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comparison SMART/galaxy/clusterize.xml @ 15:440ceca58672

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Uploaded
author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
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14:c79b9ae3f65f 15:440ceca58672
1 <tool id="MergingDataClusterize" name="Clusterize"> 1 <tool id="MergingDataClusterize" name="Clusterize">
2 <description>Clusterizes the reads when their genomic intervals overlap.</description> 2 <description>Clusterize features when their genomic intervals overlap.</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 ../Java/Python/clusterize.py -i $formatType.inputFileName 4 ../Java/Python/clusterize.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'bed': 5 #if $formatType.FormatInputFileName == 'bed':
6 -f bed 6 -f bed
7 #elif $formatType.FormatInputFileName == 'gff': 7 #elif $formatType.FormatInputFileName == 'gff':
8 -f gff 8 -f gff
9 #elif $formatType.FormatInputFileName == 'gff2': 9 #elif $formatType.FormatInputFileName == 'gff2':
10 -f gff2 10 -f gff2
11 #elif $formatType.FormatInputFileName == 'gff3': 11 #elif $formatType.FormatInputFileName == 'gff3':
12 -f gff3 12 -f gff3
13 #elif $formatType.FormatInputFileName == 'csv':
14 -f csv
15 #elif $formatType.FormatInputFileName == 'sam': 13 #elif $formatType.FormatInputFileName == 'sam':
16 -f sam 14 -f sam
17 #end if 15 #end if
18 -o $outputFileGff 16 -o $outputFileGff
19 $colinear 17 $colinear
27 <param name="FormatInputFileName" type="select" label="Input File Format"> 25 <param name="FormatInputFileName" type="select" label="Input File Format">
28 <option value="bed">bed</option> 26 <option value="bed">bed</option>
29 <option value="gff">gff</option> 27 <option value="gff">gff</option>
30 <option value="gff2">gff2</option> 28 <option value="gff2">gff2</option>
31 <option value="gff3">gff3</option> 29 <option value="gff3">gff3</option>
32 <option value="csv">csv</option>
33 <option value="sam">sam</option> 30 <option value="sam">sam</option>
34 </param> 31 </param>
35 <when value="bed"> 32 <when value="bed">
36 <param name="inputFileName" format="bed" type="data" label="Input File"/> 33 <param name="inputFileName" format="bed" type="data" label="Input File"/>
37 </when> 34 </when>
42 <param name="inputFileName" format="gff2" type="data" label="Input File"/> 39 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
43 </when> 40 </when>
44 <when value="gff3"> 41 <when value="gff3">
45 <param name="inputFileName" format="gff3" type="data" label="Input File"/> 42 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
46 </when> 43 </when>
47 <when value="csv">
48 <param name="inputFileName" format="csv" type="data" label="Input File"/>
49 </when>
50 <when value="sam"> 44 <when value="sam">
51 <param name="inputFileName" format="sam" type="data" label="Input File"/> 45 <param name="inputFileName" format="sam" type="data" label="Input File"/>
52 </when> 46 </when>
53 </conditional> 47 </conditional>
54 48
55 <param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="colinear option" help="This option clusterizes only the same strand reads"/> 49 <param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Only merge collinear data"/>
56 <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!!!!!)"/> 50 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Normalize data." help="This only works if the tag nbOccurrences is set."/>
57 <param name="log" type="boolean" truevalue="-l" falsevalue="" checked="false" label="log option" help="This option create a log file"/> 51 <param name="distance" type="integer" value="0" label="Merge features if their relative distance is withing N nt"/>
58 <param name="distance" type="integer" value="0" label="distance option" help="Limit the maximum distance between two reads"/>
59 </inputs> 52 </inputs>
60 53
61 <outputs> 54 <outputs>
62 <data name="outputFileGff" format="gff3" label="[clusterize]output file"/> 55 <data name="outputFileGff" format="gff3" label="[clusterize]output file"/>
63 <data name="outputFileLog" format="txt" label="[clusterize]output file">
64 <filter>log</filter>
65 </data>
66 </outputs> 56 </outputs>
67 </tool> 57 </tool>