Mercurial > repos > nikhil-joshi > ceas
changeset 2:012afa77c724 draft default tip
Uploaded
| author | nikhil-joshi |
|---|---|
| date | Tue, 09 Dec 2014 06:54:34 -0500 |
| parents | d59bf233d184 |
| children | |
| files | README ceas.xml ceas_tables.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 173 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue Dec 09 06:54:34 2014 -0500 @@ -0,0 +1,2 @@ +You can find the CEAS databases here: +http://liulab.dfci.harvard.edu/CEAS/download.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ceas.xml Tue Dec 09 06:54:34 2014 -0500 @@ -0,0 +1,156 @@ +<tool id="ceas" name="CEAS" version="1.0.2"> + <description>Get stats on ChIP enrichment and infer genes regulated by binding factors</description> + + <command> + mkdir -p "$pdf_out.files_path" && + cd "$pdf_out.files_path" && + + ceas + + -g "$refgene_table.fields.path" + #if $analysis_files.wig_or_bed == "bed" or $analysis_files.wig_or_bed == "both1" or $analysis_files.wig_or_bed == "both2": + -b $chip_bed + #end if + + #if $analysis_files.wig_or_bed == "wig" or $analysis_files.wig_or_bed == "both1" or $analysis_files.wig_or_bed == "both2": + -w $chip_wig + #end if + + #if $analysis_files.wig_or_bed == "both2": + --bg + #end if + + #if str($extra_bed) != 'None': + -e $extra_bed + #end if + + #if str($sizes) != "": + --sizes=$sizes + #end if + + #if str($bisizes) != "": + --bisizes=$bisizes + #end if + + #if str($span) != "": + --span=$span + #end if + + #if str($pfres) != "": + --pf-res=$pfres + #end if + + #if str($reldist) != "": + --rel-dist=$reldist + #end if + + --name=ceas_out + + 2> /dev/null + + && + + #if $analysis_files.wig_or_bed != "wig": + mv $pdf_out.files_path/ceas_out.xls $annot_out && + #end if + mv $pdf_out.files_path/ceas_out.R $r_out && + mv $pdf_out.files_path/ceas_out.pdf $pdf_out && + + rm -r "$pdf_out.files_path" + </command> + + <inputs> + <conditional name="analysis_files"> + <param name="wig_or_bed" type="select" optional="false" label="Select the type of analysis"> + <option value="bed" selected="true">Run only ChIP region and gene-centered annotation</option> + <option value="wig">Run only average signal profiling</option> + <option value="both1">Run both annotation and profiling</option> + <option value="both2">Run genome background annotation</option> + </param> + + <when value="bed"> + <param format="bed" name="chip_bed" type="data" label="BED file of ChIP regions"/> + </when> + + <when value="wig"> + <param format="wig" name="chip_wig" type="data" label="WIG file with ChiP enrichment signal"/> + </when> + + <when value="both1"> + <param format="bed" name="chip_bed" type="data" label="BED file of ChIP regions"/> + <param format="wig" name="chip_wig" type="data" label="WIG file with ChiP enrichment signal"/> + </when> + + <when value="both2"> + <param format="bed" name="chip_bed" type="data" label="BED file of ChIP regions"/> + <param format="wig" name="chip_wig" type="data" label="WIG file for genome background annotation"/> + </when> + </conditional> + + <param name="refgene_table" label="Gene annotation table" type="select"> + <options from_data_table="ceas_refgene_tables"> + <filter type="sort_by" column="1"/> + <validator type="no_options" message="No indexes are available for the selected dataset"/> + </options> + </param> + + <param format="bed" name="extra_bed" type="data" optional="true" label="BED file of extra regions of interest (e.g. non-coding regions)"/> + + <param name="sizes" type="integer" optional="true" label="Promoter (also downstream) sizes for ChIP region annotation" help="Three comma-separated integers or a single integer. Leave blank for default."/> + + <param name="bisizes" type="integer" optional="true" label="Bidirectional promoter sizes for ChIP region annotation" help="Two comma-separated integers or a single integer. Leave blank for default."/> + + <param name="span" type="integer" optional="true" label="Span from TSS and TTS in the gene-centered annotation" help="Leave blank for default."/> + <param name="pfres" type="integer" optional="true" label="WIG profiling resolution" help="Leave blank for default."/> + <param name="reldist" type="integer" optional="true" label="Relative distance to TSS/TTS in wig profiling" help="Leave blank for default."/> + + </inputs> + + <outputs> + <data format="tabular" name="annot_out" label="Gene-centered annotation from ${tool.name} on ${on_string} (XLS)"> + <filter>(analysis_files['wig_or_bed'] != 'wig')</filter> + </data> + <data format="txt" name="r_out" label="R script for graph results from ${tool.name} on ${on_string}" /> + <data format="pdf" name="pdf_out" label="Graph results from ${tool.name} on ${on_string} (PDF)" /> + </outputs> + + <help> +Options: + -b BED, --bed=BED BED file of ChIP regions. + -w WIG, --wig=WIG WIG file for either wig profiling or genome background + annotation. WARNING: --bg flag must be set for genome + background re-annotation. + -e EBED, --ebed=EBED BED file of extra regions of interest (eg, non-coding + regions) + -g GDB, --gt=GDB Gene annotation table (eg, a refGene table in sqlite3 + db format provided through the CEAS web, + http://liulab.dfci.harvard.edu/CEAS/download.html). + --sizes=SIZES Promoter (also dowsntream) sizes for ChIP region + annotation. Comma-separated three values or a single + value can be given. If a single value is given, it + will be segmented into three equal fractions (ie, 3000 + is equivalent to 1000,2000,3000), DEFAULT: + 1000,2000,3000. WARNING: Values > 10000bp are + automatically set to 10000bp. + --bisizes=BISIZES Bidirectional-promoter sizes for ChIP region + annotation Comma-separated two values or a single + value can be given. If a single value is given, it + will be segmented into two equal fractions (ie, 5000 + is equivalent to 2500,5000) DEFAULT: 2500,5000bp. + WARNING: Values > 20000bp are automatically set to + 20000bp. + --bg Run genome BG annotation again. WARNING: This flag is + effective only if a WIG file is given through -w + (--wig). Otherwise, ignored. + --span=SPAN Span from TSS and TTS in the gene-centered annotation. + ChIP regions within this range from TSS and TTS are + considered when calculating the coverage rates in + promoter and downstream, DEFAULT=3000bp + --pf-res=PF_RES Wig profiling resolution, DEFAULT: 50bp. WARNING: + Value smaller than the wig interval (resolution) may + cause aliasing error. + --rel-dist=REL_DIST Relative distance to TSS/TTS in wig profiling, + DEFAULT: 3000bp + </help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ceas_tables.loc.sample Tue Dec 09 06:54:34 2014 -0500 @@ -0,0 +1,8 @@ +ce4 C. elegans ce4 /opt/galaxy/tool-data/ceas_tables/ce4.refGene +ce6 C. elegans ce6 /opt/galaxy/tool-data/ceas_tables/ce6.refGene +dm2 D. melanogaster dm2 /opt/galaxy/tool-data/ceas_tables/dm2.refGene +dm3 D. melanogaster dm3 /opt/galaxy/tool-data/ceas_tables/dm3.refGene +mm8 M. musculus mm8 /opt/galaxy/tool-data/ceas_tables/mm8.refGene +mm9 M. musculus mm9 /opt/galaxy/tool-data/ceas_tables/mm9.refGene +hg18 H. sapiens hg18 /opt/galaxy/tool-data/ceas_tables/hg18.refGene +hg19 H. sapiens hg19 /opt/galaxy/tool-data/ceas_tables/hg19.refGene
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Dec 09 06:54:34 2014 -0500 @@ -0,0 +1,7 @@ +<tables> + <table name="ceas_refgene_tables" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/ceas_tables.loc" /> + </table> +</tables> +