Mercurial > repos > iuc > macs2
changeset 8:16dc0e3d659b draft
Uploaded
author | iuc |
---|---|
date | Thu, 23 Jan 2014 07:30:06 -0500 |
parents | da0a1fcf7fe0 |
children | 8e2039b920bf |
files | macs2_bdgbroadcall.xml macs2_bdgcmp.xml macs2_bdgdiff.xml macs2_bdgpeakcall.xml macs2_callpeak.xml macs2_filterdup.xml macs2_predict.xml macs2_randsample.xml macs2_refinepeak.xml |
diffstat | 9 files changed, 28 insertions(+), 29 deletions(-) [+] |
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--- a/macs2_bdgbroadcall.xml Tue Jan 21 13:14:33 2014 -0500 +++ b/macs2_bdgbroadcall.xml Thu Jan 23 07:30:06 2014 -0500 @@ -1,5 +1,5 @@ -<tool id="macs2_bdgbroadcall" name="Call broad peaks" version="2.0.10.0"> - <description>from bedGraph</description> +<tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="2.0.10.0"> + <description>Call broad peaks from bedGraph output</description> <expand macro="requirements" /> <expand macro="version_command" /> <macros>
--- a/macs2_bdgcmp.xml Tue Jan 21 13:14:33 2014 -0500 +++ b/macs2_bdgcmp.xml Thu Jan 23 07:30:06 2014 -0500 @@ -1,5 +1,5 @@ -<tool id="macs2_bdgcmp" name="Deduct noise" version="2.0.10.0"> - <description>by comparing two signal tracks in bedGraph (bdgcmp)</description> +<tool id="macs2_bdgcmp" name="MACS2 bdgcmp" version="2.0.10.0"> + <description>Deduct noise by comparing two signal tracks in bedGraph</description> <expand macro="requirements" /> <expand macro="version_command" /> <macros>
--- a/macs2_bdgdiff.xml Tue Jan 21 13:14:33 2014 -0500 +++ b/macs2_bdgdiff.xml Thu Jan 23 07:30:06 2014 -0500 @@ -1,5 +1,5 @@ -<tool id="macs2_bdgdiff" name="Differential peak detection" version="2.0.10.0"> - <description>based on paired four bedgraph files</description> +<tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="2.0.10.0"> + <description>Differential peak detection based on paired four bedgraph files</description> <expand macro="requirements" /> <expand macro="version_command" /> <macros>
--- a/macs2_bdgpeakcall.xml Tue Jan 21 13:14:33 2014 -0500 +++ b/macs2_bdgpeakcall.xml Thu Jan 23 07:30:06 2014 -0500 @@ -1,5 +1,5 @@ -<tool id="macs2_bdgpeakcall" name="Call peaks" version="2.0.10.0"> - <description>from bedGraph output</description> +<tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="2.0.10.0"> + <description>Call peaks from bedGraph output</description> <expand macro="requirements" /> <expand macro="version_command" /> <macros>
--- a/macs2_callpeak.xml Tue Jan 21 13:14:33 2014 -0500 +++ b/macs2_callpeak.xml Thu Jan 23 07:30:06 2014 -0500 @@ -1,5 +1,5 @@ -<tool id="macs2_callpeak" name="Call peaks" version="2.0.10.0"> - <description>from alignment results</description> +<tool id="macs2_callpeak" name="MACS2 callpeak" version="2.0.10.0"> + <description>Call peaks from alignment results</description> <expand macro="requirements"> <requirement type="package" version="3.0.1">R_3_0_1</requirement> <!-- awk and R is missing --> @@ -62,8 +62,8 @@ ## TODO ## run R to create pdf from model script - ##if os.path.exists( os.path.join( tmp_dir, "MACS2_PREFIX_model.r" ) ): - ## cmdline = 'Rscript "MACS2_PREFIX_model.r" > "MACS2_PREFIX_model.r.log"' ) + ##if os.path.exists( os.path.join( tmp_dir, "MACS2_model.r" ) ): + ## cmdline = 'Rscript "MACS2_model.r" > "MACS2_model.r.log"' ) ## proc = subprocess.Popen( args=cmdline, shell=True, cwd=tmp_dir ) ## proc.wait() @@ -89,7 +89,7 @@ ##parse xls files to interval files as needed ##TODO is in working dir #if 'peaks_interval' in str($outputs).split(','): - #set $file = os.path.join( $tmp_dir, 'MACS2_PREFIX_peaks.xls' ) + #set $file = os.path.join( $tmp_dir, 'MACS2_peaks.xls' ) #if os.path.exists( $file ): echo '#peaks file' > $output_xls_to_interval_peaks_file; awk '$2-=1' $file >> $output_xls_to_interval_peaks_file; @@ -145,14 +145,13 @@ </conditional> <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs"> - <option value="peaks_bed" selected="True">Peaks as bed file</option> + <option value="peaks_bed" selected="True">Peaks as BED file</option> <option value="html">Summary page (html)</option> <option value="narrow">narrow Peaks</option> <option value="broad">broad Peaks</option> <option value="gapped">gapped Peaks</option> <option value="summits" selected="true">summits</option> <option value="peaks_interval">Peaks as interval file</option> - <validator type="no_options" message="Please select at least one output file." /> </param> @@ -181,19 +180,19 @@ </inputs> <outputs> <!--callpeaks output--> - <data name="output_bed" format="tabular" from_work_dir="MACS2_PREFIX_peaks.xls" label="${tool.name} on ${on_string} (peaks: xls)"> + <data name="output_bed" format="tabular" from_work_dir="MACS2_peaks.bed" label="${tool.name} on ${on_string} (peaks in BED)"> <filter>'peaks_bed' in outputs</filter> </data> - <data name="output_narrowpeaks" format="tabular" from_work_dir="MACS2_PREFIX_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)"> + <data name="output_narrowpeaks" format="tabular" from_work_dir="MACS2_peaks.encodePeak" label="${tool.name} on ${on_string} (narrow Peaks)"> <filter>'narrow' in outputs</filter> </data> - <data name="output_broadpeaks" format="tabular" from_work_dir="MACS2_PREFIX_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)"> + <data name="output_broadpeaks" format="tabular" from_work_dir="MACS2_broad_peaks.bed" label="${tool.name} on ${on_string} (broad Peaks)"> <filter>'broad' in outputs</filter> </data> - <data name="output_gappedpeaks" format="tabular" from_work_dir="MACS2_PREFIX_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)"> + <data name="output_gappedpeaks" format="tabular" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)"> <filter>'gapped' in outputs</filter> </data> - <data name="output_summits" format="bed" from_work_dir="MACS2_PREFIX_summits.bed" label="${tool.name} on ${on_string} (summits)"> + <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" label="${tool.name} on ${on_string} (summits in BED)"> <filter>'summits' in outputs</filter> </data> <data name="output_xls_to_interval_peaks_file" format="interval" label="${tool.name} on ${on_string} (peaks: interval)">
--- a/macs2_filterdup.xml Tue Jan 21 13:14:33 2014 -0500 +++ b/macs2_filterdup.xml Thu Jan 23 07:30:06 2014 -0500 @@ -1,5 +1,5 @@ -<tool id="macs2_filterdup" name="Remove duplicate reads" version="2.0.10.0"> - <description>at the same position</description> +<tool id="macs2_filterdup" name="MACS2 filterdup" version="2.0.10.0"> + <description>Remove duplicate reads at the same position</description> <expand macro="requirements" /> <expand macro="version_command" /> <macros>
--- a/macs2_predict.xml Tue Jan 21 13:14:33 2014 -0500 +++ b/macs2_predict.xml Thu Jan 23 07:30:06 2014 -0500 @@ -1,5 +1,5 @@ -<tool id="macs2_predict" name="Predict" version="2.0.10.0"> - <description>d or fragment size from alignment results</description> +<tool id="macs2_predict" name="MACS2 predictd" version="2.0.10.0"> + <description>Predict 'd' or fragment size from alignment results</description> <expand macro="requirements"> <requirement type="package" version="3.0.1">R_3_0_1</requirement> </expand> @@ -8,7 +8,7 @@ <import>macs2_macros.xml</import> </macros> <command> - macs2 predict + macs2 predictd -i #echo ','.join($infiles)# --tsize $tsize @effective_genome_size@
--- a/macs2_randsample.xml Tue Jan 21 13:14:33 2014 -0500 +++ b/macs2_randsample.xml Thu Jan 23 07:30:06 2014 -0500 @@ -1,5 +1,5 @@ -<tool id="macs2_randsamoke" name="Randomly sample number or percentage" version="2.0.10.0"> - <description>of total reads</description> +<tool id="macs2_randsamoke" name="MACS2" version="2.0.10.0"> + <description>Randomly sample number or percentage of total reads</description> <expand macro="requirements" /> <expand macro="version_command" /> <macros>
--- a/macs2_refinepeak.xml Tue Jan 21 13:14:33 2014 -0500 +++ b/macs2_refinepeak.xml Thu Jan 23 07:30:06 2014 -0500 @@ -1,5 +1,5 @@ -<tool id="macs2_refinepeak" name="Refine peak summits" version="2.0.10.0"> - <description></description> +<tool id="macs2_refinepeak" name="MACS2 refinepeak" version="2.0.10.0"> + <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description> <expand macro="requirements" /> <expand macro="version_command" /> <macros>