Mercurial > repos > iuc > macs2
changeset 12:836578426f44 draft
Uploaded
author | bgruening |
---|---|
date | Fri, 24 Jan 2014 10:35:51 -0500 |
parents | ac24388a0fda |
children | b680eea82cf3 |
files | macs2_callpeak.xml macs2_macros.xml macs2_predict.xml macs2_predictd.xml tool_dependencies.xml |
diffstat | 5 files changed, 43 insertions(+), 135 deletions(-) [+] |
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--- a/macs2_callpeak.xml Thu Jan 23 11:31:32 2014 -0500 +++ b/macs2_callpeak.xml Fri Jan 24 10:35:51 2014 -0500 @@ -3,7 +3,6 @@ <expand macro="requirements"> <requirement type="package" version="3.0.1">R_3_0_1</requirement> <requirement type="set_environment">MACS2_SCRIPT_PATH</requirement> - <!-- awk and R is missing --> </expand> <expand macro="version_command" /> <macros> @@ -29,7 +28,7 @@ --bw='$band_width' - ##advanced options + ## advanced options #if str( $advanced_options.advanced_options_selector ) == 'on': --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi $advanced_options.nolambda @@ -44,57 +43,28 @@ --mfold 10 30 #end if - $bdg + ## With --bdg two additional output files will be generated. + #if 'bdg' in str($outputs).split(','): + --bdg + #end if - ##pq value select options + ## pq value select options #if str( $pq_options.pq_options_selector ) == 'qvalue': --qvalue $pq_options.qvalue #else: --pvalue $pq_options.pvalue #end if - ##model options + ## model options #if str( $nomodel_type.nomodel_type_selector ) == 'nomodel': --nomodel --shiftsize='$nomodel_type.shiftsize' #end if 2> $temp_stderr; - ####################################################### - ## move files generated by callpeak command - ## TODO ## run R to create pdf from model script - #if os.path.exists( os.getcwd(), "MACS2_model.r" ) ): - Rscript "MACS2_model.r" > "MACS2_model.r.log"; - #end if - - - ## move bed out to proper output file - ##set $file = os.path.join( $tmp_dir, "%s_peaks.bed" % $experiment_name ) - ##if os.path.exists( $file ): - ## mv $file $output_bed_file - ##end if - - ## OICR peak_xls file - ##set $file = os.path.join( $tmp_dir, "%s_peaks.xls" % $experiment_name ) - ##if os.path.exists( $file ): - ## mv $file output_peaks $output_peaks_file - ##end if - - ### peaks.encodepeaks (narrowpeaks) file - ##set $file = os.path.join ( $tmp_dir, "%s_peaks.encodePeak" % $experiment_name ) - ##if os.path.exists( $file ): - ## mv $file $output_narrowpeaks_file - - - ##parse xls files to interval files as needed - ##TODO is in working dir - #if 'peaks_interval' in str($outputs).split(','): - #if os.path.exists( 'MACS2_peaks.xls' ): - echo '#peaks file' > $output_xls_to_interval_peaks_file; - awk '$2-=1' MACS2_peaks.xls >> $output_xls_to_interval_peaks_file; - ##xls_to_interval( create_peak_xls_file, output_xls_to_interval_peaks_file, header = 'peaks file' ) - #end if + #if 'pdf' in str($outputs).split(','): + Rscript MACS2_model.r > MACS2_model.r.log; #end if #if 'html' in str($outputs).split(','): @@ -103,7 +73,7 @@ if [ \$count != 0 ]; then mkdir $output_extra_files.extra_files_path; - mv MACS2* $output_extra_files.extra_files_path; + cp MACS2* $output_extra_files.extra_files_path; python \$MACS2_SCRIPT_PATH/dir2html.py $output_extra_files.extra_files_path $temp_stderr > $output_extra_files; fi; #end if @@ -119,7 +89,6 @@ <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size" help="This value is only used while building the shifting model." /> - <param name="bdg" type="boolean" truevalue="-B" falsevalue="" checked="False" label="Save fragment pileup, control lambda, -log10pvalue/qvalue in bedGraph" help="Files are located in the html report."/> <conditional name="pq_options"> <param name="pq_options_selector" type="select" label="Peak detection based on" help="default uses q-value"> @@ -146,13 +115,11 @@ <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs"> <option value="peaks_bed" selected="True">Peaks as BED file</option> + <option value="narrow">narrow Peaks</option> + <option value="summits" selected="true">summits</option> + <option value="bdg" selected="true">Scores in bedGraph files (--bdg)</option> <option value="html">Summary page (html)</option> - <option value="narrow">narrow Peaks</option> - <option value="broad">broad Peaks</option> - <option value="gapped">gapped Peaks</option> - <option value="summits" selected="true">summits</option> - <option value="peaks_interval">Peaks as interval file</option> - <option value="plot">Plot in PDF</option> + <option value="pdf">Plot in PDF</option> <validator type="no_options" message="Please select at least one output file." /> </param> @@ -188,10 +155,12 @@ <filter>'narrow' in outputs</filter> </data> <data name="output_broadpeaks" format="tabular" from_work_dir="MACS2_broad_peaks.bed" label="${tool.name} on ${on_string} (broad Peaks)"> - <filter>'broad' in outputs</filter> - </data> - <data name="output_gappedpeaks" format="tabular" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)"> - <filter>'gapped' in outputs</filter> + <filter> + (( + advanced_options['advanced_options_selector'] == "on" and + advanced_options['broad_options']['broad_options_selector'] == "--broad" + )) + </filter> </data> <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" label="${tool.name} on ${on_string} (summits in BED)"> <filter>'summits' in outputs</filter> @@ -199,8 +168,11 @@ <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" label="${tool.name} on ${on_string} (plot)"> <filter>'pdf' in outputs</filter> </data> - <data name="output_xls_to_interval_peaks_file" format="interval" label="${tool.name} on ${on_string} (peaks: interval)"> - <filter>'peaks_interval' in outputs</filter> + <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" label="${tool.name} on ${on_string} (Bedgraph Treatment)"> + <filter>'bdg' in outputs</filter> + </data> + <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" label="${tool.name} on ${on_string} (Bedgraph Control)"> + <filter>'bdg' in outputs</filter> </data> <data name="output_extra_files" format="html" label="${tool.name} on ${on_string} (html report)"> <filter>'html' in outputs</filter> @@ -225,6 +197,9 @@ **Peak Calling**: Main MACS2 Function to Call peaks from alignment results. +If you choose "Scores in bedGraph files" MACS will output the fragment pileup, control lambda, -log10-pvalue and -log10-qvalue scores in bedGraph files. + + **Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph.
--- a/macs2_macros.xml Thu Jan 23 11:31:32 2014 -0500 +++ b/macs2_macros.xml Fri Jan 24 10:35:51 2014 -0500 @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.0.10.2">macs2</requirement> + <requirement type="package" version="2.0.10.3">macs2</requirement> <requirement type="package" version="1.7.1">numpy</requirement> <yield /> </requirements>
--- a/macs2_predict.xml Thu Jan 23 11:31:32 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -<tool id="macs2_predict" name="MACS2 predictd" version="2.0.10.0"> - <description>Predict 'd' or fragment size from alignment results</description> - <expand macro="requirements"> - <requirement type="package" version="3.0.1">R_3_0_1</requirement> - </expand> - <expand macro="version_command" /> - <macros> - <import>macs2_macros.xml</import> - </macros> - <command> - macs2 predictd - -i #echo ','.join($infiles)# - --tsize $tsize - @effective_genome_size@ - --bw $band_width - --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi - > $outfile; - - Rscript predicted_model.R > $outfile_image - </command> - <expand macro="stdio" /> - <inputs> - <repeat name="infiles" title="ChIP-seq alignment files" min="1" - help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command."> - - <param name="infile" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-seq alignment file" help="-i" /> - </repeat> - - <expand macro="conditional_effective_genome_size" /> - <expand macro="tag_size" /> - - <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size" - help="This value is only used while building the shifting model. (--bw)" /> - - <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5" - help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/> - <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50" - help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/> - - </inputs> - - <outputs> - <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" /> - <data name="outfile_image" format="png" label="${tool.name} on ${on_string} - X-correlation image" /> - </outputs> - <tests> - <!--none yet for macs2--> - </tests> - <help> -**What it does** - -bdgdiff from macs2 - - -Note that pair-end data is not supposed to work with this command. - - -@citation@ - </help> -</tool>
--- a/macs2_predictd.xml Thu Jan 23 11:31:32 2014 -0500 +++ b/macs2_predictd.xml Fri Jan 24 10:35:51 2014 -0500 @@ -1,5 +1,5 @@ -<tool id="macs2_predict" name="Predict" version="2.0.10.0"> - <description>d or fragment size from alignment results</description> +<tool id="macs2_predictd" name="MACS2 predictd" version="2.0.10.0"> + <description>Predict 'd' or fragment size from alignment results</description> <expand macro="requirements"> <requirement type="package" version="3.0.1">R_3_0_1</requirement> </expand> @@ -8,24 +8,19 @@ <import>macs2_macros.xml</import> </macros> <command> - macs2 predict - -i #echo ','.join($infiles)# + macs2 predictd + -i #echo ','.join( map( str, $infiles) )# --tsize $tsize @effective_genome_size@ --bw $band_width - --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi + --mfold $mfoldlo $mfoldhi > $outfile; Rscript predicted_model.R > $outfile_image </command> - <expand macro="stdio" /> + <expand macro="stdio" /> <inputs> - <repeat name="infiles" title="ChIP-seq alignment files" min="1" - help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command."> - - <param name="infile" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-seq alignment file" help="-i" /> - </repeat> - + <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" /> <expand macro="conditional_effective_genome_size" /> <expand macro="tag_size" /> @@ -55,12 +50,6 @@ Note that pair-end data is not supposed to work with this command. ------- - -**Citation** - -For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. - -Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org. +@citation@ </help> </tool>
--- a/tool_dependencies.xml Thu Jan 23 11:31:32 2014 -0500 +++ b/tool_dependencies.xml Fri Jan 24 10:35:51 2014 -0500 @@ -12,10 +12,14 @@ <set_environment version="1.0"> <environment_variable action="set_to" name="MACS2_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> - <package name="macs2" version="2.0.10.2"> + <!-- 2.0.10 12162013 --> + <package name="macs2" version="2.0.10.3"> <install version="1.0"> <actions> - <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.0.10.07132012.tar.gz</action> + <action type="shell_command">git clone --recursive https://github.com/taoliu/MACS.git</action> + <action type="shell_command">git checkout 7ccb571d2f2dcb5be1d75f323b1d17a59b926deb</action> + <action type="shell_command">git submodule update --recursive</action> + <action type="set_environment_for_install"> <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> <package name="numpy" version="1.7.1" />