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comparison SMART/galaxy/clusterizeBySlidingWindows.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 <tool id="clusterizeBySlidingWindows" name="clusterize by sliding windows"> 1 <tool id="clusterizeBySlidingWindows" name="clusterize By SlidingWindows">
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> 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) and keep only highest peaks.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> 3 <command interpreter="python">
7 ../Java/Python/clusterizeBySlidingWindows.py -i $formatType.inputFileName 4 ../Java/Python/clusterizeBySlidingWindows.py -i $formatType.inputFileName
8 #if $formatType.FormatInputFileName == 'bed': 5 #if $formatType.FormatInputFileName == 'bed':
9 -f bed 6 -f bed
10 #elif $formatType.FormatInputFileName == 'gff': 7 #elif $formatType.FormatInputFileName == 'gff':
74 </conditional> 71 </conditional>
75 72
76 73
77 <param name="size" type="text" value="50000" label="Size option" help="Size of the regions."/> 74 <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."/> 75 <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)"/> 76 <param name="normalize" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Normalize option for only GFF3 file format" help="This option normalizes (Warning!! Only for GFF3 file!)"/>
80 <param name="strands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="Consider the two strands separately"/> 77 <param name="strands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="strands option" help="Consider the two strands separately."/>
81 78
82 <conditional name="OptionTag"> 79 <conditional name="OptionTag">
83 <param name="tag" type="select" label="Use a given tag as input (instead of summing number of features)"> 80 <param name="tag" type="select" label="use a given tag as input (instead of summing number of features)">
84 <option value="Yes">Yes</option> 81 <option value="Yes">Yes</option>
85 <option value="No" selected="true">No</option> 82 <option value="No" selected="true">No</option>
86 </param> 83 </param>
87 <when value="Yes"> 84 <when value="Yes">
88 <param name="value" type="select" label="tag name"/> 85 <param name="value" type="text" value="None" label="tag option" help="write a tag name you want to observe."/>
89 </when> 86 </when>
90 <when value="No"> 87 <when value="No">
91 </when> 88 </when>
92 </conditional> 89 </conditional>
93 90
94 91
95 <conditional name="OptionsOperation"> 92 <conditional name="OptionsOperation">
96 <param name="operation" type="select" label="combine tag value with given operation"> 93 <param name="operation" type="select" label="combine tag value with given operation [choice (sum, avg, med, min, max)]">
97 <option value="Yes">Yes</option> 94 <option value="Yes">Yes</option>
98 <option value="No" selected="true">No</option> 95 <option value="No" selected="true">No</option>
99 </param> 96 </param>
100 <when value="Yes"> 97 <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."> 98 <param name="value" type="text" value="None" label="operation option" help="You can ONLY choose one of fowlling 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> 99 </when>
109 <when value="No"> 100 <when value="No">
110 </when> 101 </when>
111 </conditional> 102 </conditional>
112 103
121 </when> 112 </when>
122 <when value="No"> 113 <when value="No">
123 </when> 114 </when>
124 </conditional> 115 </conditional>
125 116
117 <param name="strand" type="boolean" truevalue="-2" falsevalue="" checked="false" label="strand option" help="This option considers the two strands separately."/>
118 <param name="plot" type="boolean" truevalue="-p" falsevalue="" checked="false" label="plot option" help="This option creates a png file."/>
119 <param name="excel" type="boolean" truevalue="-x" falsevalue="" checked="false" label="excel option" help="This option creates a csv file."/>
120
126 </inputs> 121 </inputs>
127 122
128 <outputs> 123 <outputs>
129 <data name="outputFileGff" format="gff3"/> 124 <data name="outputFileGff" format="gff3"/>
125 <data name="excelOutput" format="csv">
126 <filter>excel</filter>
127 </data>
128 <data name="plotPng" format="png">
129 <filter>plot</filter>
130 </data>
130 </outputs> 131 </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> 132 </tool>