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comparison unionBedGraphs.xml @ 10:71af3ebbbb7a draft

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author iuc
date Wed, 29 Apr 2015 12:06:53 -0400
parents 0d3aa592ce27
children a2d4c30ba2f9
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9:21f1d1c5467b 10:71af3ebbbb7a
1 <tool id="bedtools_unionbedgraph" 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>
9 <![CDATA[
10 unionBedGraphs
11 $header
12 -filler "${filler}"
13 #if $zero.value == True:
14 -empty
15 -g $genome
16 #end if
17
18 #if str($tag.tag_select) == "tag":
19 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
20 -i "${files}"
21 #else:
22 -i
23 #for $bg in $tag.bedgraphs:
24 "${bg.input}"
25 #end for
26 -names
27 #for $bg in $tag.bedgraphs:
28 "${bg.custom_name}"
29 #end for
30 #end if
31 > "${output}"
32 ]]>
33 </command>
34 <inputs>
35 <conditional name="tag">
36 <param name="tag_select" type="select" label="Sample name">
37 <option value="tag" selected="true">Use input's tag</option>
38 <option value="custom">Enter custom name per file</option>
39 </param>
40 <when value="tag">
41 <param name="inputs" format="bedgraph" type="data" multiple="True" label="BedGraph files" />
42 </when>
43 <when value="custom">
44 <repeat name="bedgraphs" title="Add BedGraph files" min="2" >
45 <param name="input" format="bedgraph" type="data" multiple="True" label="BedGraph file" />
46 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
47 </repeat>
48 </when>
49 </conditional>
50 <expand macro="genome" />
51 <param name="zero" type="boolean" checked="true"
52 label="Report regions with zero coverage"
53 help="If set, regions without any coverage will also be reported. Requires a valid organism key for all input datasets" />
54 <param name="filler" type="text" value="N/A"
55 label="Text to use for no-coverage value"
56 help="Can be 0.0, N/A, - or any other value. (-filler)" />
57 <expand macro="print_header" />
58 </inputs>
59 <outputs>
60 <data name="output" format="bedgraph" />
61 </outputs>
62 <tests>
63 <test>
64 <param name="tag_select" value="tag"/>
65 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
66 <param name="zero" value="False"/>
67 <output name="output" file="unionBedGraphs_result1.bg" ftype="bedgraph" />
68 </test>
69 <test>
70 <param name="tag_select" value="tag"/>
71 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
72 <param name="header" value="True"/>
73 <param name="zero" value="False"/>
74 <output name="output" file="unionBedGraphs_result2.bg" ftype="bedgraph" />
75 </test>
76 <test>
77 <param name="tag_select" value="tag"/>
78 <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
79 <param name="zero" value="True"/>
80 <param name="genome" value="unionBedGraphs1.len"/>
81 <output name="output" file="unionBedGraphs_result3.bg" ftype="bedgraph" />
82 </test>
83 <test>
84 <param name="tag_select" value="custom"/>
85 <repeat name="bedgraphs">
86 <param name="input" value="unionBedGraphs1.bg" />
87 <param name="custom_name" value="first" />
88 </repeat>
89 <repeat name="bedgraphs">
90 <param name="input" value="unionBedGraphs2.bg" />
91 <param name="custom_name" value="second" />
92 </repeat>
93 <repeat name="bedgraphs">
94 <param name="input" value="unionBedGraphs3.bg" />
95 <param name="custom_name" value="third" />
96 </repeat>
97 <param name="zero" value="True"/>
98 <param name="genome" value="unionBedGraphs1.len"/>
99 <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" />
100 </test>
101 </tests>
102 <help>
103 <![CDATA[
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 <expand macro="citations" />
232 </tool>