Mercurial > repos > pjbriggs > ceas
comparison ceas_wrapper.xml @ 4:4e2883bb058d draft
Synchronise version with one on main toolshed (version of 30/06/2015)
author | pjbriggs |
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date | Wed, 10 Aug 2016 11:04:42 -0400 |
parents | 82df5af2995f |
children | c9c4792d0876 |
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3:82df5af2995f | 4:4e2883bb058d |
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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>&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> |