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comparison SMART/galaxy/clusterizeBySlidingWindows.xml @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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children 5f5c9b74c2dd
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37:d22fadc825e3 38:2c0c0a89fad7
1 <tool id="clusterizeBySlidingWindows" name="clusterize by sliding windows">
2 <description>Produces a GFF3 file that clusters a list of transcripts using a sliding window. Cluster the data into regions (defined by size and overlap with next region).</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python">
7 ../Java/Python/clusterizeBySlidingWindows.py -i $formatType.inputFileName
8 #if $formatType.FormatInputFileName == 'bed':
9 -f bed
10 #elif $formatType.FormatInputFileName == 'gff':
11 -f gff
12 #elif $formatType.FormatInputFileName == 'gff2':
13 -f gff2
14 #elif $formatType.FormatInputFileName == 'gff3':
15 -f gff3
16 #elif $formatType.FormatInputFileName == 'sam':
17 -f sam
18 #elif $formatType.FormatInputFileName == 'gtf':
19 -f gtf
20 #end if
21 -s $size
22 -e $overlap
23 -o $outputFileGff
24 $normalize
25 $strands
26
27 #if $OptionTag.tag == "Yes":
28 -g $OptionTag.value
29 #end if
30
31 #if $OptionsOperation.operation == "Yes":
32 -r $OptionsOperation.value
33 #end if
34
35 #if $OptionWriteTag.writeTag == "Yes":
36 -w $OptionWriteTag.value
37 #end if
38
39 $strand
40 $plot $plotPng
41 $excel $excelOutput
42
43
44 </command>
45
46 <inputs>
47 <conditional name="formatType">
48 <param name="FormatInputFileName" type="select" label="Input File Format">
49 <option value="bed">bed</option>
50 <option value="gff">gff</option>
51 <option value="gff2">gff2</option>
52 <option value="gff3">gff3</option>
53 <option value="sam">sam</option>
54 <option value="gtf">gtf</option>
55 </param>
56 <when value="bed">
57 <param name="inputFileName" format="bed" type="data" label="Input File"/>
58 </when>
59 <when value="gff">
60 <param name="inputFileName" format="gff" type="data" label="Input File"/>
61 </when>
62 <when value="gff2">
63 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
64 </when>
65 <when value="gff3">
66 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
67 </when>
68 <when value="sam">
69 <param name="inputFileName" format="sam" type="data" label="Input File"/>
70 </when>
71 <when value="gtf">
72 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
73 </when>
74 </conditional>
75
76
77 <param name="size" type="text" value="50000" label="Size option" help="Size of the regions."/>
78 <param name="overlap" type="text" value="50" label="Overlap option" help="Overlap between two consecutive regions."/>
79 <param name="normalize" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Normalize option for only GFF3 file format" help="(only work if the tag nbOccurrences is set)"/>
80 <param name="strands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="Consider the two strands separately"/>
81
82 <conditional name="OptionTag">
83 <param name="tag" type="select" label="Use a given tag as input (instead of summing number of features)">
84 <option value="Yes">Yes</option>
85 <option value="No" selected="true">No</option>
86 </param>
87 <when value="Yes">
88 <param name="value" type="select" label="tag name"/>
89 </when>
90 <when value="No">
91 </when>
92 </conditional>
93
94
95 <conditional name="OptionsOperation">
96 <param name="operation" type="select" label="combine tag value with given operation">
97 <option value="Yes">Yes</option>
98 <option value="No" selected="true">No</option>
99 </param>
100 <when value="Yes">
101 <param name="value" type="select" label="operation" help="You can ONLY choose one of following operation : sum, avg, med, min, max.">
102 <option value="sum">sum</option>
103 <option value="avg">average</option>
104 <option value="med">median</option>
105 <option value="min">minimum</option>
106 <option value="max">maximum</option>
107 </param>
108 </when>
109 <when value="No">
110 </when>
111 </conditional>
112
113
114 <conditional name="OptionWriteTag">
115 <param name="writeTag" type="select" label="write a new tag in output file">
116 <option value="Yes">Yes</option>
117 <option value="No" selected="true">No</option>
118 </param>
119 <when value="Yes">
120 <param name="value" type="text" value="nbElements" label="write tag option" help="print the result in the given tag (default usually is 'nbElements')"/>
121 </when>
122 <when value="No">
123 </when>
124 </conditional>
125
126 </inputs>
127
128 <outputs>
129 <data name="outputFileGff" format="gff3"/>
130 </outputs>
131
132 <help>
133 Sliding windows are a convenient ways to clusterize data mapped on the genome. There are two important parameters of a sliding window: the size of the window and the size of the overlap.
134
135 By default, sliding windows count the number of reads in each window. However, you can basically merge any information which is contained in the tags. You can compute the average, sum, median, max or min of the tags for each window. For instance, every window can contain the average cluster size, if you merge clusters instead of reads.
136
137 The output file is a GFF3 file, where each element is a window. There is a special tag for each window, whose name is **nbElements** if you counted the number of transcripts per sliding window. However, if you performed a **min** (resp. **max**, **sum**, **median**, **average**) operation on the tags **value** of the transcripts, then the tag of the window will be **minValue** (resp. **maxValue**, **sumValue**, **medValue**, **avgValue**). You can also specify the name of your tag (which is actually advised: **nbReadsInSample1** will always be more informative than **nbElements**).
138
139 You also have different option, which can select the *n* % highest regions, or the regions with at least *n* features in it, or even the regions with at least *n* unique features. This last option is useful when you want to cluster the reads which have mapped only once, for instance.
140 </help>
141 </tool>