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comparison unionBedGraphs.xml @ 0:4fb5ea02b441 draft

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author iuc
date Tue, 15 Jul 2014 14:42:23 -0400
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1 <tool id="bedtools_mergebedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command>unionBedGraphs
9 $header
10 -filler '$filler'
11 #if $zero.value == True:
12 -empty
13 -g ${chromInfo}
14 #end if
15
16 -i '$input1'
17 '$input2'
18 #for $q in $bedgraphs
19 '${q.input}'
20 #end for
21
22 -names
23 #if $name1.choice == "tag":
24 '${input1.name}'
25 #else
26 '${name1.custom_name}'
27 #end if
28
29 #if $name2.choice == "tag":
30 '${input2.name}'
31 #else
32 '${name2.custom_name}'
33 #end if
34
35 #for $q in $bedgraphs
36 #if $q.name.choice == "tag":
37 '${q.input.name}'
38 #else
39 '${q.input.custom_name}'
40 #end if
41 #end for
42 &gt; '$output'
43 </command>
44 <inputs>
45 <!-- Make it easy for the user, first two input files are always shown -->
46 <!-- INPUT 1 -->
47 <param name="input1" format="bedgraph" type="data" label="First BedGraph file" />
48
49 <conditional name="name1">
50 <param name="choice" type="select" label="Sample name">
51 <option value="tag" selected="true">Use input's tag</option>
52 <option value="custom">Enter custom table name</option>
53 </param>
54 <when value="tag">
55 </when>
56 <when value="custom">
57 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
58 </when>
59 </conditional>
60
61 <!-- INPUT 2 -->
62 <param name="input2" format="bedgraph" type="data" label="Second BedGraph file" />
63
64 <conditional name="name2">
65 <param name="choice" type="select" label="Sample name">
66 <option value="tag" selected="true">Use input's tag</option>
67 <option value="custom">Enter custom table name</option>
68 </param>
69 <when value="tag">
70 </when>
71 <when value="custom">
72 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
73 </when>
74 </conditional>
75
76 <!-- Additional files, if the user needs more -->
77 <repeat name="bedgraphs" title="Add'l BedGraph files" >
78 <param name="input" format="bedgraph" type="data" label="BedGraph file" />
79 <conditional name="name">
80 <param name="choice" type="select" label="Sample name">
81 <option value="tag" selected="true">Use input's tag</option>
82 <option value="custom">Enter custom table name</option>
83 </param>
84 <when value="tag">
85 </when>
86 <when value="custom">
87 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
88 </when>
89 </conditional>
90 </repeat>
91
92 <param name="header" type="boolean" checked="true" truevalue="-header" falsevalue="" label="Print header line" help="The first line will include the name of each sample." />
93
94 <param name="zero" type="boolean" checked="true" label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported. Requires a valid organism key for all input datasets" />
95
96 <param name="filler" type="text" value="0" label="Text to use for no-coverage value" help="Can be 0.0, N/A, - or any other value." />
97 </inputs>
98
99 <outputs>
100 <data format="tabular" name="output" metadata_source="input1" label="Merged BedGraphs of ${input1.name}, ${input2.name} and so on." />
101 </outputs>
102 <help>
103
104 **What it does**
105
106 This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files.
107
108 .. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/ubg.png
109
110
111 .. class:: warningmark
112
113 This tool requires that each BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file).
114
115
116 ------
117
118 **Example input**::
119
120 # 1.bedgraph
121 chr1 1000 1500 10
122 chr1 2000 2100 20
123
124 # 2.bedgraph
125 chr1 900 1600 60
126 chr1 1700 2050 50
127
128 # 3.bedgraph
129 chr1 1980 2070 80
130 chr1 2090 2100 20
131
132
133 ------
134
135 **Examples using the Zero Coverage checkbox**
136
137 Output example (*without* checking "Report regions with zero coverage")::
138
139 chr1 900 1000 0 60 0
140 chr1 1000 1500 10 60 0
141 chr1 1500 1600 0 60 0
142 chr1 1700 1980 0 50 0
143 chr1 1980 2000 0 50 80
144 chr1 2000 2050 20 50 80
145 chr1 2050 2070 20 0 80
146 chr1 2070 2090 20 0 0
147 chr1 2090 2100 20 0 20
148
149
150 Output example (*with* checking "Report regions with zero coverage"). The lines marked with (*) are not covered in any input file, but are still reported (The asterisk marking does not appear in the file).::
151
152 chr1 0 900 0 0 0 (*)
153 chr1 900 1000 0 60 0
154 chr1 1000 1500 10 60 0
155 chr1 1500 1600 0 60 0
156 chr1 1600 1700 0 0 0 (*)
157 chr1 1700 1980 0 50 0
158 chr1 1980 2000 0 50 80
159 chr1 2000 2050 20 50 80
160 chr1 2050 2070 20 0 80
161 chr1 2070 2090 20 0 0
162 chr1 2090 2100 20 0 20
163 chr1 2100 247249719 0 0 0 (*)
164
165
166 ------
167
168 **Examples adjusting the "Filler value" for no-covered intervals**
169
170 The default value is '0', but you can use any other value.
171
172 Output example with **filler = N/A**::
173
174 chr1 900 1000 N/A 60 N/A
175 chr1 1000 1500 10 60 N/A
176 chr1 1500 1600 N/A 60 N/A
177 chr1 1600 1700 N/A N/A N/A
178 chr1 1700 1980 N/A 50 N/A
179 chr1 1980 2000 N/A 50 80
180 chr1 2000 2050 20 50 80
181 chr1 2050 2070 20 N/A 80
182 chr1 2070 2090 20 N/A N/A
183 chr1 2090 2100 20 N/A 20
184
185
186 ------
187
188 **Examples using the "sample name" labels**::
189
190 chrom start end WT-1 WT-2 KO-1
191 chr1 900 1000 N/A 60 N/A
192 chr1 1000 1500 10 60 N/A
193 chr1 1500 1600 N/A 60 N/A
194 chr1 1600 1700 N/A N/A N/A
195 chr1 1700 1980 N/A 50 N/A
196 chr1 1980 2000 N/A 50 80
197 chr1 2000 2050 20 50 80
198 chr1 2050 2070 20 N/A 80
199 chr1 2070 2090 20 N/A N/A
200 chr1 2090 2100 20 N/A 20
201
202
203 ------
204
205 **Non-numeric values**
206
207 The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value.
208
209 Input Example::
210
211 File-1 File-2
212 chr1 200 300 Sample1 chr1 100 240 0.75
213 chr1 400 450 Sample1 chr1 250 700 0.43
214 chr1 530 600 Sample2
215
216 Output Example::
217
218 chr1 100 200 0 0.75
219 chr1 200 240 Sample1 0.75
220 chr1 240 250 Sample1 0
221 chr1 250 300 Sample1 0.43
222 chr1 300 400 0 0.43
223 chr1 400 450 Sample1 0.43
224 chr1 450 530 0 0.43
225 chr1 530 600 Sample2 0.43
226 chr1 600 700 0 0.43
227
228 @REFERENCES@
229
230 </help>
231 </tool>