Mercurial > repos > jjohnson > cistrome_ceas
diff ceas.xml @ 0:4e52505adaa6
Imported from capsule None
| author | jjohnson |
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| date | Wed, 17 Sep 2014 15:03:26 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ceas.xml Wed Sep 17 15:03:26 2014 -0400 @@ -0,0 +1,288 @@ +<tool name="CEAS: Enrichment on chromosome and annotation" id="ceas_ceas" version="0.1.0"> + <description>Annotate the given intervals and scores with genome features such as gene body</description> + <macros> + <import>ceas_macros.xml</import> + </macros> + <expand macro="requirements_bx" /> + <command> +#import os.path +#if $genegroup.enable == "yes" +#set $gngroups = str($genegroup.genelist) +#set $gnlabels = str($genegroup.label) +#for $m in $genegroup.more +#set $gngroups = $gngroups+","+str($m.genelist) +#set $gnlabels = $gnlabels+","+str($m.label) +#end for +#set $gngroupspara = "--gn-groups="+$gngroups +#set $gnlabelspara = "--gn-group-names='"+$gnlabels+"'"+str($genegroup.idtype.value) +#else +#set $gngroupspara = "" +#set $gnlabelspara = "" +#end if +#set $sizes = str($lowersize) + "," + str($middlesize) + "," + str($uppersize) +#set $bisizes = str($lowerbisize) + "," + str($upperbisize) +#if $wfile: + #if $wfile.extension == "bigwig" + ceasBW -w $wfile + #set dbkey = $wfile.metadata.dbkey + #set $length_file = os.path.join( os.path.abspath($__app__.config.len_file_path), $dbkey+".len" ) + -l $length_file + #else + ceas -w $wfile + #end if +#else + ceas +#end if +#if $bfile: + -b $bfile +#end if +#include source=$gtpath_ceasdb_ref# +--span=$span --pf-res=$pfres --sizes=$sizes --bisizes=$bisizes +--rel-dist=$reldist $gngroupspara $gnlabelspara --name=$name &> $log && +Rscript ceas_out.R && +#if $imagetype.__str__ == "PNG": +convert ceas_out.pdf ceas_out.png && convert ceas_out-*.png -append ceas_out_joint.png && +cp ceas_out_joint.png $output +#else +cp ceas_out.pdf $output +#end if + </command> + <inputs> + <expand macro="ceasdb_ref" /> + <param name="name" type="hidden" value="ceas_out"/> + <param format="wig,bigwig" name="wfile" type="data" label="wig / bigwig file" optional="true"> + <validator type="unspecified_build" /> + </param> + <param format="bed" name="bfile" type="data" label="BED file(maximum 100000 lines)" optional="true"> + <validator type="unspecified_build" /> + </param> + <param name="span" type="integer" label="Span" value="3000"> + <validator type="in_range" max="1000000" min="100" message="The Span is out of range, the parameter has to be between 100 to 1000000" /> + </param> + <param name="pfres" type="integer" label="Profiling resolution" value="50"> + <validator type="in_range" max="1000" min="10" message="The Profiling Resolution is out of range, the parameter has to be between 10 to 1000" /> + </param> + <param name="lowersize" type="text" label="Promoter/downstream lower-interval" value="1000" > + <validator type="in_range" max="10000" min="100" message="The lower-interval is out of range, the parameter has to be between 100 to 10000" /> + </param> + <param name="middlesize" type="text" label="Promoter/downstream middle-interval" value="2000" > + <validator type="in_range" max="10000" min="100" message="The middle-interval is out of range, the parameter has to be between 100 to 10000" /> + </param> + <param name="uppersize" type="text" label="Promoter/downstream upper-interval" value="3000"> + <validator type="in_range" max="10000" min="100" message="The upper-interval is out of range, the parameter has to be between 100 to 10000" /> + </param> + <param name="lowerbisize" type="text" label="Bi-Promoter lower range" value="2500"> + <validator type="in_range" max="10000" min="100" message="The lower-range is out of range, the parameter has to be between 100 to 10000" /> + </param> + <param name="upperbisize" type="text" label="Bi-Promoter upper range" value="5000"> + <validator type="in_range" max="10000" min="100" message="The upper-range is out of range, the parameter has to be between 100 to 10000" /> + </param> + <param name="reldist" type="integer" label="Relative distance" value="3000"> + <validator type="in_range" max="10000" min="100" message="The Relative distance is out of range, the parameter has to be between 100 to 10000" /> + </param> + <param type="select" name="imagetype" display="radio" label="Image Type"> + <option value="PNG">PNG format</option> + <option value="PDF">PDF format</option> + </param> + + <conditional name="genegroup"> + <param name="enable" type="select" label="Specify gene list in the signal profiling" force_select="true"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + + <when value="no"> + </when> + + <when value="yes"> + <param format="text" name="genelist" type="data" label="Gene List" optional="false"/> + <param name="label" type="text" label="Gene List Label" optional="false" /> + <repeat name="more" title="Gene Lists"> + <param format="text" name="genelist" type="data" label="Gene List" optional="false"/> + <param name="label" type="text" label="Gene List Label" optional="false" /> + </repeat> + <param name="idtype" type="select" label="Are they ..."> + <option value="">refseq</option> + <option value=" --gname2">genesymbol</option> + </param> + </when> + </conditional> + + </inputs> + + <outputs> + <data format="png" name="output"> + <change_format> + <when input="imagetype" value="PDF" format="pdf" /> + </change_format> + </data> + <data format="txt" name="log" label="ceas job log" /> + </outputs> + <expand macro="stdio" /> + <tests> + <test> + <param name="wfile" value="treatment.wig" /> + <param name="bfile" value="peaks.bed" /> + <param name="span" value="3000" /> + <param name="pfres" value="50" /> + <param name="lowersize" value="1000" /> + <param name="middlesize" value="2000" /> + <param name="uppersize" value="3000" /> + <param name="lowerbisize" value="2500" /> + <param name="upperbisize" value="5000" /> + <param name="reldist" value="3000" /> + <param name="refsrc" value="history"/> + <param name="gdb" ftype="ceasdb" value="mm9.refGene.ceasdb"/> + <param name="imagetype" value="PDF" /> + <param name="enable" value="no" /> + <output name="log"> + <assert_contents> + <has_text_matching expression="See ceas_out.pdf for the graphical results of CEAS" /> + </assert_contents> + </output> + </test> + <test> + <param name="wfile" value="treatment.bigwig" /> + <param name="bfile" value="peaks.bed" /> + <param name="span" value="3000" /> + <param name="pfres" value="50" /> + <param name="lowersize" value="1000" /> + <param name="middlesize" value="2000" /> + <param name="uppersize" value="3000" /> + <param name="lowerbisize" value="2500" /> + <param name="upperbisize" value="5000" /> + <param name="reldist" value="3000" /> + <param name="refsrc" value="history"/> + <param name="gdb" ftype="ceasdb" value="mm9.refGene.ceasdb"/> + <param name="imagetype" value="PDF" /> + <param name="enable" value="no" /> + <output name="log"> + <assert_contents> + <has_text_matching expression="See ceas_out.pdf for the graphical results of CEAS" /> + </assert_contents> + </output> + </test> + </tests> + <help> +** CEAS ** +This tool annotates the given intervals and scores with genome +features such as gene body. It's the major module in CEAS package +which is written by Hyunjin Gene Shin, published in Bioinformatics +(pubmed id:19689956). + +@EXTERNAL_DOCUMENTATION@ + +@CITATION_SECTION@ + + +.. class:: warningmark + +**NEED IMPROVEMENT** + +----- + +**Parameters** + +- **WIGGLE file** contains the scores for the experiment in a wiggle + format file. Normally, it's produced by the peak calling tool. It's + optional. +- **BED file** contains the peak locations for the experiment in a BED + format file. +- **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. +- **Profiling resolution** is the WIGGLE profiling resolution. +- **Promoter/downstream intervals** for ChIP region annotation are + 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) +- **BiPromoter ranges** is for ChIP region annotation. It's + 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) +- **Relative distance** is the relative distance to TSS/TTS in WIGGLE file + profiling +- **Genome Annotation Version** to specify the annotations according to + the data set. The annotations are downloaded from UCSC genome site. +- **Image type** specify the output image format, either in PNG or in + PDF format. +- If **Specify gene list in the signal profiling** is set, you can specify + different gene groups for CEAS to put them together in the profile + figure. You need to select several **Gene List** files from history which + contains the RefSeq ids or Gene Symbols for each row, and + **Gene List Label** for each gene list file. + +----- + +**Outputs** + +- **PNG/PDF file** is the result for CEAS analysis, containing 5 pages. +- **LOG file** for job log. If you see errors, please attached this in + the bug report + +----- + +**script parameter list of CEAS 0.9.8** + +Options: + --version show program's version number and exit + -h, --help Show this help message and exit. + -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). + --name=NAME Experiment name. This will be used to name the output + files. If an experiment name is not given, the stem of + the input BED file name will be used instead (eg, if + 'peaks.bed', 'peaks' will be used as a name.) + --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 + --gn-groups=GN_GROUPS + Gene-groups of particular interest in wig profiling. + Each gene group file must have gene names in the 1st + column. The file names are separated by commas w/ no + space (eg, --gn-groups=top10.txt,bottom10.txt) + --gn-group-names=GN_NAMES + The names of the gene groups in --gn-groups. The gene + group names are separated by commas. (eg, --gn-group- + names='top 10%,bottom 10%'). These group names appear + in the legends of the wig profiling plots. If no group + names given, the groups are represented as 'Group 1, + Group2,...Group n'. + --gname2 Whether or not use the 'name2' column of the gene + annotation table when reading the gene IDs in the + files given through --gn-groups. This flag is + meaningful only with --gn-groups. + + </help> + +</tool>