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1 <tool id="ConvertTranscriptFile" name="convert transcript file">
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2 <description>Convert a file from a format to another.</description>
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3 <requirements>
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4 <requirement type="set_environment">PYTHONPATH</requirement>
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5 </requirements>
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56
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6 <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName -f $inputFormatType.FormatInputFileName -g $outputFormatType.outFormat -n $name $strand -o $outputFile </command>
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7 <inputs>
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8 <conditional name="inputFormatType">
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9 <param name="FormatInputFileName" type="select" label="Input File Format">
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10 <option value="gff3">GFF3</option>
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11 <option value="bed">BED</option>
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12 <option value="sam">SAM</option>
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13 <option value="bam">BAM</option>
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14 <option value="gtf">GTF</option>
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15 </param>
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16 <when value="gff3">
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17 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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18 </when>
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19 <when value="bed">
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20 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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21 </when>
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22 <when value="sam">
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23 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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24 </when>
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25 <when value="bam">
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26 <param name="inputFileName" format="bam" type="data" label="Input File"/>
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27 </when>
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28 <when value="gtf">
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29 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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30 </when>
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31 </conditional>
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32
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33
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34 <conditional name="outputFormatType">
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35 <param name="outFormat" type="select" label="Please choose the format that you want to convert to (corresponding to your input file format).">
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36 <option value="gff3">GFF3</option>
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37 <option value="bed">BED</option>
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38 <option value="wig">WIG</option>
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39 <option value="sam">SAM</option>
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40 <option value="csv">CSV</option>
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41 <option value="gtf">GTF</option>
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42 </param>
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43 <when value="gff3">
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44 </when>
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45 <when value="bed">
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46 </when>
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47 <when value="wig">
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48 </when>
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49 <when value="sam">
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50 </when>
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51 <when value="csv">
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52 </when>
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53 <when value="gtf">
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54 </when>
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55 </conditional>
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56
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57 <param name="name" type="text" value="SMART" label="name for the transcripts"/>
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58
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59 <param name="strand" type="boolean" truevalue="-t" falsevalue="" checked="false" label="consider the 2 strands as different (only useful for writing WIG files)"/>
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60
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61 </inputs>
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62
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63 <outputs>
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64 <data name="outputFile" format="gff3" label="$inputFormatType.FormatInputFileName to $outputFormatType.outFormat">
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65 <change_format>
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66 <when input="outputFormatType.outFormat" value="bed" format="bed" />
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67 <when input="outputFormatType.outFormat" value="gff" format="gff" />
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68 <when input="outputFormatType.outFormat" value="wig" format="wig" />
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69 <when input="outputFormatType.outFormat" value="sam" format="sam" />
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70 <when input="outputFormatType.outFormat" value="csv" format="csv" />
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71 <when input="outputFormatType.outFormat" value="gtf" format="gtf" />
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72 </change_format>
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73 </data>
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74 </outputs>
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75
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76 <help>
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77 Simple conversion tool.
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78 </help>
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79 </tool>
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