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comparison macs2_macros.xml @ 18:640d3af5d833 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
author iuc
date Sat, 02 Apr 2022 21:37:38 +0000
parents acbd3fb47f90
children 86e2413cf3f8
comparison
equal deleted inserted replaced
17:424aefbd7777 18:640d3af5d833
1 <macros> 1 <macros>
2 <token name="@VERSION_STRING@">2.1.1.20160309</token> 2 <token name="@TOOL_VERSION@">2.2.7.1</token>
3 3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@VERSION_STRING@">macs2</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">macs2</requirement>
7 <requirement type="package" version="3.4">r-base</requirement> 7 <requirement type="package" version="3.4">r-base</requirement>
8 <yield /> 8 <yield />
9 </requirements> 9 </requirements>
10 </xml> 10 </xml>
11 11 <xml name="bio_tools">
12 <xrefs>
13 <xref type="bio.tools">macs</xref>
14 </xrefs>
15 </xml>
12 <token name="@home_dir@"><![CDATA[ 16 <token name="@home_dir@"><![CDATA[
13 export PYTHON_EGG_CACHE=`pwd` && 17 export PYTHON_EGG_CACHE=`pwd` &&
14 ]]></token> 18 ]]></token>
15 19
16 <xml name="conditional_effective_genome_size"> 20 <xml name="conditional_effective_genome_size">
52 <when value="auto" /> 56 <when value="auto" />
53 </conditional> 57 </conditional>
54 </xml> 58 </xml>
55 59
56 <xml name="mfold_options"> 60 <xml name="mfold_options">
57 <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)" > 61 <section name="mfold" title="Mfold settings" expanded="True"
62 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" >
58 <param name="lower" type="integer" value="5" label="Set lower mfold bound" /> 63 <param name="lower" type="integer" value="5" label="Set lower mfold bound" />
59 <param name="upper" type="integer" value="50" label="Set upper mfold bound" /> 64 <param name="upper" type="integer" value="50" label="Set upper mfold bound" />
60 </section> 65 </section>
61 </xml> 66 </xml>
62 67
70 #else: 75 #else:
71 --gsize '${ effective_genome_size_options.effective_genome_size_options_selector }' 76 --gsize '${ effective_genome_size_options.effective_genome_size_options_selector }'
72 #end if 77 #end if
73 </token> 78 </token>
74 79
80 <xml name="buffer_size">
81 <param argument="--buffer-size" type="integer" min="0" value="100000" label="Buffer size"
82 help="Buffer size for incrementally increasing internal array size to store reads alignment information. In most cases, you don't have to change this parameter.
83 However, if there are large number of chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size in order to
84 decrease memory usage (but it will take longer time to read alignment files)." />
85 </xml>
86
87 <token name="@buffer_size@">
88 --buffer-size $buffer_size
89 </token>
90
75 <xml name="version_command"> 91 <xml name="version_command">
76 <version_command>macs2 --version</version_command> 92 <version_command>macs2 --version</version_command>
77 </xml> 93 </xml>
78 94
79 <xml name="tag_size"> 95 <xml name="tag_size">
80 <param name="tsize" type="integer" label="Tag size" value="" optional="true" 96 <param argument="--tsize" type="integer" label="Tag size" value="" optional="true"
81 help="This will override the auto detected tag size. Per default that option is deactivated: -1.0 (--tsize)" /> 97 help="This will override the auto detected tag size. Per default that option is deactivated: -1.0 " />
82 </xml> 98 </xml>
83 <xml name="band_width"> 99 <xml name="band_width">
84 <param name="band_width" type="integer" value="300" 100 <param name="band_width" type="integer" value="300"
85 label="Band width for picking regions to compute fragment size" 101 label="Band width for picking regions to compute fragment size"
86 help=" You can set this parameter as the medium fragment size expected from sonication or size selection. (--bw)" /> 102 help=" You can set this parameter as the medium fragment size expected from sonication or size selection. (--bw)" />
103 </xml>
104
105 <xml name="fragment_size">
106 <param argument="--d-min" type="integer" value="20"
107 label="Minimum fragment size in basepair"
108 help="Any predicted fragment size less than this will be excluded."/>
87 </xml> 109 </xml>
88 110
89 <token name="@tag_size@"> 111 <token name="@tag_size@">
90 #if $tsize: 112 #if $tsize:
91 --tsize '${ tsize }' 113 --tsize '${ tsize }'