38
+ − 1 <tool id="CleanTranscriptFile" name="clean transcript file">
+ − 2 <description>Clean a transcript file so that it is useable for S-MART.</description>
+ − 3 <requirements>
+ − 4 <requirement type="set_environment">PYTHONPATH</requirement>
+ − 5 </requirements>
+ − 6 <command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName
+ − 7 #if $formatType.FormatInputFileName == 'gff':
+ − 8 -f gff
+ − 9 #elif $formatType.FormatInputFileName == 'gtf':
+ − 10 -f gtf
+ − 11 #elif $formatType.FormatInputFileName == 'gff3':
+ − 12 -f gff3
+ − 13 #end if
+ − 14 #if $optionType.type == 'Yes':
+ − 15 -t $optionType.value
+ − 16 #end if
+ − 17 -o $outputFile
+ − 18 </command>
+ − 19
+ − 20 <inputs>
+ − 21 <conditional name="formatType">
+ − 22 <param name="FormatInputFileName" type="select" label="Input File Format">
+ − 23 <option value="gff">gff</option>
+ − 24 <option value="gtf">gtf</option>
+ − 25 <option value="gff3">gff3</option>
+ − 26 </param>
+ − 27 <when value="gff">
+ − 28 <param name="inputFileName" format="gff" type="data" label="Input File"/>
+ − 29 </when>
+ − 30 <when value="gtf">
+ − 31 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
+ − 32 </when>
+ − 33 <when value="gff3">
+ − 34 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
+ − 35 </when>
+ − 36 </conditional>
+ − 37
+ − 38 <conditional name="optionType">
+ − 39
+ − 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)">
+ − 41 <option value="Yes">Yes</option>
+ − 42 <option value="No" selected="true">No</option>
+ − 43 </param>
+ − 44 <when value="Yes">
+ − 45 <param name="value" type="text" value="tRNA,rRNA,ncRNA,CDS,exon"/>
+ − 46 </when>
+ − 47 <when value="No">
+ − 48 </when>
+ − 49 </conditional>
+ − 50
+ − 51 </inputs>
+ − 52
+ − 53
+ − 54 <outputs>
+ − 55 <data name="outputFile" format="gtf">
+ − 56 <change_format>
+ − 57 <when input="formatType.FormatInputFileName" value="gtf" format="gtf" />
+ − 58 <when input="formatType.FormatInputFileName" value="gff" format="gff" />
+ − 59 <when input="formatType.FormatInputFileName" value="gff3" format="gff3" />
+ − 60 </change_format>
+ − 61 </data>
+ − 62
+ − 63 </outputs>
+ − 64 <tests>
+ − 65 <test>
+ − 66 <param name="FormatInputFileName" value="gtf" />
+ − 67 <param name="inputFileName" value="genes.gtf" />
+ − 68 <param name="type" value="No" />
+ − 69 <output name="outputFile" file="exp_cleantranscriptfile_genes.gtf" />
+ − 70 </test>
+ − 71 </tests>
+ − 72
+ − 73 <help>
+ − 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).
+ − 75 </help>
+ − 76
+ − 77 </tool>
