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annotate SMART/galaxy/clusterize.xml @ 16:6135c3075bc5

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author m-zytnicki
date Mon, 22 Apr 2013 11:09:41 -0400
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1 <tool id="MergingDataClusterize" name="Clusterize">
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2 <description>Clusterize features when their genomic intervals overlap.</description>
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3 <command interpreter="python">
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4 ../Java/Python/clusterize.py -i $formatType.inputFileName
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5 #if $formatType.FormatInputFileName == 'bed':
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6 -f bed
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7 #elif $formatType.FormatInputFileName == 'gff':
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8 -f gff
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9 #elif $formatType.FormatInputFileName == 'gff2':
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10 -f gff2
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11 #elif $formatType.FormatInputFileName == 'gff3':
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12 -f gff3
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13 #elif $formatType.FormatInputFileName == 'sam':
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14 -f sam
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15 #end if
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16 -o $outputFileGff
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17 $colinear
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18 $normalize
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19 -d $distance
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20 $log $outputFileLog
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21 </command>
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22
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23 <inputs>
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24 <conditional name="formatType">
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25 <param name="FormatInputFileName" type="select" label="Input File Format">
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26 <option value="bed">bed</option>
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27 <option value="gff">gff</option>
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28 <option value="gff2">gff2</option>
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29 <option value="gff3">gff3</option>
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30 <option value="sam">sam</option>
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31 </param>
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32 <when value="bed">
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33 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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34 </when>
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35 <when value="gff">
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36 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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37 </when>
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38 <when value="gff2">
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39 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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40 </when>
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41 <when value="gff3">
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42 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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43 </when>
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44 <when value="sam">
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45 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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46 </when>
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47 </conditional>
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48
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49 <param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Only merge collinear data"/>
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50 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Normalize data." help="This only works if the tag nbOccurrences is set."/>
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51 <param name="distance" type="integer" value="0" label="Merge features if their relative distance is withing N nt"/>
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52 </inputs>
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53
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54 <outputs>
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55 <data name="outputFileGff" format="gff3" label="[clusterize]output file"/>
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56 </outputs>
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57 </tool>