| Previous changeset 5:199989365def (2016-04-04) Next changeset 7:007d99e2ae91 (2016-04-04) |
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Commit message:
Uploaded |
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modified:
chipsequtil/map_to_known_genes.xml chipsequtil/tool_dependencies.xml |
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added:
chipsequtil/._map_to_known_genes.py chipsequtil/._map_to_known_genes.xml |
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| diff -r 199989365def -r 124231ed2402 chipsequtil/._map_to_known_genes.py |
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| Binary file chipsequtil/._map_to_known_genes.py has changed |
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| diff -r 199989365def -r 124231ed2402 chipsequtil/._map_to_known_genes.xml |
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| Binary file chipsequtil/._map_to_known_genes.xml has changed |
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| diff -r 199989365def -r 124231ed2402 chipsequtil/map_to_known_genes.xml --- a/chipsequtil/map_to_known_genes.xml Mon Apr 04 14:52:25 2016 -0400 +++ b/chipsequtil/map_to_known_genes.xml Mon Apr 04 14:56:51 2016 -0400 |
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| @@ -28,14 +28,14 @@ <param name="upst_win" type="integer" label="Upstream Window" help="Window width in base pairs to consider promoter region [default: %default]" optional="false" value="5500" /> <param name="dnst_win" type="integer" label="Downstream Window" help="Window width in base pairs to consider downstream region [default: %default]" optional="false" value="2500" /> - <param name="tss" checked="true" label="calculate downstream window from transcription start site instead of transcription end site" type="boolean" truevalue="--tss" falsevalue="" help="" /> + <param name="tss" checked="true" label="Calculate downstream window from transcription start site instead of transcription end site" type="boolean" truevalue="--tss" falsevalue="" help="" /> <param name="peaks_fmt" type="select" label="Peaks Format" help="Format of peaks input file" optional="false"> <option value="MACS">MACS</option> <option selected="true" value="BED">BED</option> </param> - <param name="detail" checked="true" label="Add extra fields to output" type="boolean" truevalue="--detail" falsevalue="" help="" /> + <param name="detail" checked="true" label="Append the following fields to each row: peak loc, dist from feature, map type, map subtype" type="boolean" truevalue="--detail" falsevalue="" help="" /> <param name="intergenic" checked="false" label="Write intergenic peaks to the gene file as well with None as gene ID" type="boolean" truevalue="--intergenic" falsevalue="" help="" /> </inputs> <outputs> |
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| diff -r 199989365def -r 124231ed2402 chipsequtil/tool_dependencies.xml --- a/chipsequtil/tool_dependencies.xml Mon Apr 04 14:52:25 2016 -0400 +++ b/chipsequtil/tool_dependencies.xml Mon Apr 04 14:56:51 2016 -0400 |
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| @@ -3,7 +3,7 @@ <package name="chipsequtil" version="1.0"> <install version="1.0"> <actions> - <action type="download_by_url">https://github.com/adamlabadorf/chipsequtil/archive/master.zip</action> + <action type="download_by_url">https://github.com/fraenkel-lab/chipsequtil/archive/master.zip</action> <action type="shell_command">cp org_settings.cfg src/chipsequtil/</action> <action type="shell_command">python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action> <action type="set_environment"> |