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comparison macs2_macros.xml @ 19:05aca18fd8dc draft

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author iuc
date Wed, 23 Apr 2014 18:25:51 -0400
parents ab352bb83cb2
children f63ccb331626
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18:ab352bb83cb2 19:05aca18fd8dc
9 </xml> 9 </xml>
10 10
11 <xml name="conditional_effective_genome_size"> 11 <xml name="conditional_effective_genome_size">
12 <conditional name="effective_genome_size_options"> 12 <conditional name="effective_genome_size_options">
13 <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" help="--gsize"> 13 <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" help="--gsize">
14 <option value="3300000000">Human (3.300.000.000)</option> 14 <option value="2451960000">Human (2.451.960.000)</option>
15 <option value="3000000000">Mouse (3.000.000.000)</option> 15 <option value="2150570000">Mouse (2.150.570.000)</option>
16 <option value="190000000">Fly (190.000.000)</option> 16 <option value="121400000">Fly (121.400.000)</option>
17 <option value="130000000">Worm (130.000.000)</option> 17 <option value="93260000">Worm (93.260.000)</option>
18 <option value="user_defined">User defined</option> 18 <option value="user_defined">User defined</option>
19 </param> 19 </param>
20 <when value="user_defined"> 20 <when value="user_defined">
21 <param name="gsize" type="integer" size="12" label="Effective genome size" value=""/> 21 <param name="gsize" type="integer" size="12" label="Effective genome size" value=""/>
22 </when> 22 </when>
23 </conditional> 23 </conditional>
24 </xml> 24 </xml>
25 25
26 <token name="@effective_genome_size@"> 26 <token name="@effective_genome_size@">
27 #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined': 27 #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined':
28 --gsize $effective_genome_size_options.gsize 28 --gsize "${ effective_genome_size_options.gsize }"
29 #else: 29 #else:
30 --gsize $effective_genome_size_options.effective_genome_size_options_selector 30 --gsize "${ effective_genome_size_options.effective_genome_size_options_selector }"
31 #end if 31 #end if
32 </token> 32 </token>
33 33
34 <xml name="version_command"> 34 <xml name="version_command">
35 <version_command>macs2 --version</version_command> 35 <version_command>macs2 --version</version_command>
43 help="This value is only used while building the shifting model. (--bw)" /> 43 help="This value is only used while building the shifting model. (--bw)" />
44 </xml> 44 </xml>
45 45
46 <token name="@tag_size@"> 46 <token name="@tag_size@">
47 #if $tsize == -1.0: 47 #if $tsize == -1.0:
48 --tsize $tsize 48 --tsize "${ tsize }"
49 #end if 49 #end if
50 </token> 50 </token>
51 51
52 <xml name="stdio"> 52 <xml name="stdio">
53 <stdio> 53 <stdio>