Mercurial > repos > charles > cytosine_report_to_bedgraph
comparison cytosine_report_to_bedgraph.xml @ 0:b3f6f58f454c draft default tip
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author | charles |
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date | Mon, 14 Nov 2016 04:53:25 -0500 |
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-1:000000000000 | 0:b3f6f58f454c |
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1 <tool id="cytosine_report_to_bedgraph" name="Cytosine Report To Bedgraphs" version="0.0.0"> | |
2 | |
3 <description>Converts genome-wide cytosine methylation report to Bedgraphs</description> | |
4 | |
5 <requirements> | |
6 <requirement type="package" version="2.3.32">igvtools</requirement> | |
7 </requirements> | |
8 | |
9 <command interpreter="python"> | |
10 <![CDATA[ | |
11 cytosine_report_to_bedgraph_wrapper.py | |
12 | |
13 --tool_dir "$__tool_directory__" | |
14 | |
15 --cytosine_report "$cytosine_report" | |
16 | |
17 --coverage_bedgraph "$coverage_bedgraph" | |
18 #if $tdf['tdf_selector']: | |
19 --tdf | |
20 --igv_genome "${tdf.built_in_igv_genomes_chr_sizes.fields.path}" | |
21 --coverage_tdf "$coverage_tdf" | |
22 #end if | |
23 | |
24 #if $context: | |
25 --context | |
26 --CpG_bedgraph "$CpG_bedgraph" | |
27 --CHG_bedgraph "$CHG_bedgraph" | |
28 --CHH_bedgraph "$CHH_bedgraph" | |
29 #if $tdf['tdf_selector']: | |
30 --CpG_tdf "$CpG_tdf" | |
31 --CHG_tdf "$CHG_tdf" | |
32 --CHH_tdf "$CHH_tdf" | |
33 #end if | |
34 #else | |
35 --CXX "$CXX_bedgraph" | |
36 #if $tdf['tdf_selector']: | |
37 --CXX "$CXX_tdf" | |
38 #end if | |
39 #end if | |
40 | |
41 --log "$log_report" | |
42 ]]> | |
43 </command> | |
44 <inputs> | |
45 <param name="cytosine_report" type="data" format="txt" label="Submit a genome-wide cytosine methylation report" optional="False" /> | |
46 <param name="context" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Create a bedGraph for each cytosine methylation context?" /> | |
47 <conditional name="tdf"> | |
48 <param name="tdf_selector" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a tdf file from each resulting bedGraph?" /> | |
49 <when value="true"> | |
50 <param name="built_in_igv_genomes_chr_sizes" type="select" label="Select Reference Genome (igv genomes chr.sizes)" help="If your genome of interest is not listed, contact your Galaxy admin"> | |
51 <options from_data_table="igv_genomes_chr_sizes"> | |
52 <filter type="sort_by" column="name"/> | |
53 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | |
54 </options> | |
55 </param> | |
56 </when> | |
57 <when value="false"></when> | |
58 </conditional> | |
59 </inputs> | |
60 | |
61 <outputs> | |
62 <data name="log_report" format="txt" label="${tool.name} on ${on_string}: Log Report" /> | |
63 <data name="CpG_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CpG context"> | |
64 <filter>context is True</filter> | |
65 </data> | |
66 <data name="CHG_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CHG context"> | |
67 <filter>context is True</filter> | |
68 </data> | |
69 <data name="CHH_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CHH context"> | |
70 <filter>context is True</filter> | |
71 </data> | |
72 <data name="CXX_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CXX"> | |
73 <filter>context is False</filter> | |
74 </data> | |
75 <data name="coverage_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: Coverage" /> | |
76 <data name="CpG_tdf" format="tdf" label="${tool.name} on ${on_string}: CpG context (tdf)"> | |
77 <filter>tdf['tdf_selector'] is True and context is True</filter> | |
78 </data> | |
79 <data name="CHG_tdf" format="tdf" label="${tool.name} on ${on_string}: CHG context (tdf)"> | |
80 <filter>tdf['tdf_selector'] is True and context is True</filter> | |
81 </data> | |
82 <data name="CHH_tdf" format="tdf" label="${tool.name} on ${on_string}: CHH context (tdf)"> | |
83 <filter>tdf['tdf_selector'] is True and context is True</filter> | |
84 </data> | |
85 <data name="CXX_tdf" format="tdf" label="${tool.name} on ${on_string}: CXX (tdf)"> | |
86 <filter>context is False and tdf['tdf_selector'] is True</filter> | |
87 </data> | |
88 <data name="coverage_tdf" format="tdf" label="${tool.name} on ${on_string}: Coverage (tdf)" > | |
89 <filter>tdf['tdf_selector'] is True</filter> | |
90 </data> | |
91 </outputs> | |
92 | |
93 <tests></tests> | |
94 | |
95 <help> | |
96 <![CDATA[ | |
97 | |
98 **What it does** | |
99 | |
100 | This tool takes as input a genome-wide cytosine methylation report (generated by the tool *Bismark Meth. Extractor*) and converts it into a bedGraph for each cytosine context (CpG, CHG and CHH). | |
101 | These bedGraphs display, for a given context, the ratio of methylation of each covered cytosine in the genome. | |
102 | | |
103 | It also produces a bedGraph displaying the coverage count of each cytosine in the genome (non-covered cytosine are ignored). | |
104 | | |
105 | |
106 .. class:: infomark | |
107 | |
108 | The tool outputs offer the possibility to vizualise the methylation signal of covered cytosines thanks to softwares like IGV (*Integrative Genomics Viewer*). | |
109 | In this respect, the tool can optionally generate a tdf binary file (*Tiled Data Format*) from each converted bedGraph. Tdf format is indeed better handled by IGV than bedGraph. | |
110 ]]> | |
111 </help> | |
112 </tool> |