Mercurial > repos > pjbriggs > ceas
annotate ceas_wrapper.xml @ 3:df54f8fcc7a7 draft
Version 1.0.2-3: move to conda-based dependency resolution.
| author | pjbriggs |
|---|---|
| date | Wed, 28 Feb 2018 10:22:32 -0500 |
| parents | d2283cca00cd |
| children | cd6a48ffd093 |
| rev | line source |
|---|---|
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d2283cca00cd
CEAS tool version 1.0.2-3: updates to get R 3.1.2 and bx-python 0.7.1 dependencies from the toolshed.
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1 <tool id="ceas" name="CEAS" version="1.0.2-3"> |
| 0 | 2 <description>Annotate intervals and scores with genome features</description> |
| 3 <requirements> | |
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df54f8fcc7a7
Version 1.0.2-3: move to conda-based dependency resolution.
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4 <requirement type="package" version="1.0.2b1">cistrome-ceas</requirement> |
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df54f8fcc7a7
Version 1.0.2-3: move to conda-based dependency resolution.
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5 <requirement type="package" version="357">ucsc-fetchchromsizes</requirement> |
| 0 | 6 </requirements> |
| 7 <version_command>ceas --version 2>&1 | tail -1</version_command> | |
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8 <command><![CDATA[ |
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df54f8fcc7a7
Version 1.0.2-3: move to conda-based dependency resolution.
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9 bash $__tool_directory__/ceas_wrapper.sh |
| 0 | 10 $bed_file ${gdb_file.fields.path} |
| 11 $log_output $pdf_report $xls_output | |
| 12 #if (str($wig_file) != 'None') | |
| 13 #if (str($wig_file.ext) == 'bigwig') | |
| 14 --bigwig $wig_file | |
| 15 --length $GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${bed_file.dbkey}.len | |
| 16 #else | |
| 17 --wig $wig_file | |
| 18 #end if | |
| 19 #end if | |
| 20 #if (str($extra_bed_file) != 'None') | |
| 21 --ebed $extra_bed_file | |
| 22 #end if | |
| 23 #if (str($span) and int(str($span)) > 0) | |
| 24 --span $span | |
| 25 #end if | |
| 26 --sizes $sizes_lower,$sizes_middle,$sizes_upper | |
| 27 --bisizes $bisizes_lower,$bisizes_upper | |
| 28 --pf-res $profiling_resolution | |
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29 --rel-dist $relative_distance |
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df54f8fcc7a7
Version 1.0.2-3: move to conda-based dependency resolution.
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30 ]]></command> |
| 0 | 31 <inputs> |
| 32 <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" /> | |
| 33 <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true" | |
| 34 help="If not supplied then only perform ChIP region annotation and gene-centered annotation" /> | |
| 35 <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="gdb_file" type="select" label="Gene annotation table"> | |
| 37 <options from_data_table="ceas_annotations"> | |
| 38 </options> | |
| 39 <filter name="dbkey" type="data_meta" ref="bed_file" key="dbkey" column="1" /> | |
| 40 <validator type="no_options" message="No tables are available for the selected input"/> | |
| 41 </param> | |
| 42 <param name="span" type="integer" | |
| 43 label="Span from TSS and TTS in the gene-centered annotation (bp)" | |
| 44 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" /> | |
| 45 <param name="sizes_lower" type="integer" | |
| 46 label="Lower interval for promoter/downstream sizes for ChIP region annotation (bp)" | |
| 47 value="1000" help=" (--sizes)" /> | |
| 48 <param name="sizes_middle" type="integer" | |
| 49 label="Middle interval for promoter/downstream sizes (bp)" value="2000" | |
| 50 help="Values > 10000bp are automatically fixed to 10000bp (--sizes)" /> | |
| 51 <param name="sizes_upper" type="integer" | |
| 52 label="Upper interval for promoter/downstream sizes (bp)" value="3000" | |
| 53 help="Values > 10000bp are automatically fixed to 10000bp (--sizes)" /> | |
| 54 <param name="bisizes_lower" type="integer" | |
| 55 label="Lower interval for bidirectional-promoter sizes for ChIP region annotation (bp)" value="2500" | |
| 56 help="(--bisizes)" /> | |
| 57 <param name="bisizes_upper" type="integer" | |
| 58 label="Upper interval for bidirectional-promoter sizes (bp)" value="5000" | |
| 59 help="Values > 20000bp are automatically fixed to 20000bp (--bisizes)" /> | |
| 60 <param name="profiling_resolution" type="integer" | |
| 61 label="Wig profiling resolution (bp)" value="50" | |
| 62 help="Warning: a number smaller than the wig interval (resolution) may cause aliasing error (--pf-res)" /> | |
| 63 <param name="relative_distance" type="integer" | |
| 64 label="Relative distance to TSS/TTS in wig profiling (bp)" value="3000" | |
| 65 help="(--rel-dist)" /> | |
| 66 </inputs> | |
| 67 <outputs> | |
| 68 <data name="log_output" format="txt" label="CEAS on ${on_string} (log output)" /> | |
| 69 <data name="pdf_report" format="pdf" label="CEAS on ${on_string} (PDF report)" /> | |
| 70 <data name="xls_output" format="interval" label="CEAS on ${on_string} (XLS output)" /> | |
| 71 </outputs> | |
| 72 <tests> | |
| 73 <test> | |
| 74 <!-- Test with bed input only --> | |
| 75 <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" /> | |
| 76 <param name="gdb_file" value="galGal3_test" /> | |
| 77 <output name="log_output" file="ceas_out1.log.re_match" compare="re_match"/> | |
| 78 <output name="pdf_report" file="ceas_out1.pdf" /> | |
| 79 <output name="xls_output" file="ceas_out1.xls" /> | |
| 80 </test> | |
| 81 <test> | |
| 82 <!-- Test with bed & very small wig input --> | |
| 83 <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" /> | |
| 84 <param name="wig_file" value="ceas_in.wig" ftype="wig" /> | |
| 85 <param name="gdb_file" value="galGal3_test" /> | |
| 86 <output name="log_output" file="ceas_out2.log.re_match" compare="re_match"/> | |
| 87 <output name="pdf_report" file="ceas_out2.pdf" /> | |
| 88 <output name="xls_output" file="ceas_out2.xls" /> | |
| 89 </test> | |
| 90 <test> | |
| 91 <!-- Test with bed & bigwig input --> | |
| 92 <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" /> | |
| 93 <param name="wig_file" value="ceas_in.bigwig" ftype="bigwig" /> | |
| 94 <param name="gdb_file" value="galGal3_test" /> | |
| 95 <output name="log_output" file="ceas_out3.log.re_match" compare="re_match"/> | |
| 96 <output name="pdf_report" file="ceas_out3.pdf" /> | |
| 97 <output name="xls_output" file="ceas_out3.xls" /> | |
| 98 </test> | |
| 99 </tests> | |
| 100 <help> | |
| 101 **What it does** | |
| 102 | |
| 103 CEAS (Cis-regulatory Element Annotation System) is a tool for characterizing genome-wide | |
| 104 protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad | |
| 105 binding factors. It provides statistics on ChIP enrichment at important genome features | |
| 106 such as specific chromosome, promoters, gene bodies, or exons, and infers genes most | |
| 107 likely to be regulated by a binding factor. | |
| 108 | |
| 109 CEAS also enables biologists to visualize the average ChIP enrichment signals over | |
| 110 specific genomic features, allowing continuous and broad ChIP enrichment to be perceived | |
| 111 which might be too subtle to detect from ChIP peaks alone. | |
| 112 | |
| 113 **Usage** | |
| 114 | |
| 115 CEAS takes the following inputs: | |
| 116 | |
| 117 * BED file with discrete ChIP regions (for example, the 'summits' output from the MACS | |
| 118 peak caller) | |
| 119 * WIG or bigWIG file with a continuous ChIP enrichment signal | |
| 120 * Gene annotation table (provided as reference data) | |
| 121 | |
| 122 Optionally it can also take a BED file describing extra regions of interest (for example | |
| 123 non-coding regions). | |
| 124 | |
| 125 The analysis modules are: | |
| 126 | |
| 127 * **ChIP region annotation:** estimates the relative enrichment level of ChIP regions in | |
| 128 each gene feature with respect to the whole genome. | |
| 129 * **Gene-centered annotation:** identifies genes associated with ChIP regions to infer | |
| 130 the direct regulatory gene targets of the binding factor of interest. | |
| 131 * **Average signal profiling within/near important genomic features:** displays continuous | |
| 132 ChIP enrichment signal within/around important gene features to help visualize the | |
| 133 average binding patterns. | |
| 134 | |
| 135 **Background** | |
| 136 | |
| 137 This tool is compatible with the ceasBW version of CEAS from the Cistrome package | |
| 138 obtained from | |
| 139 | |
| 140 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview | |
| 141 | |
| 142 (commit id d8c0751, datestamp 20140929). The CEAS code is under the | |
| 143 published-packages/CEAS/ subdirectory. | |
| 144 | |
| 145 Cistrome data files and documentation can be found at | |
| 146 | |
| 147 http://liulab.dfci.harvard.edu/CEAS/index.html | |
| 148 | |
| 149 The CEAS user manual is available at http://liulab.dfci.harvard.edu/CEAS/usermanual.html | |
| 150 </help> | |
| 151 <citations> | |
| 152 <!-- | |
| 153 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set | |
| 154 Can be either DOI or Bibtex | |
| 155 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex | |
| 156 --> | |
| 157 <citation type="doi">10.1093/bioinformatics/btp479</citation> | |
| 158 </citations> | |
| 159 </tool> |