Mercurial > repos > pjbriggs > ceas

annotate ceas_wrapper.xml @ 3:82df5af2995f draft

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