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