6
+ − 1 <tool id="CleanTranscriptFile" name="Clean Transcript File">
+ − 2 <description> Clean a transcript file so that it is useable for S-MART.</description>
+ − 3 <command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName
+ − 4 #if $formatType.FormatInputFileName == 'gff':
+ − 5 -f gff
+ − 6 #elif $formatType.FormatInputFileName == 'gtf':
+ − 7 -f gtf
+ − 8 #elif $formatType.FormatInputFileName == 'gff3':
+ − 9 -f gff3
+ − 10 #end if
+ − 11 #if $optionType.type == 'Yes':
+ − 12 -t $optionType.value
+ − 13 #end if
+ − 14 -o $outputFile
+ − 15 </command>
+ − 16
+ − 17 <inputs>
+ − 18 <conditional name="formatType">
+ − 19 <param name="FormatInputFileName" type="select" label="Input File Format">
+ − 20 <option value="gff">gff</option>
+ − 21 <option value="gtf">gtf</option>
+ − 22 <option value="gff3">gff3</option>
+ − 23 </param>
+ − 24 <when value="gff">
+ − 25 <param name="inputFileName" format="gff" type="data" label="Input File"/>
+ − 26 </when>
+ − 27 <when value="gtf">
+ − 28 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
+ − 29 </when>
+ − 30 <when value="gff3">
+ − 31 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
+ − 32 </when>
+ − 33 </conditional>
+ − 34
+ − 35 <conditional name="optionType">
+ − 36
+ − 37 <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)">
+ − 38 <option value="Yes">Yes</option>
+ − 39 <option value="No" selected="true">No</option>
+ − 40 </param>
+ − 41 <when value="Yes">
+ − 42 <param name="value" type="text" value="tRNA,rRNA,ncRNA,CDS,exon"/>
+ − 43 </when>
+ − 44 <when value="No">
+ − 45 </when>
+ − 46 </conditional>
+ − 47
+ − 48 </inputs>
+ − 49
+ − 50
+ − 51 <outputs>
+ − 52 <data name="outputFile" format="gtf">
+ − 53 <change_format>
+ − 54 <when input="formatType.FormatInputFileName" value="gff" format="gff" />
+ − 55 <when input="formatType.FormatInputFileName" value="gff3" format="gff3" />
+ − 56 </change_format>
+ − 57 </data>
+ − 58
+ − 59 </outputs>
+ − 60 </tool>