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comparison ceas_wrapper.xml @ 3:82df5af2995f draft

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Renamed from "ceasbw..." to "ceas...".
author pjbriggs
date Wed, 22 Apr 2015 05:34:06 -0400
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children 4e2883bb058d
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2:695d61decd06 3:82df5af2995f
1 <tool id="ceas" name="CEAS" version="1.0.2-1">
2 <requirements>
3 <requirement type="package" version="1.2.5">python_mysqldb</requirement>
4 <requirement type="package" version="0.7.1">bx_python</requirement>
5 <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement>
6 <requirement type="package" version="3.1.2">R</requirement>
7 </requirements>
8 <description>Annotate intervals and scores with genome features</description>
9 <command interpreter="bash">ceas_wrapper.sh $bed_file $gdb_file $extra_bed_file $log_output $pdf_report $xls_output
10 #if (str($wig_file.ext) == 'bigwig')
11 --bigwig $wig_file
12 --length $GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${bed_file.dbkey}.len
13 # else
14 --wig $wig_file
15 #end if
16 #if (str($span) and int(str($span)) > 0)
17 --span $span
18 #end if
19 --sizes $sizes_lower,$sizes_middle,$sizes_upper
20 --bisizes $bisizes_lower,$bisizes_upper
21 --pf-res $profiling_resolution
22 --rel-dist $relative_distance</command>
23 <inputs>
24 <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" />
25 <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true" />
26 <param name="extra_bed_file" type="data" format="bed" label="BED file with extra regions of interest (e.g. non-coding regions)" optional="true" />
27 <param name="gdb_file" type="select" label="Gene annotation table">
28 <options from_data_table="ceas_annotations">
29 <filter name="dbkey" type="data_meta" ref="bed_file" key="dbkey" column="0" />
30 <validator type="no_options" message="No tables are available for the selected input"/>
31 </options>
32 </param>
33 <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" />
34 <param name="sizes_lower" type="integer" label="Lower interval for promoter/downstream sizes for ChIP region annotation (bp)" value="1000" />
35 <param name="sizes_middle" type="integer" label="Middle interval for promoter/downstream sizes (bp)" value="2000" help="Values > 10000bp are automatically fixed to 10000bp" />
36 <param name="sizes_upper" type="integer" label="Upper interval for promoter/downstream sizes (bp)" value="3000" help="Values > 10000bp are automatically fixed to 10000bp" />
37 <param name="bisizes_lower" type="integer" label="Lower interval for bidirectional-promoter sizes for ChIP region annotation (bp)" value="2500" />
38 <param name="bisizes_upper" type="integer" label="Upper interval for bidirectional-promoter sizes (bp)" value="5000" help="Values > 20000bp are automatically fixed to 20000bp" />
39 <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" />
40 <param name="relative_distance" type="integer" label="Relative distance to TSS/TTS in wig profiling (bp)" value="3000" />
41 </inputs>
42 <outputs>
43 <data name="log_output" format="txt" label="CEAS on ${on_string} (log output)" />
44 <data name="pdf_report" format="pdf" label="CEAS on ${on_string} (PDF report)" />
45 <data name="xls_output" format="interval" label="CEAS on ${on_string} (XLS output)" />
46 </outputs>
47 <help>
48 **What it does**
49
50 CEAS (Cis-regulatory Element Annotation System) is a tool for characterizing genome-wide
51 protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad
52 binding factors. It provides statistics on ChIP enrichment at important genome features
53 such as specific chromosome, promoters, gene bodies, or exons, and infers genes most
54 likely to be regulated by a binding factor.
55
56 CEAS also enables biologists to visualize the average ChIP enrichment signals over
57 specific genomic features, allowing continuous and broad ChIP enrichment to be perceived
58 which might be too subtle to detect from ChIP peaks alone.
59
60 This tool is compatible with the ceasBW version of CEAS from the Cistrome package
61 obtained from
62
63 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
64
65 (commit id d8c0751, datestamp 20140929). The CEAS code is under the
66 published-packages/CEAS/ subdirectory.
67
68 Cistrome data files and documentation can be found at
69
70 http://liulab.dfci.harvard.edu/CEAS/index.html
71
72 The CEAS user manual is available at http://liulab.dfci.harvard.edu/CEAS/usermanual.html
73 </help>
74 </tool>