Mercurial > repos > iuc > macs2
changeset 6:97449a3c1f27 draft
Uploaded
author | bgruening |
---|---|
date | Tue, 21 Jan 2014 11:50:01 -0500 |
parents | a83ea372ddd1 |
children | da0a1fcf7fe0 |
files | macs2_macros.xml macs2_predict.xml macs2_predictd.xml tool_dependencies.xml |
diffstat | 4 files changed, 68 insertions(+), 70 deletions(-) [+] |
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--- a/macs2_macros.xml Thu Jan 16 17:53:00 2014 -0500 +++ b/macs2_macros.xml Tue Jan 21 11:50:01 2014 -0500 @@ -1,8 +1,6 @@ <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 />
--- a/macs2_predict.xml Thu Jan 16 17:53:00 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ -<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 ${on_string} - X-correlation image" /> - </outputs> - <tests> - <!--none yet for macs2--> - </tests> - <help> -**What it does** - -bdgdiff from macs2 - - -Note that pair-end data is not supposed to work with this command. - - ------- - -**Citation** - -For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. - -Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org. - </help> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macs2_predictd.xml Tue Jan 21 11:50:01 2014 -0500 @@ -0,0 +1,66 @@ +<tool id="macs2_predict" name="Predict" version="2.0.10.0"> + <description>d or fragment size from alignment results</description> + <expand macro="requirements"> + <requirement type="package" version="3.0.1">R_3_0_1</requirement> + </expand> + <expand macro="version_command" /> + <macros> + <import>macs2_macros.xml</import> + </macros> + <command> + macs2 predict + -i #echo ','.join($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 ${on_string} - X-correlation image" /> + </outputs> + <tests> + <!--none yet for macs2--> + </tests> + <help> +**What it does** + +bdgdiff from macs2 + + +Note that pair-end data is not supposed to work with this command. + + +------ + +**Citation** + +For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. + +Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org. + </help> +</tool>
--- a/tool_dependencies.xml Thu Jan 16 17:53:00 2014 -0500 +++ b/tool_dependencies.xml Tue Jan 21 11:50:01 2014 -0500 @@ -7,7 +7,7 @@ <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="R_3_0_1" version="3.0.1"> - <repository changeset_revision="0a395bcd7efd" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="1d5b86c2e93d" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="macs2" version="2.0.10.2"> <install version="1.0"> @@ -24,7 +24,7 @@ <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command"> export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && - python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $env.INSTALL_DIR/bin + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin </action> <action type="set_environment"> <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>