class:: infomark
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34
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35 2L DmelCaf1_2_2_REPET_TEs match 47519 52563 0.0 + . ID=ms1_dmel_chr2L_RIX-comp_DmelCaf1_2_2-B-P58.20-Map11;Target=RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 6 5050;Identity=99.8
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36
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37
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38 -----
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39
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40 **output format :**
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41
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42 2L 47519 52563 ms1_dmel_chr2L_RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 RIX-comp_DmelCaf1_2_2-B-P58.20-Map11 6 5050 +
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43
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44 -----
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45
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46
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47 -----
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48
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49 **reference :**
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50
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51 ]]>
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52 </help>
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53 </tool>
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