Mercurial > repos > yufei-luo > s_mart
diff SMART/galaxy/ConvertTranscriptFile.xml @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/galaxy/ConvertTranscriptFile.xml Tue Apr 30 15:02:29 2013 -0400 @@ -0,0 +1,95 @@ +<tool id="ConvertTranscriptFile" name="convert transcript file"> + <description>Convert a file from a format to another.</description> + <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName + #if $inputFormatType.FormatInputFileName == 'gff3': + -f gff3 + #elif $inputFormatType.FormatInputFileName == 'bed': + -f bed + #elif $inputFormatType.FormatInputFileName == 'bam': + -f blast + #elif $inputFormatType.FormatInputFileName == 'sam': + -f sam + #elif $inputFormatType.FormatInputFileName == 'gtf': + -f gtf + #end if + + -g $outputFormatType.outFormat + + -n $name + $strand + -o $outputFile + + </command> + <inputs> + <conditional name="inputFormatType"> + <param name="FormatInputFileName" type="select" label="Input File Format"> + <option value="gff3">GFF3</option> + <option value="bed">BED</option> + <option value="bam">BAM</option> + <option value="sam">SAM</option> + <option value="gtf">GTF</option> + </param> + <when value="gff3"> + <param name="inputFileName" format="gff3" type="data" label="Input File"/> + </when> + <when value="bed"> + <param name="inputFileName" format="bed" type="data" label="Input File"/> + </when> + <when value="bam"> + <param name="inputFileName" format="bam" type="data" label="Input File"/> + </when> + <when value="sam"> + <param name="inputFileName" format="sam" type="data" label="Input File"/> + </when> + <when value="gtf"> + <param name="inputFileName" format="gtf" type="data" label="Input File"/> + </when> + </conditional> + + + <conditional name="outputFormatType"> + <param name="outFormat" type="select" label="Please choose the format that you want to convert to (corresponding to your input file format)."> + <option value="gff3">GFF3</option> + <option value="bed">BED</option> + <option value="wig">WIG</option> + <option value="sam">SAM</option> + <option value="csv">CSV</option> + <option value="gtf">GTF</option> + </param> + <when value="gff3"> + </when> + <when value="bed"> + </when> + <when value="wig"> + </when> + <when value="sam"> + </when> + <when value="csv"> + </when> + <when value="gtf"> + </when> + </conditional> + + <param name="name" type="text" value="SMART" label="name for the transcripts"/> + + <param name="strand" type="boolean" truevalue="-t" falsevalue="" checked="false" label="consider the 2 strands as different (only useful for writing WIG files)"/> + + </inputs> + + <outputs> + <data name="outputFile" format="gff3" label="$inputFormatType.FormatInputFileName to $outputFormatType.outFormat"> + <change_format> + <when input="outputFormatType.outFormat" value="bed" format="bed" /> + <when input="outputFormatType.outFormat" value="gff" format="gff" /> + <when input="outputFormatType.outFormat" value="wig" format="wig" /> + <when input="outputFormatType.outFormat" value="sam" format="sam" /> + <when input="outputFormatType.outFormat" value="csv" format="csv" /> + <when input="outputFormatType.outFormat" value="gtf" format="gtf" /> + </change_format> + </data> + </outputs> + + <help> +Simple conversion tool. + </help> +</tool>