Mercurial > repos > nikhil-joshi > ceas
view ceas/ceas.xml @ 0:a5b3f7cf458e draft
Uploaded
| author | nikhil-joshi |
|---|---|
| date | Tue, 09 Dec 2014 06:50:43 -0500 |
| parents | |
| children |
line wrap: on
line source
<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>