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comparison macs2_macros.xml @ 5:beb902da6e5f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
author iuc
date Sat, 08 Apr 2017 08:28:57 -0400
parents 6d4babad010f
children e8a060164e11
comparison
equal deleted inserted replaced
4:56e104999978 5:beb902da6e5f
1 <macros> 1 <macros>
2 <token name="@VERSION_STRING@">2.1.1.20160309</token>
3
2 <xml name="requirements"> 4 <xml name="requirements">
3 <requirements> 5 <requirements>
4 <requirement type="package" version="2.1.0.20151222">macs2</requirement> 6 <requirement type="package" version="@VERSION_STRING@">macs2</requirement>
5 <requirement type="package" version="1.7.1">numpy</requirement>
6 <requirement type="package" version="0.12.0">scipy</requirement>
7 <yield /> 7 <yield />
8 </requirements> 8 </requirements>
9 </xml> 9 </xml>
10 10
11 <token name="@VERSION_STRING@">2.1.0.20151222</token>
12
13 <xml name="conditional_effective_genome_size"> 11 <xml name="conditional_effective_genome_size">
14 <conditional name="effective_genome_size_options"> 12 <conditional name="effective_genome_size_options">
15 <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" 13 <param name="effective_genome_size_options_selector" type="select" label="Effective genome size"
16 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. 14 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of Ns that should be discarded.
17 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. 15 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. (--gsize)">
18 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes. (--gsize)"> 16 <option value="2451960000">H. sapiens (2,451,960,000)</option>
19 <option value="2451960000">Human (2,451,960,000)</option> 17 <option value="2150570000">M. musculus (2,150,570,000)</option>
20 <option value="2150570000">Mouse (2,150,570,000)</option> 18 <option value="121400000">D. melanogaster (121,400,000)</option>
21 <option value="121400000">Fly (121,400,000)</option> 19 <option value="93260000">C. elegans (93,260,000)</option>
22 <option value="93260000">Worm (93,260,000)</option> 20 <option value="12400000">S. cerevisiae (12,400,000)</option>
23 <option value="user_defined">User defined</option> 21 <option value="user_defined">User defined</option>
24 </param> 22 </param>
25 <when value="2451960000" /> 23 <when value="2451960000" />
26 <when value="2150570000" /> 24 <when value="2150570000" />
27 <when value="121400000" /> 25 <when value="121400000" />
28 <when value="93260000" /> 26 <when value="93260000" />
27 <when value="12400000" />
29 <when value="user_defined"> 28 <when value="user_defined">
30 <param name="gsize" type="integer" label="Effective genome size" value=""/> 29 <param name="gsize" type="integer" label="Effective genome size" value=""/>
31 </when> 30 </when>
32 </conditional> 31 </conditional>
33 </xml> 32 </xml>
49 <when value="all" /> 48 <when value="all" />
50 <when value="auto" /> 49 <when value="auto" />
51 </conditional> 50 </conditional>
52 </xml> 51 </xml>
53 52
53 <xml name="mfold_options">
54 <section name="mfold" title="Mfold settings" expanded="True" help="Select the regions within MFOLD range of highconfidence enrichment ratio against background to build model. Fold-enrichment in regions must be lower than upper limit, and higher than the lower limit. Default is 5 for lower and 50 for upper (--mfold)" >
55 <param name="lower" type="integer" value="5" label="Set lower mfold bound" />
56 <param name="upper" type="integer" value="50" label="Set upper mfold bound" />
57 </section>
58 </xml>
59
60 <token name="@mfold_command@">
61 --mfold '${mfold.lower}' '${mfold.upper}'
62 </token>
63
54 <token name="@effective_genome_size@"> 64 <token name="@effective_genome_size@">
55 #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined': 65 #if $effective_genome_size_options.effective_genome_size_options_selector == "user_defined":
56 --gsize "${ effective_genome_size_options.gsize }" 66 --gsize '${ effective_genome_size_options.gsize }'
57 #else: 67 #else:
58 --gsize "${ effective_genome_size_options.effective_genome_size_options_selector }" 68 --gsize '${ effective_genome_size_options.effective_genome_size_options_selector }'
59 #end if 69 #end if
60 </token> 70 </token>
61 71
62 <xml name="version_command"> 72 <xml name="version_command">
63 <version_command>macs2 --version</version_command> 73 <version_command>macs2 --version</version_command>
64 </xml> 74 </xml>
65 75
66 <xml name="tag_size"> 76 <xml name="tag_size">
67 <param name="tsize" type="float" label="Tag size" value="-1.0" help="This will override the auto detected tag size. Per default that option is deactivated: -1.0 (--tsize)" /> 77 <param name="tsize" type="integer" label="Tag size" value="" optional="true"
78 help="This will override the auto detected tag size. Per default that option is deactivated: -1.0 (--tsize)" />
68 </xml> 79 </xml>
69 <xml name="band_width"> 80 <xml name="band_width">
70 <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size" 81 <param name="band_width" type="integer" value="300"
71 help="This value is only used while building the shifting model. (--bw)" /> 82 label="Band width for picking regions to compute fragment size"
83 help=" You can set this parameter as the medium fragment size expected from sonication or size selection. (--bw)" />
72 </xml> 84 </xml>
73 85
74 <token name="@tag_size@"> 86 <token name="@tag_size@">
75 #if $tsize == -1.0: 87 #if $tsize:
76 --tsize "${ tsize }" 88 --tsize '${ tsize }'
77 #end if 89 #end if
78 </token> 90 </token>
79 91
80 <xml name="stdio"> 92 <xml name="stdio">
81 <stdio> 93 <stdio>
87 </xml> 99 </xml>
88 100
89 <token name="@citation@"> 101 <token name="@citation@">
90 ------ 102 ------
91 103
92 **Citation** 104 Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening.
93 105
94 For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
95
96 Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening.
97 </token> 106 </token>
98 <xml name="citations"> 107 <xml name="citations">
99 <citations> 108 <citations>
100 <citation type="doi">10.1186/gb-2008-9-9-r137</citation> 109 <citation type="doi">10.1186/gb-2008-9-9-r137</citation>
110 <citation type="doi">10.1038/nprot.2012.101</citation>
101 </citations> 111 </citations>
102 </xml> 112 </xml>
103 </macros> 113 </macros>