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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 <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName
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4 #if $inputFormatType.FormatInputFileName == 'gff3':
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5 -f gff3
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6 #elif $inputFormatType.FormatInputFileName == 'bed':
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7 -f bed
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8 #elif $inputFormatType.FormatInputFileName == 'bam':
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9 -f blast
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10 #elif $inputFormatType.FormatInputFileName == 'sam':
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11 -f sam
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12 #elif $inputFormatType.FormatInputFileName == 'gtf':
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13 -f gtf
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14 #end if
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15
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16 -g $outputFormatType.outFormat
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17
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18 -n $name
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19 $strand
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20 -o $outputFile
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21
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22 </command>
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23 <inputs>
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24 <conditional name="inputFormatType">
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25 <param name="FormatInputFileName" type="select" label="Input File Format">
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26 <option value="gff3">GFF3</option>
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27 <option value="bed">BED</option>
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28 <option value="bam">BAM</option>
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29 <option value="sam">SAM</option>
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30 <option value="gtf">GTF</option>
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31 </param>
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32 <when value="gff3">
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33 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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34 </when>
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35 <when value="bed">
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36 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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37 </when>
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38 <when value="bam">
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39 <param name="inputFileName" format="bam" type="data" label="Input File"/>
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40 </when>
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41 <when value="sam">
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42 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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43 </when>
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44 <when value="gtf">
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45 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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46 </when>
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47 </conditional>
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48
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49
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50 <conditional name="outputFormatType">
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51 <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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52 <option value="gff3">GFF3</option>
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53 <option value="bed">BED</option>
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54 <option value="wig">WIG</option>
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55 <option value="sam">SAM</option>
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56 <option value="csv">CSV</option>
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57 <option value="gtf">GTF</option>
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58 </param>
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59 <when value="gff3">
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60 </when>
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61 <when value="bed">
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62 </when>
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63 <when value="wig">
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64 </when>
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65 <when value="sam">
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66 </when>
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67 <when value="csv">
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68 </when>
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69 <when value="gtf">
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70 </when>
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71 </conditional>
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72
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73 <param name="name" type="text" value="SMART" label="name for the transcripts"/>
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74
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75 <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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76
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77 </inputs>
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78
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79 <outputs>
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80 <data name="outputFile" format="gff3" label="$inputFormatType.FormatInputFileName to $outputFormatType.outFormat">
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81 <change_format>
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82 <when input="outputFormatType.outFormat" value="bed" format="bed" />
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83 <when input="outputFormatType.outFormat" value="gff" format="gff" />
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84 <when input="outputFormatType.outFormat" value="wig" format="wig" />
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85 <when input="outputFormatType.outFormat" value="sam" format="sam" />
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86 <when input="outputFormatType.outFormat" value="csv" format="csv" />
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87 <when input="outputFormatType.outFormat" value="gtf" format="gtf" />
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88 </change_format>
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89 </data>
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90 </outputs>
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91
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92 <help>
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93 Simple conversion tool.
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94 </help>
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95 </tool>
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