| Previous changeset 0:a5b3f7cf458e (2014-12-09) Next changeset 2:012afa77c724 (2014-12-09) |
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Commit message:
Deleted selected files |
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removed:
ceas/README ceas/ceas.xml ceas/ceas_tables.loc.sample |
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| diff -r a5b3f7cf458e -r d59bf233d184 ceas/README --- a/ceas/README Tue Dec 09 06:50:43 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -You can find the CEAS databases here: -http://liulab.dfci.harvard.edu/CEAS/download.html |
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| diff -r a5b3f7cf458e -r d59bf233d184 ceas/ceas.xml --- a/ceas/ceas.xml Tue Dec 09 06:50:43 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,156 +0,0 @@ -<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> |
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| diff -r a5b3f7cf458e -r d59bf233d184 ceas/ceas_tables.loc.sample --- a/ceas/ceas_tables.loc.sample Tue Dec 09 06:50:43 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -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 |