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comparison ceas_wrapper.xml @ 4:4e2883bb058d draft

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Synchronise version with one on main toolshed (version of 30/06/2015)
author pjbriggs
date Wed, 10 Aug 2016 11:04:42 -0400
parents 82df5af2995f
children c9c4792d0876
comparison
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3:82df5af2995f 4:4e2883bb058d
1 <tool id="ceas" name="CEAS" version="1.0.2-1"> 1 <tool id="ceas" name="CEAS" version="1.0.2-2">
2 <description>Annotate intervals and scores with genome features</description>
2 <requirements> 3 <requirements>
3 <requirement type="package" version="1.2.5">python_mysqldb</requirement> 4 <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="0.7.1">bx_python</requirement>
5 <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement> 6 <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement>
7 <requirement type="package" version="1.0">ucsc_fetchChromSizes</requirement>
6 <requirement type="package" version="3.1.2">R</requirement> 8 <requirement type="package" version="3.1.2">R</requirement>
7 </requirements> 9 </requirements>
8 <description>Annotate intervals and scores with genome features</description> 10 <version_command>ceas --version 2&gt;&amp;1 | tail -1</version_command>
9 <command interpreter="bash">ceas_wrapper.sh $bed_file $gdb_file $extra_bed_file $log_output $pdf_report $xls_output 11 <command interpreter="bash">ceas_wrapper.sh
10 #if (str($wig_file.ext) == 'bigwig') 12 $bed_file ${gdb_file.fields.path}
11 --bigwig $wig_file 13 $log_output $pdf_report $xls_output
12 --length $GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${bed_file.dbkey}.len 14 #if (str($wig_file) != 'None')
13 # else 15 #if (str($wig_file.ext) == 'bigwig')
14 --wig $wig_file 16 --bigwig $wig_file
17 --length $GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${bed_file.dbkey}.len
18 #else
19 --wig $wig_file
20 #end if
21 #end if
22 #if (str($extra_bed_file) != 'None')
23 --ebed $extra_bed_file
15 #end if 24 #end if
16 #if (str($span) and int(str($span)) > 0) 25 #if (str($span) and int(str($span)) > 0)
17 --span $span 26 --span $span
18 #end if 27 #end if
19 --sizes $sizes_lower,$sizes_middle,$sizes_upper 28 --sizes $sizes_lower,$sizes_middle,$sizes_upper
20 --bisizes $bisizes_lower,$bisizes_upper 29 --bisizes $bisizes_lower,$bisizes_upper
21 --pf-res $profiling_resolution 30 --pf-res $profiling_resolution
22 --rel-dist $relative_distance</command> 31 --rel-dist $relative_distance</command>
23 <inputs> 32 <inputs>
24 <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" /> 33 <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" /> 34 <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true"
35 help="If not supplied then only perform ChIP region annotation and gene-centered annotation" />
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" /> 36 <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"> 37 <param name="gdb_file" type="select" label="Gene annotation table">
28 <options from_data_table="ceas_annotations"> 38 <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> 39 </options>
40 <filter name="dbkey" type="data_meta" ref="bed_file" key="dbkey" column="1" />
41 <validator type="no_options" message="No tables are available for the selected input"/>
32 </param> 42 </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" /> 43 <param name="span" type="integer"
34 <param name="sizes_lower" type="integer" label="Lower interval for promoter/downstream sizes for ChIP region annotation (bp)" value="1000" /> 44 label="Span from TSS and TTS in the gene-centered annotation (bp)"
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" /> 45 help="ChIP regions within this range from TSS and TTS are considered when calculating the coverage rates of promoter and downstream by ChIP regions (--span)" value="3000" />
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" /> 46 <param name="sizes_lower" type="integer"
37 <param name="bisizes_lower" type="integer" label="Lower interval for bidirectional-promoter sizes for ChIP region annotation (bp)" value="2500" /> 47 label="Lower interval for promoter/downstream sizes for ChIP region annotation (bp)"
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" /> 48 value="1000" help=" (--sizes)" />
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" /> 49 <param name="sizes_middle" type="integer"
40 <param name="relative_distance" type="integer" label="Relative distance to TSS/TTS in wig profiling (bp)" value="3000" /> 50 label="Middle interval for promoter/downstream sizes (bp)" value="2000"
51 help="Values > 10000bp are automatically fixed to 10000bp (--sizes)" />
52 <param name="sizes_upper" type="integer"
53 label="Upper interval for promoter/downstream sizes (bp)" value="3000"
54 help="Values > 10000bp are automatically fixed to 10000bp (--sizes)" />
55 <param name="bisizes_lower" type="integer"
56 label="Lower interval for bidirectional-promoter sizes for ChIP region annotation (bp)" value="2500"
57 help="(--bisizes)" />
58 <param name="bisizes_upper" type="integer"
59 label="Upper interval for bidirectional-promoter sizes (bp)" value="5000"
60 help="Values > 20000bp are automatically fixed to 20000bp (--bisizes)" />
61 <param name="profiling_resolution" type="integer"
62 label="Wig profiling resolution (bp)" value="50"
63 help="Warning: a number smaller than the wig interval (resolution) may cause aliasing error (--pf-res)" />
64 <param name="relative_distance" type="integer"
65 label="Relative distance to TSS/TTS in wig profiling (bp)" value="3000"
66 help="(--rel-dist)" />
41 </inputs> 67 </inputs>
42 <outputs> 68 <outputs>
43 <data name="log_output" format="txt" label="CEAS on ${on_string} (log output)" /> 69 <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)" /> 70 <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)" /> 71 <data name="xls_output" format="interval" label="CEAS on ${on_string} (XLS output)" />
46 </outputs> 72 </outputs>
73 <tests>
74 <test>
75 <!-- Test with bed input only -->
76 <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
77 <param name="gdb_file" value="galGal3_test" />
78 <output name="log_output" file="ceas_out1.log.re_match" compare="re_match"/>
79 <output name="pdf_report" file="ceas_out1.pdf" />
80 <output name="xls_output" file="ceas_out1.xls" />
81 </test>
82 <test>
83 <!-- Test with bed & very small wig input -->
84 <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
85 <param name="wig_file" value="ceas_in.wig" ftype="wig" />
86 <param name="gdb_file" value="galGal3_test" />
87 <output name="log_output" file="ceas_out2.log.re_match" compare="re_match"/>
88 <output name="pdf_report" file="ceas_out2.pdf" />
89 <output name="xls_output" file="ceas_out2.xls" />
90 </test>
91 <test>
92 <!-- Test with bed & bigwig input -->
93 <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
94 <param name="wig_file" value="ceas_in.bigwig" ftype="bigwig" />
95 <param name="gdb_file" value="galGal3_test" />
96 <output name="log_output" file="ceas_out3.log.re_match" compare="re_match"/>
97 <output name="pdf_report" file="ceas_out3.pdf" />
98 <output name="xls_output" file="ceas_out3.xls" />
99 </test>
100 </tests>
47 <help> 101 <help>
48 **What it does** 102 **What it does**
49 103
50 CEAS (Cis-regulatory Element Annotation System) is a tool for characterizing genome-wide 104 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 105 protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad
54 likely to be regulated by a binding factor. 108 likely to be regulated by a binding factor.
55 109
56 CEAS also enables biologists to visualize the average ChIP enrichment signals over 110 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 111 specific genomic features, allowing continuous and broad ChIP enrichment to be perceived
58 which might be too subtle to detect from ChIP peaks alone. 112 which might be too subtle to detect from ChIP peaks alone.
113
114 **Usage**
115
116 CEAS takes the following inputs:
117
118 * BED file with discrete ChIP regions (for example, the 'summits' output from the MACS
119 peak caller)
120 * WIG or bigWIG file with a continuous ChIP enrichment signal
121 * Gene annotation table (provided as reference data)
122
123 Optionally it can also take a BED file describing extra regions of interest (for example
124 non-coding regions).
125
126 The analysis modules are:
127
128 * **ChIP region annotation:** estimates the relative enrichment level of ChIP regions in
129 each gene feature with respect to the whole genome.
130 * **Gene-centered annotation:** identifies genes associated with ChIP regions to infer
131 the direct regulatory gene targets of the binding factor of interest.
132 * **Average signal profiling within/near important genomic features:** displays continuous
133 ChIP enrichment signal within/around important gene features to help visualize the
134 average binding patterns.
135
136 **Background**
59 137
60 This tool is compatible with the ceasBW version of CEAS from the Cistrome package 138 This tool is compatible with the ceasBW version of CEAS from the Cistrome package
61 obtained from 139 obtained from
62 140
63 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview 141 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
69 147
70 http://liulab.dfci.harvard.edu/CEAS/index.html 148 http://liulab.dfci.harvard.edu/CEAS/index.html
71 149
72 The CEAS user manual is available at http://liulab.dfci.harvard.edu/CEAS/usermanual.html 150 The CEAS user manual is available at http://liulab.dfci.harvard.edu/CEAS/usermanual.html
73 </help> 151 </help>
152 <citations>
153 <!--
154 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
155 Can be either DOI or Bibtex
156 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
157 -->
158 <citation type="doi">10.1093/bioinformatics/btp479</citation>
159 </citations>
74 </tool> 160 </tool>