Mercurial > repos > jjohnson > cistrome_beta
changeset 0:20453b656907
Imported from capsule None
| author | jjohnson |
|---|---|
| date | Tue, 16 Sep 2014 13:35:24 -0400 |
| parents | |
| children | 7f023a22da15 |
| files | beta_basic.xml beta_macros.xml beta_minus.xml beta_plus.xml test-data/diff_expr.xls test-data/peaks.bed tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 9 files changed, 1289 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/beta_basic.xml Tue Sep 16 13:35:24 2014 -0400 @@ -0,0 +1,188 @@ +<tool id="beta_basic" name="BETA-basic: Binding and Expression Target Analysis" version="0.1.0"> + <description>Predict the factors (TFs or CRs) direct target genes by combining the binding and expression data</description> + <macros> + <import>beta_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> + BETA basic + #include source=$common_opts# + #include source=$genome_opts# + #include source=$extended_opts# + &> $log + </command> + <inputs> + <expand macro="common_params" /> + <expand macro="genome_params" /> + <expand macro="extended_params" /> + </inputs> + <expand macro="stdio" /> + <outputs> + <data format="txt" name="log" label="Log of BETA basic"/> + <data format="pdf" name="functionoutput" label="BETA functional prediction on ${peakfile.name}" from_work_dir="BETA_OUTPUT/NA_function_prediction.pdf"/> + <data format="tabular" name="uptargetsoutput" label="BETA direct targets prediction on up regulated genes" from_work_dir="BETA_OUTPUT/NA_uptarget.txt"/> + <data format="tabular" name="downtargetsoutput" label="BETA direct targets prediction on down regulated genes" from_work_dir="BETA_OUTPUT/NA_downtarget.txt"/> + <data format="bed" name="uptargetpeaks" label="BETA Uptarget associated peaks" from_work_dir="BETA_OUTPUT/NA_uptarget_associate_peaks.bed"/> + <data format="bed" name="downtargetpeaks" label="BETA Downtarget associated peaks" from_work_dir="BETA_OUTPUT/NA_downtarget_associate_peaks.bed"/> + </outputs> + <tests> + <test> + <param name='peakfile' value="peaks.bed" ftype="bed" dbkey="hg19"/> + <param name="distance" value="100000"/> + <param name="peaknumber" value="10000"/> + <param name="genomeName" value="hg19"/> + <param name='exprefile' value="diff_expr.xls" ftype="tabular" dbkey="hg19"/> + <param name="kind" value="LIM"/> + <param name="expreinfo" type="text" value="2,5,7"/> + <param name="gname2" value="Refseq"/> + <param name="diff_fdr" value="1.0"/> + <param name="diff_amount" value="0.5"/> + <param name="method" value="score"/> + <output name="log"> + <assert_contents> + <has_text_matching expression="Finished" /> + </assert_contents> + </output> + <output name="targetsoutput"> + <assert_contents> + <has_text_matching expression="chr19\t4675243\t4723855\tNM_139159\t1.1.*\t-\tDPP" /> + </assert_contents> + </output> + <output name="targetpeaks"> + <assert_contents> + <has_text_matching expression="chr19\t4723422\t4724314\tregion_9\tNM_139159\tDPP9\t13\t0.6.*" /> + </assert_contents> + </output> + </test> + </tests> + <help> +** BETA basic ** + +@EXTERNAL_DOCUMENTATION@ + +@CITATION_SECTION@ + +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). + +.. class:: warningmark + +**NEED IMPROVEMENT** + +----- + +**Parameters** + +- **PEAKFILE file** contains peaks for the experiment in a bed + format file. Normally, it's produced by the peak calling tool. It's + required. +- **EXPREFILE file** contains the differentially expressed genes in a tab + delimited text file. It's required. +- **Kind** The kind of your expression file format, LIM for LIMMA standard + output with Microarray, CUF for Cuffdiffs standard output with RNA-seq, + BSF for BETA specific format, and O for other formats. +- **genome** hg19 for human and mm9 for mouse. Others, don't set this parameter. +- **gname2** If this switch is on, gene or transcript IDs in files given + through -e will be considered as official gene symbols, DEFAULT=FALSE +- **EXPREINFO** is the columns info of the geneID, up/down status and statistcal + values column of your expression data,NOTE: use a comma as an connector. + for example: 2,5,7 means geneID in the 2nd column, Tscore in 5th column + and FDR in 7 column. +- **REFERENCE** is the refgene info file downloaded from UCSC genome browser. + It is a tab delimited text file with gene annotation with refseq and gene symbol. + Input this file only if your genome is neither hg19 nor mm9. + profiling +- **OUTPUT** to specify the output files directory +- **bl** Whether or not to use CTCF boundary file to get the contributed peaks +- **BOUNDARYFILE** is the file with reasonable boundaries if --bl is on and genome + is neither hg19 nor mm9. +- **NAME** specify the name of the output files. +- **DISTANCE** specify the distance wich peaks within it will be considered. +- **DIFF_FDR** specify the differential genes by the 3rd column in file input + via -e, genes with less than this value will be considered as the differentially + changed genes. +- **DIFF_AMOUNT** specify the differential genes the top #(DIFF_AMOUNT) ranked by + the 3rd column in file input via -e, genes ranked in the top # will be considered + as the differentially expressed genes. +- **CUTOFF** specify a cutoff of ks-test in the function prediction part + +----- + +**Script parameter list of BETA basic** + +:: + + -h, --help show this help message and exit + -p PEAKFILE, --peakfile PEAKFILE + The bed format of peaks binding sites. (BETA support 3 + or 5 columns bed format, CHROM, START, END (NAME, + SCORE)) + -e EXPREFILE, --diff_expr EXPREFILE + The differential expression file get from limma for + MicroArray ddata and cuffdiff for RNAseq data + -k {LIM,CUF,BSF,O}, --kind {LIM,CUF,BSF,O} + The kind of your expression file,this is required,it + can be LIM, CUF, BSF, O. LIM for LIMMA standard + format. CUF for CUFDIFF standard format, BSF for BETA + specific format and O for other formats, if is 'O', + columns infor required via --info + -g {hg19,mm9}, --genome {hg19,mm9} + Specify your species, hg19, mm9. For other genome + assembily versions of human and mouse or other + species, ignore this parameter. + --gname2 If this switch is on, gene or transcript IDs in files + given through -e will be considered as official gene + symbols, DEFAULT=FALSE + --info EXPREINFO Specify the geneID, up/down status and statistcal + values column of your expression data,NOTE: use a + comma as an connector. for example: 2,5,7 means geneID + in the 2nd column, Tscore in 5th column and FDR in 7 + column DEFAULT:2,5,7 for LIMMA; 2,10,13 for Cuffdiff + and 1,2,3 for BETA specific format + -r REFERENCE, --reference REFERENCE + The refgene info file downloaded from UCSC genome + browser.input this file only if your genome is neither + hg19 nor mm9 + -o OUTPUT, --output OUTPUT + The directory to store all the output files, if you + don't set this, files will be output into the current + directory + --bl Whether or not use CTCF boundary to filter peaks + around a gene, DEFAULT=FALSE + --bf BOUNDARYFILE CTCF conserved peaks bed file, use this only when you + set --bl and the genome is neither hg19 nor mm9 + --pn PEAKNUMBER The number of peaks you want to consider, + DEFAULT=10000 + --method {score,distance} + Define the method to do the TF/CR function prediction, + score for regulatory potential, distance for the + distance to the proximal binding peak. DEFAULT:SCORE + -n NAME, --name NAME This argument is used to name the result file.If not + set, the peakfile name will be used instead + -d DISTANCE, --distance DISTANCE + Set a number which unit is 'base'. It will get peaks + within this distance from gene TSS. default:100000 + (100kb) + --df DIFF_FDR Input a number 0~1 as a threshold to pick out the most + significant differential expressed genes by FDR, + DEFAULT = 1, that is select all the genes + --da DIFF_AMOUNT Get the most significant differential expressed genes + by the percentage(0-1) or number(larger than 1)Input a + number between 0-1, the rank based on fdr for example, + 2000, so that the script will only consider top 2000 + genes as the differentially expressed genes. DEFAULT = + 0.5, that is select top 50 percent genes of up and + down seprately. NOTE: if you want to use diff_fdr, + please set this parameter to 1, otherwise it will get + the intersection of these two parameters + -c CUTOFF, --cutoff CUTOFF + Input a number between 0~1 as a threshold to select + the closer target gene list(up regulate or down + regulate or both) with the p value was called by one + side ks-test, DEFAULT = 0.001 + + </help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/beta_macros.xml Tue Sep 16 13:35:24 2014 -0400 @@ -0,0 +1,185 @@ + +<macros> + <macro name="requirements"> + <requirements> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="2.15.0">R</requirement> + <requirement type="package" version="1.0.6">beta</requirement> + </requirements> + </macro> + + <macro name="stdio"> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </macro> + + <macro name="common_params"> + <param format="bed" name="peakfile" type="data" label="BED file for Peaks"> + <validator type="unspecified_build" /> + </param> + <param name="output_dir" type="hidden" label="Name for the output files" value="BETA_OUTPUT"/> + <param name="name" type="hidden" label="Name for the output files" value="NA"/> + <param name="distance" type="integer" label="the distance from gene TSS within which peaks will be selected" value="100000"> + <validator type="in_range" max="20000000" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 20000000" /> + </param> + <param name="peaknumber" type="integer" label="Peaks considered to contribute to the genes" value="10000"> + <validator type="in_range" max="200000" min="100" message="The Relative distance is out of range, the parameter has to be between 100 to 10000" /> + </param> + </macro> + + <macro name="boundary"> + <conditional name="boundary"> + <param name="boundaryLimit" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Use CTCF boundary to filter peaks around a gene"/> + <when value="no"/> + <when value="yes"> + <yield /> + </when> + </conditional> + </macro> + + <macro name="genome_params"> + <conditional name="refGenome"> + <param name="genomeName" type="select" label="genome reference"> + <option value="hg19">hg19 (built-in)</option> + <option value="mm9">mm9 (built-in)</option> + <option value="other">other</option> + </param> + <when value="hg19"> + <expand macro="boundary" /> + </when> + <when value="mm9"> + <expand macro="boundary" /> + </when> + <when value="other"> + <param name="refseq" type="data" format="tabular" label="UCSC Refseq Genes (From UCSC Table Browser)" + help="Columns: name,chrom,strand,txStart,txEnd,name"/> + <expand macro="boundary"> + <param name="bl_bed" type="data" format="bed" label="BED format boundary file"/> + </expand> + </when> + </conditional> + </macro> + + <macro name="refGenomeSourceConditional"> + <conditional name="refGenomeSource"> + <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Genome Reference Fasta sequence"> + <option value="cached" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from history</option> + </param> + <when value="cached"> + <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"/> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> + </when> <!-- history --> + </conditional> <!-- refGenomeSource --> + </macro> + + <macro name="extended_params"> + <param format="txt" name="exprefile" type="data" label="TEXT file for differential expression data"> + <validator type="unspecified_build" /> + </param> + <conditional name="expression"> + <param name="kind" type="select" label="Expression FIle Type" help="Preset columns for Cuffdiff, LIMMA, and BETA Specific Format"> + <option value="CUF">RNA-seq data with Cuffdiff default format</option> + <option value="LIM">MicroArray data with LIMMA default format</option> + <option value="BSF">BETA Specific Format</option> + <option value="O">Other tools processed data with BETA specific format</option> + </param> + <when value="CUF"> + <param name="expreinfo" type="text" value="2,10,13" label="Column number of the geneid, regulate status and statistics value"/> + </when> + <when value="LIM"> + <param name="expreinfo" type="text" value="2,5,7" label="Column number of the geneid, regulate status and statistics value"/> + </when> + <when value="BSF"> + <param name="expreinfo" type="text" value="1,2,3" label="Column number of the geneid, regulate status and statistics value"/> + </when> + <when value="O"> + <param name="expreinfo" type="text" value="" label="Column number of the geneid, regulate status and statistics value is required"> + <validator type="regex" message="Enter column numbers:geneid,test_stat,value">^\d+,\d+,\d+$</validator> + </param> + </when> + </conditional> + <param name="gname2" type="select" label="TRUE if gene ID in expression file identified by official gene symbol"> + <option value="Refseq">Refseq</option> + <option value="Gene_Symbol">Gene Symbol</option> + </param> + <param name="diff_fdr" type="float" label="get the most significant expression differentially changed genes by this cutoff based on fdr or pvalue" value="1.0"> + <validator type="in_range" max="1.0" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 1.0" /> + </param> + <param name="diff_amount" type="float" label="get the most significant expression differentially changed genes by amount" value="0.5"> + <validator type="in_range" max="20000" min="0" message="The Relative distance is out of range, the parameter has to be between 0 to 20000" /> + </param> + <param name="method" type="select" label="method to do the TF/CR function prediction" optional="true"> + <option value="score">regulatory potential</option> + <option value="distance">distance to the nearest peak</option> + </param> + + </macro> + + <template name="common_opts"> + -p "$peakfile" + -d $distance --pn $peaknumber -o $output_dir -n $name + </template> + + <template name="genome_opts"> +#if $refGenome.genomeName == 'hg19': + -g $refGenome.genomeName + ## -r \$BETA_LIB_PATH/BETA/references/hg19.refseq + #if $refGenome.boundary.boundaryLimit: + --bl + ## --bf \$BETA_LIB_PATH/BETA/references/hg19_CTCF_bound.bed + #end if +#elif $refGenome.genomeName == 'mm9': + -g $refGenome.genomeName + ## -r \$BETA_LIB_PATH/BETA/references/mm9.refseq + #if $refGenome.boundary.boundaryLimit: + --bl + ## --bf \$BETA_LIB_PATH/BETA/references/mm9_CTCF_bound.bed + #end if +#else + -r $refGenome.refseq + #if $refGenome.boundary.boundaryLimit: + --bl + --bf $refGenome.boundary.bl_bed + #end if +#end if + </template> + <template name="ref_genome_seq_opts"> +#if $refGenomeSource.genomeSource == 'cached': + --gs $refGenomeSource.all_fasta_source.fields.path +#else + --gs $refGenomeSource.ownFile +#end if + </template> + + <template name="extended_opts"> + -e "$exprefile" + -k $expression.kind --info $expression.expreinfo --method $method + --da $diff_amount --df $diff_fdr -c 1 +#if $gname2 == "Gene_Symbol": + --gname2" +#end if + </template> + + <token name="@EXTERNAL_DOCUMENTATION@"> + +For details about this application, please go to: + http://cistrome.org/BETA/index.html + + </token> + <token name="@CITATION_SECTION@">------ + +**Citation** + +For the underlying tool, please cite the following publication: +Wang, S., Sun, H., Ma, J., Zang, C., Wang, C., Wang, J., Tang Q, Meyer CA, Zhang Y, Liu, X. S. (2013). Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nature protocols, 8(12), 2502-2515. +PMID: 24263090 + </token> +</macros> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/beta_minus.xml Tue Sep 16 13:35:24 2014 -0400 @@ -0,0 +1,111 @@ +<tool id="beta_minus" name="BETA-minus: Targets prediction with binding only" version="0.1.0"> + <description>Predict the factors (TFs or CRs) direct target genes by only binding data</description> + <macros> + <import>beta_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> + BETA minus + #include source=$common_opts# + #include source=$genome_opts# + &> $log + </command> + <inputs> + <expand macro="common_params" /> + <expand macro="genome_params" /> + </inputs> + <expand macro="stdio" /> + <outputs> + <data format="txt" name="log" label="Log of BETA minus"/> + <data format="tabular" name="targetsoutput" label="BETA predicted Targets" from_work_dir="BETA_OUTPUT/NA_targets.txt"/> + <data format="tabular" name="targetpeaks" label="BETA Target gene's associated peaks" from_work_dir="BETA_OUTPUT/NA_targets_associated_peaks.txt"/> + </outputs> + <tests> + <test> + <param name='peakfile' value="peaks.bed" ftype="bed" dbkey="hg19"/> + <param name="distance" value="100000"/> + <param name="peaknumber" value="10000"/> + <param name="genomeName" value="hg19"/> + <output name="log"> + <assert_contents> + <has_text_matching expression="Finished" /> + </assert_contents> + </output> + <output name="targetsoutput"> + <assert_contents> + <has_text_matching expression="chr19\t4675243\t4723855\tNM_139159\t1.1.*\t-\tDPP" /> + </assert_contents> + </output> + <output name="targetpeaks"> + <assert_contents> + <has_text_matching expression="chr19\t4723422\t4724314\tregion_9\tNM_139159\tDPP9\t13\t0.6.*" /> + </assert_contents> + </output> + </test> + </tests> + <help> +** BETA minus ** + +@EXTERNAL_DOCUMENTATION@ + +@CITATION_SECTION@ + +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). + +.. class:: warningmark + +**NEED IMPROVEMENT** + +----- + +**Parameters** + +- **PEAKFILE file** contains peaks for the experiment in a bed + format file. Normally, it's produced by the peak calling tool. It's + required. +- **genome** hg19 for human and mm9 for mouse. Others, don't set this parameter. +- **REFERENCE** is the refgene info file downloaded from UCSC genome browser. + It is a tab delimited text file with gene annotation with refseq and gene symbol. + Input this file only if your genome is neither hg19 nor mm9. + profiling +- **OUTPUT** to specify the output files directory +- **bl** Whether or not to use CTCF boundary file to get the contributed peaks +- **NAME** specify the name of the output files. +- **DISTANCE** specify the distance wich peaks within it will be considered. + + +----- + +**script parameter list of BETA minus** + +:: + + -h, --help show this help message and exit + -p PEAKFILE, --peakfile PEAKFILE + The bed format of peaks binding sites. + BETA supports 3 or 5 columns bed format: CHROM, START, END [NAME, SCORE] + -g {hg19,mm9}, --genome {hg19,mm9} + Specify your species, {hg19, mm9} + -r REFERENCE, --reference REFERENCE + the refgene info file downloaded from UCSC genome + browser.input this file only if your genome is neither + hg19 nor mm9 + -o OUTPUT, --output OUTPUT + the directory to store all the output files, if you + don't set this, files will be output into the current + directory + --bl whether or not use CTCF boundary to filter peaks + around a gene, DEFAULT=FALSE + --pn PEAKNUMBER the number of peaks you want to consider, DEFAULT=10000 + -n NAME, --name NAME this argument is used to name the result file.If not + set, the peakfile name will be used instead + -d DISTANCE, --distance DISTANCE + Set a number which unit is 'base'. It will get peaks + within this distance from gene TSS. default:100000 (100kb) + + </help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/beta_plus.xml Tue Sep 16 13:35:24 2014 -0400 @@ -0,0 +1,215 @@ +<tool id="beta_plus" name="BETA-plus: Binding and Expression Target prediction and motif analysis" version="0.1.0"> + <description>Predict the factors (TFs or CRs) direct target genes by combining the binding and expression data, then do motif analysis on target regions</description> + <macros> + <import>beta_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> + BETA plus + #include source=$common_opts# + #include source=$genome_opts# + #include source=$ref_genome_seq_opts# + #include source=$extended_opts# + --mn $motifs + &> $log && + mkdir -p $motifresult.extra_files_path && + cp BETA_OUTPUT/motifresult/betamotif.html $motifresult && + cp BETA_OUTPUT/motifresult/*.js $motifresult.extra_files_path && + cp BETA_OUTPUT/motifresult/*.css $motifresult.extra_files_path && + cp -r BETA_OUTPUT/motifresult/img $motifresult.extra_files_path + + </command> + <inputs> + <expand macro="common_params" /> + <expand macro="genome_params" /> + <expand macro="refGenomeSourceConditional" /> + <expand macro="extended_params" /> + <param name="motifs" type="float" value="10" optional="true" label="Motifs to retrieve" + help="a number between 0 and 1 as the p-value cutoff or an integer larger than 1 as the number of motifs"> + <validator type="in_range" max="20000" min="0" message="A float between 0 and 1 or an integer greater than 1" /> + </param> + </inputs> + <expand macro="stdio" /> + <outputs> + <data format="txt" name="log" label="Log of BETA plus"/> + <data format="pdf" name="functionoutput" label="BETA functional prediction on ${peakfile.name}" from_work_dir="BETA_OUTPUT/NA_function_prediction.pdf"/> + <data format="tabular" name="uptargetsoutput" label="BETA direct targets prediction on up regulated genes" from_work_dir="BETA_OUTPUT/NA_uptarget.txt"/> + <data format="tabular" name="downtargetsoutput" label="BETA direct targets prediction on down regulated genes" from_work_dir="BETA_OUTPUT/NA_downtarget.txt"/> + <data format="bed" name="uptargetpeaks" label="BETA Uptarget associated peaks" from_work_dir="BETA_OUTPUT/NA_uptarget_associate_peaks.bed"/> + <data format="bed" name="downtargetpeaks" label="BETA Downtarget associated peaks" from_work_dir="BETA_OUTPUT/NA_downtarget_associate_peaks.bed"/> + <data format="txt" name="upmotifs" label="BETA Motifs in up-target regions" from_work_dir="BETA_OUTPUT/motifresult/UP_MOTIFS.txt" /> + <data format="txt" name="up_non_motifs" label="BETA Motifs in up-target regions versus non-target regions" from_work_dir="BETA_OUTPUT/motifresult/UP_NON_MOTIFS.txt" /> + <data format="txt" name="downmotifs" label="BETA Motifs in down-target regions" from_work_dir="BETA_OUTPUT/motifresult/DOWN_MOTIFS.txt" /> + <data format="txt" name="down_non_motifs" label="BETA Motifs in down-target regions versus non-target regions" from_work_dir="BETA_OUTPUT/motifresult/DOWN_NON_MOTIFS.txt" /> + <data format="txt" name="differentialmotifs" label="BETA Motifs up-target regions versus down-target regions" from_work_dir="BETA_OUTPUT/motifresult/DIFFERENTIAL_MOTIF_UP_DOWN.txt" /> + <data format="html" name="motifresult" label="BETA Motif analysis on target regions"/> + </outputs> + <tests> + <test> + <param name='peakfile' value="peaks.bed" ftype="bed" dbkey="hg19"/> + <param name="distance" value="100000"/> + <param name="peaknumber" value="10000"/> + <param name="genomeName" value="hg19"/> + <param name='exprefile' value="diff_expr.xls" ftype="tabular" dbkey="hg19"/> + <param name="kind" value="LIM"/> + <param name="expreinfo" type="text" value="2,5,7"/> + <param name="gname2" value="Refseq"/> + <param name="diff_fdr" value="1.0"/> + <param name="diff_amount" value="0.5"/> + <param name="method" value="score"/> + <output name="log"> + <assert_contents> + <has_text_matching expression="Finished" /> + </assert_contents> + </output> + <output name="uptargetsoutput"> + <assert_contents> + <has_text_matching expression="NM_001002231" /> + </assert_contents> + </output> + <output name="downtargetsoutput"> + <assert_contents> + <has_text_matching expression="NM_001280" /> + </assert_contents> + </output> + <output name="differentialmotifs"> + <assert_contents> + <has_text_matching expression="CDX1\tHomeodomain Family" /> + </assert_contents> + </output> + </test> + </tests> + <help> +** BETA plus ** + +@EXTERNAL_DOCUMENTATION@ + +@CITATION_SECTION@ + +This tool annotates the given intervals and scores with genome +features such as gene body. +Predicts Direct targets of TF and the active/repressive function +prediction. Does motif analysis at targets region as well. +It's the major module in CEAS package +which is written by Hyunjin Gene Shin, published in Bioinformatics +(pubmed id:19689956). + +.. class:: warningmark + +**NEED IMPROVEMENT** + +----- + +**Parameters** + +- **PEAKFILE file** contains peaks for the experiment in a bed + format file. Normally, it's produced by the peak calling tool. It's + required. +- **EXPREFILE file** contains the differentially expressed genes in a tab + delimited text file. It's required. +- **Kind** The kind of your expression file format, LIM for LIMMA standard + output with Microarray, CUF for Cuffdiffs standard output with RNA-seq, + BSF for BETA specific format, and O for other formats. +- **genome** hg19 for human and mm9 for mouse. Others, don't set this parameter. +- **genomereference** Genome reference data with fasta format +- **gname2** If this switch is on, gene or transcript IDs in files given + through -e will be considered as official gene symbols, DEFAULT=FALSE +- **EXPREINFO** is the columns info of the geneID, up/down status and statistcal + values column of your expression data,NOTE: use a comma as an connector. + for example: 2,5,7 means geneID in the 2nd column, Tscore in 5th column + and FDR in 7 column. +- **REFERENCE** is the refgene info file downloaded from UCSC genome browser. + It is a tab delimited text file with gene annotation with refseq and gene symbol. + Input this file only if your genome is neither hg19 nor mm9. + profiling +- **OUTPUT** to specify the output files directory +- **bl** Whether or not to use CTCF boundary file to get the contributed peaks +- **BOUNDARYFILE** is the file with reasonable boundaries if --bl is on and genome + is neither hg19 nor mm9. +- **NAME** specify the name of the output files. +- **DISTANCE** specify the distance wich peaks within it will be considered. +- **DIFF_FDR** specify the differential genes by the 3rd column in file input + via -e, genes with less than this value will be considered as the differentially + changed genes. +- **DIFF_AMOUNT** specify the differential genes the top #(DIFF_AMOUNT) ranked by + the 3rd column in file input via -e, genes ranked in the top # will be considered + as the differentially expressed genes. +- **CUTOFF** specify a cutoff of ks-test in the function prediction part + + +----- + +**Script parameter list of BETA plus** + +:: + + -h, --help show this help message and exit + -p PEAKFILE, --peakfile PEAKFILE + The bed format of peaks binding sites. (BETA support 3 + or 5 columns bed format, CHROM, START, END (NAME, + SCORE)) + -e EXPREFILE, --diff_expr EXPREFILE + The differential expression file get from limma for + MicroArray ddata and cuffdiff for RNAseq data + -k {LIM,CUF,BSF,O}, --kind {LIM,CUF,BSF,O} + The kind of your expression file,this is required,it + can be LIM, CUF, BSF, O. LIM for LIMMA standard + format. CUF for CUFDIFF standard format, BSF for BETA + specific format and O for other formats, if is 'O', + columns infor required via --info + -g {hg19,mm9}, --genome {hg19,mm9} + Specify your species, hg19, mm9 + --gs GENOMEREFERNCE GenomeReference file with fasta format + --gname2 If this switch is on, gene or transcript IDs in files + given through -e will be considered as official gene + symbols, DEFAULT=FALSE + --info EXPREINFO Specify the geneID, up/down status and statistcal + values column of your expression data,NOTE: use a + comma as an connector. for example: 2,5,7 means geneID + in the 2nd column, Tscore in 5th column and FDR in 7 + column DEFAULT:2,5,7 for LIMMA; 2,10,13 for Cuffdiff + and 1,2,3 for BETA specific format + -r REFERENCE, --reference REFERENCE + The refgene info file downloaded from UCSC genome + browser.input this file only if your genome is neither + hg19 nor mm9 + -o OUTPUT, --output OUTPUT + The directory to store all the output files, if you + don't set this, files will be output into the current + directory + --bl Whether or not use CTCF boundary to filter peaks + around a gene, DEFAULT=FALSE + --bf BOUNDARYFILE CTCF conserved peaks bed file, use this only when you + set --bl and the genome is neither hg19 nor mm9 + --pn PEAKNUMBER The number of peaks you want to consider, + DEFAULT=10000 + --method {score,distance} + Define the method to do the TF/CR function prediction, + score for regulatory potential, distance for the + distance to the proximal binding peak. DEFAULT:SCORE + -n NAME, --name NAME This argument is used to name the result file.If not + set, the peakfile name will be used instead + -d DISTANCE, --distance DISTANCE + Set a number which unit is 'base'. It will get peaks + within this distance from gene TSS. default:100000 + (100kb) + --df DIFF_FDR Input a number 0~1 as a threshold to pick out the most + significant differential expressed genes by FDR, + DEFAULT = 1, that is select all the genes + --da DIFF_AMOUNT Get the most significant differential expressed genes + by the percentage(0-1) or number(larger than 1)Input a + number between 0-1, the rank based on fdr for example, + 2000, so that the script will only consider top 2000 + genes as the differentially expressed genes. DEFAULT = + 0.5, that is select top 50 percent genes of up and + down seprately. NOTE: if you want to use diff_fdr, + please set this parameter to 1, otherwise it will get + the intersection of these two parameters + -c CUTOFF, --cutoff CUTOFF + Input a number between 0~1 as a threshold to select + the closer target gene list(up regulate or down + regulate or both) with the p value was called by one + side ks-test, DEFAULT = 0.001 + + </help> +</tool>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peaks.bed Tue Sep 16 13:35:24 2014 -0400 @@ -0,0 +1,72 @@ +chr19 518572 519514 AR_LNCaP_4717 59.19 +chr19 1020702 1021980 AR_LNCaP_4725 388.32 +chr19 1094875 1095946 AR_LNCaP_4726 63.11 +chr19 1228829 1229967 AR_LNCaP_4728 54.26 +chr19 1382835 1384282 AR_LNCaP_4733 231.69 +chr19 2269491 2270735 AR_LNCaP_4741 60.70 +chr19 2543491 2544716 AR_LNCaP_4747 228.53 +chr19 3185501 3186253 AR_LNCaP_4748 52.27 +chr19 3336410 3337572 AR_LNCaP_4750 94.92 +chr19 4723422 4724314 AR_LNCaP_4753 74.30 +chr19 4724416 4725364 AR_LNCaP_4754 115.50 +chr19 5268577 5269878 AR_LNCaP_4755 290.97 +chr19 5620739 5621928 AR_LNCaP_4756 70.46 +chr19 7489621 7490513 AR_LNCaP_4760 73.95 +chr19 8372986 8374008 AR_LNCaP_4765 76.91 +chr19 10875668 10876743 AR_LNCaP_4773 72.61 +chr19 12721199 12722240 AR_LNCaP_4774 61.84 +chr19 13101849 13102755 AR_LNCaP_4777 291.05 +chr19 13318039 13318869 AR_LNCaP_4783 52.65 +chr19 13875326 13876277 AR_LNCaP_4785 51.19 +chr19 14583973 14585287 AR_LNCaP_4788 88.28 +chr19 15414587 15415713 AR_LNCaP_4789 76.29 +chr19 15489711 15490727 AR_LNCaP_4790 59.97 +chr19 16473642 16474670 AR_LNCaP_4793 70.70 +chr19 16973078 16974032 AR_LNCaP_4796 76.09 +chr19 17096748 17097899 AR_LNCaP_4797 62.09 +chr19 17345963 17347135 AR_LNCaP_4798 92.15 +chr19 18391901 18392804 AR_LNCaP_4802 51.13 +chr19 18808279 18810382 AR_LNCaP_4809 149.25 +chr19 28392798 28393702 AR_LNCaP_4818 54.45 +chr19 28426028 28427157 AR_LNCaP_4820 51.30 +chr19 28431530 28432644 AR_LNCaP_4821 63.20 +chr19 28607592 28608803 AR_LNCaP_4822 101.52 +chr19 30020337 30021328 AR_LNCaP_4827 52.78 +chr19 30211394 30212475 AR_LNCaP_4829 53.76 +chr19 30551328 30552172 AR_LNCaP_4830 52.34 +chr19 30643279 30644356 AR_LNCaP_4831 229.66 +chr19 30932770 30934129 AR_LNCaP_4833 103.59 +chr19 32210230 32211210 AR_LNCaP_4839 59.08 +chr19 32234483 32235456 AR_LNCaP_4840 51.81 +chr19 33667285 33668666 AR_LNCaP_4846 438.19 +chr19 33863966 33865008 AR_LNCaP_4847 54.29 +chr19 34663548 34664231 AR_LNCaP_4849 50.15 +chr19 34800905 34802101 AR_LNCaP_4852 292.94 +chr19 34817831 34818944 AR_LNCaP_4853 124.21 +chr19 34948706 34949438 AR_LNCaP_4854 52.96 +chr19 34962763 34963890 AR_LNCaP_4855 95.70 +chr19 38560828 38561779 AR_LNCaP_4860 61.50 +chr19 38789237 38790370 AR_LNCaP_4861 76.81 +chr19 38865927 38867149 AR_LNCaP_4863 84.08 +chr19 39892778 39893857 AR_LNCaP_4868 72.83 +chr19 39902325 39903668 AR_LNCaP_4869 84.54 +chr19 41139890 41140917 AR_LNCaP_4873 50.16 +chr19 42502780 42503773 AR_LNCaP_4877 62.07 +chr19 44198615 44199741 AR_LNCaP_4880 120.50 +chr19 45595987 45596898 AR_LNCaP_4882 51.31 +chr19 45655043 45656039 AR_LNCaP_4883 58.06 +chr19 45981823 45982582 AR_LNCaP_4886 52.62 +chr19 46246031 46247043 AR_LNCaP_4887 420.28 +chr19 47290422 47291287 AR_LNCaP_4892 51.42 +chr19 47470793 47471707 AR_LNCaP_4893 53.30 +chr19 47950633 47951639 AR_LNCaP_4896 60.92 +chr19 48204625 48205733 AR_LNCaP_4900 71.83 +chr19 50154344 50155915 AR_LNCaP_4912 84.12 +chr19 51354060 51354999 AR_LNCaP_4914 62.11 +chr19 51372841 51373704 AR_LNCaP_4915 50.33 +chr19 51392207 51393248 AR_LNCaP_4916 132.09 +chr19 55592961 55594092 AR_LNCaP_4921 68.33 +chr19 57639841 57640962 AR_LNCaP_4929 105.02 +chr19 57723651 57724464 AR_LNCaP_4931 57.62 +chr19 57873567 57875214 AR_LNCaP_4932 131.57 +chr19 58919368 58920359 AR_LNCaP_4940 58.81
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Tue Sep 16 13:35:24 2014 -0400 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Sep 16 13:35:24 2014 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Sep 16 13:35:24 2014 -0400 @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="numpy" version="1.7.1"> + <repository changeset_revision="55a7a5e9d63f" name="package_numpy_1_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="R" version="2.15.0"> + <repository changeset_revision="3a70cdc41d21" name="package_r_2_15_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="beta" version="1.0.6"> + <repository changeset_revision="26f7b1d72d3c" name="package_beta_1_0_6" owner="jjohnson" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>