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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
children 94ab73e8a190
comparison
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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 #elif $formatType.FormatInputFileName == 'gtf': 15 #elif $formatType.FormatInputFileName == 'gtf':
18 -f gtf 16 -f gtf
19 #end if 17 #end if
20 -o $outputFileGff 18 -o $outputFileGff
21 $colinear 19 $colinear
22 $normalize 20 $normalize
23 -d $distance 21 -d $distance
24 $log $outputFileLog
25 </command> 22 </command>
26 23
27 <inputs> 24 <inputs>
28 <conditional name="formatType"> 25 <conditional name="formatType">
29 <param name="FormatInputFileName" type="select" label="Input File Format"> 26 <param name="FormatInputFileName" type="select" label="Input File Format">
30 <option value="bed">bed</option> 27 <option value="bed">bed</option>
31 <option value="gff">gff</option> 28 <option value="gff">gff</option>
32 <option value="gff2">gff2</option> 29 <option value="gff2">gff2</option>
33 <option value="gff3">gff3</option> 30 <option value="gff3">gff3</option>
34 <option value="csv">csv</option>
35 <option value="sam">sam</option> 31 <option value="sam">sam</option>
36 <option value="gtf">gtf</option> 32 <option value="gtf">gtf</option>
37 </param> 33 </param>
38 <when value="bed"> 34 <when value="bed">
39 <param name="inputFileName" format="bed" type="data" label="Input File"/> 35 <param name="inputFileName" format="bed" type="data" label="Input File"/>
45 <param name="inputFileName" format="gff2" type="data" label="Input File"/> 41 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
46 </when> 42 </when>
47 <when value="gff3"> 43 <when value="gff3">
48 <param name="inputFileName" format="gff3" type="data" label="Input File"/> 44 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
49 </when> 45 </when>
50 <when value="csv">
51 <param name="inputFileName" format="csv" type="data" label="Input File"/>
52 </when>
53 <when value="sam"> 46 <when value="sam">
54 <param name="inputFileName" format="sam" type="data" label="Input File"/> 47 <param name="inputFileName" format="sam" type="data" label="Input File"/>
55 </when> 48 </when>
56 <when value="gtf"> 49 <when value="gtf">
57 <param name="inputFileName" format="gtf" type="data" label="Input File"/> 50 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
58 </when> 51 </when>
59 </conditional> 52 </conditional>
60 53
61 <param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="colinear option" help="This option clusterizes only the same strand reads"/> 54 <param name="colinear" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Only merge collinear features"/>
62 <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!!!!!)"/> 55 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Normalize counts" help="Only works if the nbOccurrences tag is set."/>
63 <param name="log" type="boolean" truevalue="-l" falsevalue="" checked="false" label="log option" help="This option create a log file"/> 56 <param name="distance" type="text" value="0" label="merge features if their relative distance is within N nt"/>
64 <param name="distance" type="text" value="0" label="distance option" help="Limit the maximum distance between two reads"/>
65 </inputs> 57 </inputs>
66 58
67 <outputs> 59 <outputs>
68 <data name="outputFileGff" format="gff3"/> 60 <data name="outputFileGff" format="gff3"/>
69 <data name="outputFileLog" format="txt">
70 <filter>log</filter>
71 </data>
72 </outputs> 61 </outputs>
62
63 <help>
64 The script clusterizes the input genomic data. Two features are clusterized when their genomic intervals overlap. The output is a GFF3 file, where each element is a cluster. The number of elements in the cluster is given by the tag **nbElements**. The name of a cluster is the concatation of the names of its reads (like **read1--read2--read3**). Note that if the size of the name of the cluster exceeds 100 characters, it is truncated to the first 100 characters.
65
66 Some options may clusterize the features which are closer than a given distance.
67
68 By default, the tool clusterizes all features which overlap (or nearly overlap), even if they are on different strands. If you want to clusterize the features which are on the same strand only, you can specify it.
69 </help>
73 </tool> 70 </tool>