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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 == 'gff2':
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9 -f gff2
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10 #elif $inputFormatType.FormatInputFileName == 'bam':
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11 -f blast
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12 #elif $inputFormatType.FormatInputFileName == 'sam':
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13 -f sam
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14 #elif $inputFormatType.FormatInputFileName == 'gtf':
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15 -f gtf
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16 #end if
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17
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18 -g $outputFormatType.outFormat
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19 #if $optionSequence.choose == 'Yes':
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20 -s $optionSequence.value
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21 #end if
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22
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23
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24 -n $name
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25 $strand
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26 -o $outputFile
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27
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28 </command>
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29 <inputs>
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30 <conditional name="inputFormatType">
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31 <param name="FormatInputFileName" type="select" label="Input File Format">
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32 <option value="gff3">GFF3</option>
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33 <option value="bed">BED</option>
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34 <option value="gff2">GFF2</option>
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35 <option value="bam">BAM</option>
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36 <option value="sam">SAM</option>
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37 <option value="gtf">GTF</option>
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38 </param>
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39 <when value="gff3">
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40 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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41 </when>
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42 <when value="bed">
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43 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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44 </when>
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45 <when value="gff2">
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46 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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47 </when>
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48 <when value="bam">
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49 <param name="inputFileName" format="bam" type="data" label="Input File"/>
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50 </when>
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51 <when value="sam">
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52 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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53 </when>
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54 <when value="gtf">
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55 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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56 </when>
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57 </conditional>
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58
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59
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60 <conditional name="outputFormatType">
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61 <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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62 <option value="gff3">GFF3</option>
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63 <option value="bed">BED</option>
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64 <option value="gff2">GFF2</option>
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65 <option value="wig">WIG</option>
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66 <option value="sam">SAM</option>
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67 <option value="csv">CSV</option>
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68 <option value="gtf">GTF</option>
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69 </param>
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70 <when value="gff3">
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71 </when>
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72 <when value="bed">
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73 </when>
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74 <when value="gff2">
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75 </when>
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76 <when value="wig">
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77 </when>
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78 <when value="sam">
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79 </when>
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80 <when value="csv">
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81 </when>
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82 <when value="gtf">
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83 </when>
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84 </conditional>
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85
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86 <param name="name" type="text" value="SMART" label="name for the transcripts"/>
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87
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88 <conditional name="optionSequence">
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89 <param name="choose" type="select" label="give the corresponding Multi-Fasta file (useful for EMBL format)">
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90 <option value="Yes">Yes</option>
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91 <option value="No" selected="true">No</option>
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92 </param>
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93 <when value="Yes">
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94 <param name="value" type="data" format="mfa" />
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95 </when>
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96 <when value="No">
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97 </when>
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98 </conditional>
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99
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100 <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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101
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102 </inputs>
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103
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104 <outputs>
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105 <data name="outputFile" format="gff3" label="$inputFormatType.FormatInputFileName to $outputFormatType.outFormat">
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106 <change_format>
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107 <when input="outputFormatType.outFormat" value="bed" format="bed" />
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108 <when input="outputFormatType.outFormat" value="gff2" format="gff2" />
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109 <when input="outputFormatType.outFormat" value="wig" format="wig" />
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110 <when input="outputFormatType.outFormat" value="sam" format="sam" />
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111 <when input="outputFormatType.outFormat" value="csv" format="csv" />
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112 <when input="outputFormatType.outFormat" value="gtf" format="gtf" />
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113 </change_format>
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114 </data>
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115 </outputs>
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116
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117 <help>
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118 </help>
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119 </tool>
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