|
0
|
1 <tool id="ceasbw" name="CEAS" version="1.0.2-0">
|
|
|
2 <description>Annotate intervals and scores with genome features (cistrome CEAS)</description>
|
|
|
3 <command interpreter="bash">ceasbw_wrapper.sh $bed_file $gdb_file $extra_bed_file $log_output $pdf_report $xls_output
|
|
|
4 #if (str($wig_file.ext) == 'bigwig')
|
|
|
5 --bigwig $wig_file
|
|
|
6 --length $GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${bed_file.dbkey}.len
|
|
|
7 # else
|
|
|
8 --wig $wig_file
|
|
|
9 #end if
|
|
|
10 #if (str($span) and int(str($span)) > 0)
|
|
|
11 --span $span
|
|
|
12 #end if
|
|
|
13 --sizes $sizes_lower,$sizes_middle,$sizes_upper
|
|
|
14 --bisizes $bisizes_lower,$bisizes_upper
|
|
|
15 --pf-res $profiling_resolution
|
|
|
16 --rel-dist $relative_distance</command>
|
|
|
17 <requirements>
|
|
|
18 <requirement type="package" version="1.2.5">python_mysqldb</requirement>
|
|
|
19 <requirement type="package" version="0.7.1">bx_python</requirement>
|
|
|
20 <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement>
|
|
|
21 </requirements>
|
|
|
22 <inputs>
|
|
|
23 <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" />
|
|
|
24 <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true" />
|
|
|
25 <param name="extra_bed_file" type="data" format="bed" label="BED file with extra regions of interest (e.g. non-coding regions)" optional="true" />
|
|
|
26 <param name="gdb_file" type="select" label="Gene annotation table">
|
|
|
27 <options from_data_table="ceas_annotations">
|
|
|
28 <filter name="dbkey" type="data_meta" ref="bed_file" key="dbkey" column="0" />
|
|
|
29 <validator type="no_options" message="No tables are available for the selected input"/>
|
|
|
30 </options>
|
|
|
31 </param>
|
|
|
32 <param name="span" type="integer" label="Span from TSS and TTS in the gene-centered annotation (bp)" help="ChIP regions within this range from TSS and TTS are considered when calculating the coverage rates of promoter and downstream by ChIP regions" value="3000" />
|
|
|
33 <param name="sizes_lower" type="integer" label="Lower interval for promoter/downstream sizes for ChIP region annotation (bp)" value="1000" />
|
|
|
34 <param name="sizes_middle" type="integer" label="Middle interval for promoter/downstream sizes (bp)" value="2000" help="Values > 10000bp are automatically fixed to 10000bp" />
|
|
|
35 <param name="sizes_upper" type="integer" label="Upper interval for promoter/downstream sizes (bp)" value="3000" help="Values > 10000bp are automatically fixed to 10000bp" />
|
|
|
36 <param name="bisizes_lower" type="integer" label="Lower interval for bidirectional-promoter sizes for ChIP region annotation (bp)" value="2500" />
|
|
|
37 <param name="bisizes_upper" type="integer" label="Upper interval for bidirectional-promoter sizes (bp)" value="5000" help="Values > 20000bp are automatically fixed to 20000bp" />
|
|
|
38 <param name="profiling_resolution" type="integer" label="Wig profiling resolution (bp)" value="50" help="Warning: a number smaller than the wig interval (resolution) may cause aliasing error" />
|
|
|
39 <param name="relative_distance" type="integer" label="Relative distance to TSS/TTS in wig profiling (bp)" value="3000" />
|
|
|
40 </inputs>
|
|
|
41 <outputs>
|
|
|
42 <data name="log_output" format="txt" label="CEAS on ${on_string} (log output)" />
|
|
|
43 <data name="pdf_report" format="pdf" label="CEAS on ${on_string} (PDF report)" />
|
|
|
44 <data name="xls_output" format="interval" label="CEAS on ${on_string} (XLS output)" />
|
|
|
45 </outputs>
|
|
|
46 <help>
|
|
|
47 **What it does**
|
|
|
48
|
|
|
49 CEAS (Cis-regulatory Element Annotation System) is a tool for characterizing genome-wide
|
|
|
50 protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad
|
|
|
51 binding factors. It provides statistics on ChIP enrichment at important genome features
|
|
|
52 such as specific chromosome, promoters, gene bodies, or exons, and infers genes most
|
|
|
53 likely to be regulated by a binding factor.
|
|
|
54
|
|
|
55 CEAS also enables biologists to visualize the average ChIP enrichment signals over
|
|
|
56 specific genomic features, allowing continuous and broad ChIP enrichment to be perceived
|
|
|
57 which might be too subtle to detect from ChIP peaks alone.
|
|
|
58
|
|
|
59 This tool is compatible with the ceasBW version of CEAS from the Cistrome package
|
|
|
60 obtained from
|
|
|
61
|
|
|
62 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
|
|
|
63
|
|
|
64 (commit id d8c0751, datestamp 20140929). The CEAS code is under the
|
|
|
65 published-packages/CEAS/ subdirectory.
|
|
|
66
|
|
|
67 Cistrome data files and documentation can be found at
|
|
|
68
|
|
|
69 http://liulab.dfci.harvard.edu/CEAS/index.html
|
|
|
70
|
|
|
71 The CEAS user manual is available at http://liulab.dfci.harvard.edu/CEAS/usermanual.html
|
|
|
72 </help>
|
|
|
73 </tool>
|
