Mercurial > repos > iuc > macs2
changeset 1:d202e3d663bb draft
Uploaded
| author | iuc |
|---|---|
| date | Thu, 16 Jan 2014 15:44:43 -0500 |
| parents | 9c157b556c33 |
| children | 1bb575b6c07c |
| files | macs2_bdgbroadcall.xml macs2_bdgcmp.xml macs2_bdgdiff.xml macs2_bdgpeakcall.xml macs2_callpeak.xml macs2_filterdup.xml macs2_macros.xml macs2_predict.xml macs2_randsample.xml macs2_refinepeak.xml tool_dependencies.xml |
| diffstat | 11 files changed, 173 insertions(+), 79 deletions(-) [+] |
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--- a/macs2_bdgbroadcall.xml Thu Jan 16 13:31:17 2014 -0500 +++ b/macs2_bdgbroadcall.xml Thu Jan 16 15:44:43 2014 -0500 @@ -1,11 +1,10 @@ <tool id="macs2_bdgbroadcall" name="Call broad peaks" version="2.0.10.0"> <description>from bedGraph</description> - <requirements> - <requirement type="python-module">macs2</requirement> - <requirement type="python-module">numpy</requirement> - <requirement type="package" version="2.0.10.2">macs2</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - </requirements> + <expand macro="requirements" /> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> <command> macs2 bdgbroadcall
--- a/macs2_bdgcmp.xml Thu Jan 16 13:31:17 2014 -0500 +++ b/macs2_bdgcmp.xml Thu Jan 16 15:44:43 2014 -0500 @@ -1,11 +1,10 @@ <tool id="macs2_bdgcmp" name="Deduct noise" version="2.0.10.0"> <description>by comparing two signal tracks in bedGraph (bdgcmp)</description> - <requirements> - <requirement type="python-module">macs2</requirement> - <requirement type="python-module">numpy</requirement> - <requirement type="package" version="2.0.10.2">macs2</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - </requirements> + <expand macro="requirements" /> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> <command> macs2 bdgcmp -t $input_treatment_file
--- a/macs2_bdgdiff.xml Thu Jan 16 13:31:17 2014 -0500 +++ b/macs2_bdgdiff.xml Thu Jan 16 15:44:43 2014 -0500 @@ -1,13 +1,11 @@ <tool id="macs2_bdgdiff" name="Differential peak detection" version="2.0.10.0"> <description>based on paired four bedgraph files</description> - <requirements> - <requirement type="python-module">macs2</requirement> - <requirement type="python-module">numpy</requirement> - <requirement type="package" version="2.0.10.2">macs2</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - </requirements> + <expand macro="requirements" /> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> <command> - macs2 bdgdiff --t1 $infile_pileup_cond1 --t2 $infile_pileup_cond2 @@ -30,7 +28,6 @@ #if '--ofile-both-conditions' in str($outputs).split(','): --ofile-both-conditions $output_both #end if - </command> <inputs> <param name="infile_pileup_cond1" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 1" /> @@ -39,7 +36,7 @@ <param name="infile_control_cond1" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 1" /> <param name="infile_control_cond2" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 2" /> - <param name="cutoff" type="float" label="Cutoff of log10 likelihood ratio cutoff" value="1.0" help="DEFAULT: 1.0 (likelihood ratio=10) (--cutoff)"/> + <param name="cutoff" type="float" label="Cutoff of log10 likelihood ratio cutoff" value="1.0" help="Default: 1.0 (likelihood ratio=10) (--cutoff)"/> <param name="minlen" type="integer" label="Minimum length of differential region" value="200"/> <param name="depth1" type="integer" value="1" label="Sequence depth of condition 1 in million reads" help="Default: 1 (--depth1)" /> <param name="depth2" type="integer" value="1" label="Sequence depth of condition 2 in million reads" help="Default: 1 (--depth2)" />
--- a/macs2_bdgpeakcall.xml Thu Jan 16 13:31:17 2014 -0500 +++ b/macs2_bdgpeakcall.xml Thu Jan 16 15:44:43 2014 -0500 @@ -1,11 +1,10 @@ <tool id="macs2_bdgpeakcall" name="Call peaks" version="2.0.10.0"> <description>from bedGraph output</description> - <requirements> - <requirement type="python-module">macs2</requirement> - <requirement type="python-module">numpy</requirement> - <requirement type="package" version="2.0.10.2">macs2</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - </requirements> + <expand macro="requirements" /> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> <command> macs2 bdgpeakcall @@ -31,7 +30,6 @@ <param name="notrackline" type="boolean" truevalue="" falsevalue="--no-trackline" checked="False" label="Include trackline into bedGraph output" help="required by USCS (--no-trackline)"/> - </inputs> <outputs> <data name="ofile" format="tabular" label="${tool.name} on ${on_string}" />
--- a/macs2_callpeak.xml Thu Jan 16 13:31:17 2014 -0500 +++ b/macs2_callpeak.xml Thu Jan 16 15:44:43 2014 -0500 @@ -1,12 +1,13 @@ <tool id="macs2_callpeak" name="Call peaks" version="2.0.10.0"> <description>from alignment results</description> - <requirements> - <requirement type="python-module">macs2</requirement> - <requirement type="python-module">numpy</requirement> - <requirement type="package" version="2.0.10.2">macs2</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> + <expand macro="requirements"> + <requirement type="package" version="3.0.1">R_3_0_1</requirement> <!-- awk and R is missing --> - </requirements> + </expand> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> <command> #set $temp_stderr = 'macs2_stderr' macs2 callpeak @@ -21,14 +22,10 @@ #for $ifile in $input_treatment_file: --format='$ifile.ext.upper()' #end for - - #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined': - --gsize $effective_genome_size_options.gsize - #else: - --gsize $effective_genome_size_options.effective_genome_size_options_selector - #end if - --bw='$bw' + @effective_genome_size@ + + --bw='$band_width' ##advanced options #if str( $advanced_options.advanced_options_selector ) == 'on': @@ -116,26 +113,15 @@ #end if cat $temp_stderr 2>&1 - </command> <inputs> <param name="input_control_file" type="data" format="bam,sam,bed" multiple="True" optional="True" label="ChIP-Seq Control File" /> <param name="input_treatment_file" type="data" format="bam,sam,bed" multiple="True" label="ChIP-Seq Treatment File" /> - <conditional name="effective_genome_size_options"> - <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" help="--gsize"> - <option value="3300000000">Human (3.300.000.000)</option> - <option value="3000000000">Mouse (3.000.000.000)</option> - <option value="190000000">Fly (190.000.000)</option> - <option value="130000000">Worm (130.000.000)</option> - <option value="user_defined">User defined</option> - </param> - <when value="user_defined"> - <param name="gsize" type="integer" size="12" label="Effective genome size" value=""/> - </when> - </conditional> + <expand macro="conditional_effective_genome_size" /> - <param name="bw" type="integer" label="Band width" value="300" help="(--bw)"/> + <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">
--- a/macs2_filterdup.xml Thu Jan 16 13:31:17 2014 -0500 +++ b/macs2_filterdup.xml Thu Jan 16 15:44:43 2014 -0500 @@ -1,11 +1,10 @@ <tool id="macs2_filterdup" name="Remove duplicate reads" version="2.0.10.0"> <description>at the same position</description> - <requirements> - <requirement type="python-module">macs2</requirement> - <requirement type="python-module">numpy</requirement> - <requirement type="package" version="2.0.10.2">macs2</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - </requirements> + <expand macro="requirements" /> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> <command> macs2 filterdup -t $infile @@ -26,7 +25,7 @@ <!--may need to add a few more formats at later time--> <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> <param name="gsize" type="float" label="Effective genome size" value="2.7e+9" help="Human: 3.3e+9, Mouse: 3.0e+9, Fly: 1.9e+8, Worm: 1.3e+8 (--gsize)" /> - <param name="tsize" type="float" label="Tag size" value="-1.0" help="This will overide the auto detected tag size. DEFAULT: Not set (-1.0) (--tsize)" /> + <expand macro="tag_size" /> <param name="pvalue" type="float" label="Pvalue cutoff for binomial distribution test" value="1e-5" help="default: 1e-5 (--pvalue)" /> <conditional name="keep_dup_options">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs2_macros.xml Thu Jan 16 15:44:43 2014 -0500 @@ -0,0 +1,49 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="python-module">macs2</requirement> + <requirement type="python-module">numpy</requirement> + <requirement type="package" version="2.0.10.2">macs2</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + <yield /> + </requirements> + </xml> + + <xml name="conditional_effective_genome_size"> + <conditional name="effective_genome_size_options"> + <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" help="--gsize"> + <option value="3300000000">Human (3.300.000.000)</option> + <option value="3000000000">Mouse (3.000.000.000)</option> + <option value="190000000">Fly (190.000.000)</option> + <option value="130000000">Worm (130.000.000)</option> + <option value="user_defined">User defined</option> + </param> + <when value="user_defined"> + <param name="gsize" type="integer" size="12" label="Effective genome size" value=""/> + </when> + </conditional> + </xml> + + <token name="@effective_genome_size@"> + #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined': + --gsize $effective_genome_size_options.gsize + #else: + --gsize $effective_genome_size_options.effective_genome_size_options_selector + #end if + </token> + + <xml name="version_command"> + <version_command>macs2 --version</version_command> + </xml> + + <xml name="tag_size"> + <param name="tsize" type="float" label="Tag size" value="-1.0" help="This will overide the auto detected tag size. DEFAULT: Not set (-1.0) (--tsize)" /> + </xml> + + <xml name="stdio"> + <stdio> + <regex match="Error:" /> + <regex match="EXception:" /> + </stdio> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs2_predict.xml Thu Jan 16 15:44:43 2014 -0500 @@ -0,0 +1,66 @@ +<tool id="macs2_predict" name="Predict" version="2.0.10.0"> + <description>d or fragment size from alignment results</description> + <expand macro="requirements"> + <requirement type="package" version="3.0.1">R_3_0_1</requirement> + </expand> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> + <command> + macs2 predict + -i #echo ','.join($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** + +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. + </help> +</tool>
--- a/macs2_randsample.xml Thu Jan 16 13:31:17 2014 -0500 +++ b/macs2_randsample.xml Thu Jan 16 15:44:43 2014 -0500 @@ -1,11 +1,10 @@ <tool id="macs2_randsamoke" name="Randomly sample number or percentage" version="2.0.10.0"> <description>of total reads</description> - <requirements> - <requirement type="python-module">macs2</requirement> - <requirement type="python-module">numpy</requirement> - <requirement type="package" version="2.0.10.2">macs2</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - </requirements> + <expand macro="requirements" /> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> <command> macs2 randsample -t $infile @@ -25,7 +24,7 @@ <!--may need to add a few more formats at later time--> <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> - <param name="tsize" type="float" label="Tag size" value="-1.0" help="This will overide the auto detected tag size. DEFAULT: Not set (-1.0) (--tsize)" /> + <expand macro="tag_size" /> <conditional name="method_options"> <param name="method_options_selector" type="select" label="Select action to be performed">
--- a/macs2_refinepeak.xml Thu Jan 16 13:31:17 2014 -0500 +++ b/macs2_refinepeak.xml Thu Jan 16 15:44:43 2014 -0500 @@ -1,11 +1,10 @@ <tool id="macs2_refinepeak" name="Refine peak summits" version="2.0.10.0"> <description></description> - <requirements> - <requirement type="python-module">macs2</requirement> - <requirement type="python-module">numpy</requirement> - <requirement type="package" version="2.0.10.2">macs2</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - </requirements> + <expand macro="requirements" /> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> <command> macs2 refinepeak @@ -21,7 +20,7 @@ <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" /> <param name="cutoff" type="float" label="Cutoff" value="5.0" help="DEFAULT: 5.0 (--cutoff)"/> - <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="DEFAULT: 200bp (--window-size)" /> + <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" /> </inputs> <outputs>
--- a/tool_dependencies.xml Thu Jan 16 13:31:17 2014 -0500 +++ b/tool_dependencies.xml Thu Jan 16 15:44:43 2014 -0500 @@ -1,10 +1,13 @@ <?xml version="1.0"?> <tool_dependency> - <package name="numpy" version="1.7.1"> - <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"> + <repository name="package_numpy_1_7" owner="iuc"/> </package> <package name="scipy" version="0.12"> - <repository changeset_revision="3c1bf479158c" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository name="package_scipy_0_12" owner="iuc"/> + </package>--> + <package name="R_3_0_1" version="3.0.1"> + <repository changeset_revision="0a395bcd7efd" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="macs2" version="2.0.10.2"> <install version="1.0">