Mercurial > repos > yufei-luo > s_mart
diff smart_toolShed/SMART/galaxy/Clusterize.xml @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
| author | yufei-luo |
|---|---|
| date | Thu, 17 Jan 2013 10:52:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smart_toolShed/SMART/galaxy/Clusterize.xml Thu Jan 17 10:52:14 2013 -0500 @@ -0,0 +1,73 @@ +<tool id="MergingDataClusterize" name="Clusterize"> + <description>Clusterizes the reads when their genomic intervals overlap.</description> + <command interpreter="python"> + ../Java/Python/clusterize.py -i $formatType.inputFileName + #if $formatType.FormatInputFileName == 'bed': + -f bed + #elif $formatType.FormatInputFileName == 'gff': + -f gff + #elif $formatType.FormatInputFileName == 'gff2': + -f gff2 + #elif $formatType.FormatInputFileName == 'gff3': + -f gff3 + #elif $formatType.FormatInputFileName == 'csv': + -f csv + #elif $formatType.FormatInputFileName == 'sam': + -f sam + #elif $formatType.FormatInputFileName == 'gtf': + -f gtf + #end if + -o $outputFileGff + $colinear + $normalize + -d $distance + $log $outputFileLog + </command> + + <inputs> + <conditional name="formatType"> + <param name="FormatInputFileName" type="select" label="Input File Format"> + <option value="bed">bed</option> + <option value="gff">gff</option> + <option value="gff2">gff2</option> + <option value="gff3">gff3</option> + <option value="csv">csv</option> + <option value="sam">sam</option> + <option value="gtf">gtf</option> + </param> + <when value="bed"> + <param name="inputFileName" format="bed" type="data" label="Input File"/> + </when> + <when value="gff"> + <param name="inputFileName" format="gff" type="data" label="Input File"/> + </when> + <when value="gff2"> + <param name="inputFileName" format="gff2" type="data" label="Input File"/> + </when> + <when value="gff3"> + <param name="inputFileName" format="gff3" type="data" label="Input File"/> + </when> + <when value="csv"> + <param name="inputFileName" format="csv" 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> + + <param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="colinear option" help="This option clusterizes only the same strand reads"/> + <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize option for only GFF3 file format" help="This option normalize (attention!! Only for GFF3 file!!!!!)"/> + <param name="log" type="boolean" truevalue="-l" falsevalue="" checked="false" label="log option" help="This option create a log file"/> + <param name="distance" type="text" value="0" label="distance option" help="Limit the maximum distance between two reads"/> + </inputs> + + <outputs> + <data name="outputFileGff" format="gff3"/> + <data name="outputFileLog" format="txt"> + <filter>log</filter> + </data> + </outputs> +</tool>