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1 <tool id="CleanTranscriptFile" name="clean transcript file">
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2 <description>Clean a transcript file so that it is useable for S-MART.</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/CleanTranscriptFile.py -i $formatType.inputFileName
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7 #if $formatType.FormatInputFileName == 'gff':
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8 -f gff
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9 #elif $formatType.FormatInputFileName == 'gtf':
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10 -f gtf
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11 #elif $formatType.FormatInputFileName == 'gff3':
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12 -f gff3
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13 #end if
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14 #if $optionType.type == 'Yes':
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15 -t $optionType.value
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16 #end if
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17 -o $outputFile
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18 </command>
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19
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20 <inputs>
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21 <conditional name="formatType">
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22 <param name="FormatInputFileName" type="select" label="Input File Format">
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23 <option value="gff">gff</option>
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24 <option value="gtf">gtf</option>
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25 <option value="gff3">gff3</option>
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26 </param>
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27 <when value="gff">
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28 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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29 </when>
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30 <when value="gtf">
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31 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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32 </when>
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33 <when value="gff3">
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34 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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35 </when>
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36 </conditional>
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37
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38 <conditional name="optionType">
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39
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40 <param name="type" type="select" label="You can choose the tag that you are interested in, like tRNA,rRNA,ncRNA,CDS,exon, etc." help="Name of the types you want to keep in GFF/GTF (list separated by commas)">
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41 <option value="Yes">Yes</option>
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42 <option value="No" selected="true">No</option>
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43 </param>
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44 <when value="Yes">
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45 <param name="value" type="text" value="tRNA,rRNA,ncRNA,CDS,exon"/>
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46 </when>
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47 <when value="No">
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48 </when>
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49 </conditional>
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50
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51 </inputs>
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52
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53
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54 <outputs>
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55 <data name="outputFile" format="gtf">
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56 <change_format>
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57 <when input="formatType.FormatInputFileName" value="gtf" format="gtf" />
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58 <when input="formatType.FormatInputFileName" value="gff" format="gff" />
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59 <when input="formatType.FormatInputFileName" value="gff3" format="gff3" />
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60 </change_format>
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61 </data>
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62
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="FormatInputFileName" value="gtf" />
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67 <param name="inputFileName" value="genes.gtf" />
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68 <param name="type" value="No" />
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69 <output name="outputFile" file="exp_cleantranscriptfile_genes.gtf" />
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70 </test>
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71 </tests>
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72
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73 <help>
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74 A GFF/GTF file (please consult http://www.sequenceontology.org/gff3.shtml to know more about the GFF3 format, and http://mblab.wustl.edu/GTF22.html for the GTF format) may contain different sources of information: chromosome size, genes, transcripts, etc. S-MART mostly works on transcripts. This scripts filters the input file to keep the information you really want, based on the feature (3rd column).
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75 </help>
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76
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77 </tool>
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