Mercurial > repos > bgruening > deeptools
changeset 5:c54d31467be4 draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 29 Nov 2013 08:59:04 -0500 |
| parents | ac935c35437a |
| children | 1ee0b1ecf500 |
| files | bamCorrelate.xml computeGCBias.xml correctGCBias.xml deepTools_macros.xml readme.rst tool_dependencies.xml |
| diffstat | 6 files changed, 73 insertions(+), 83 deletions(-) [+] |
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--- a/bamCorrelate.xml Sat Nov 16 07:54:13 2013 -0500 +++ b/bamCorrelate.xml Fri Nov 29 08:59:04 2013 -0500 @@ -15,14 +15,7 @@ bamCorrelate - #if $mode.modeOpt == "bins": - bins - --binSize '$mode.binSize' - --numberOfSamples '$mode.numberOfSamples' - #else: - BED-file - --BED $mode.region_file - #end if + $mode.modeOpt @THREADS@ @@ -40,6 +33,13 @@ --outFileCorMatrix '$outFileCorMatrix' #end if + #if $mode.modeOpt == "bins": + --binSize '$mode.binSize' + --numberOfSamples '$mode.numberOfSamples' + #else: + --BED $mode.region_file + #end if + ## options available in both modes #if $mode.advancedOpt.showAdvancedOpt == "yes":
--- a/computeGCBias.xml Sat Nov 16 07:54:13 2013 -0500 +++ b/computeGCBias.xml Fri Nov 29 08:59:04 2013 -0500 @@ -8,63 +8,52 @@ <import>deepTools_macros.xml</import> </macros> <command> - #import tempfile - #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) + ln -s $bamInput local_bamInput.bam; + ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai; - #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) - #set $temp_bam_path = $temp_bam_handle.name + '.bam' - #silent $temp_bam_handle.close() - #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path)) - #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path)) + computeGCBias - computeGCBias - - @THREADS@ + @THREADS@ - --bamfile '$temp_bam_path' - --GCbiasFrequenciesFile $outFileName - --fragmentLength $fragmentLength + --bamfile 'local_bamInput.bam' + --GCbiasFrequenciesFile $outFileName + --fragmentLength $fragmentLength - @reference_genome_source@ - + @reference_genome_source@ - #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": - --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize - #else: - --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt - #end if - + #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": + --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize + #else: + --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt + #end if - #if $advancedOpt.showAdvancedOpt == "yes": - #if str($advancedOpt.region.value) != '': - --region '$advancedOpt.region' - #end if - - --sampleSize '$advancedOpt.sampleSize' - --regionSize '$advancedOpt.regionSize' + #if $advancedOpt.showAdvancedOpt == "yes": + #if str($advancedOpt.region.value) != '': + --region '$advancedOpt.region' + #end if - #if $advancedOpt.filterOut: - --filterOut $advancedOpt.filterOut - #end if + --sampleSize '$advancedOpt.sampleSize' + --regionSize '$advancedOpt.regionSize' + + #if $advancedOpt.filterOut: + --filterOut $advancedOpt.filterOut + #end if - #if $advancedOpt.extraSampling: - --extraSampling $advancedOpt.extraSampling - #end if - - #end if + #if $advancedOpt.extraSampling: + --extraSampling $advancedOpt.extraSampling + #end if + #end if - #if $saveBiasPlot: - --biasPlot $biasPlot - #end if + #if $saveBiasPlot: + --biasPlot $biasPlot + #end if -## #if $output.showOutputSettings == "yes" -## #if $output.saveBiasPlot: -## --biasPlot biasPlot.png ; -## mv biasPlot.png $biasPlot -## #end if -## #end if - - ; rm $temp_dir -rf + ## #if $output.showOutputSettings == "yes" + ## #if $output.saveBiasPlot: + ## --biasPlot biasPlot.png ; + ## mv biasPlot.png $biasPlot + ## #end if + ## #end if </command> <inputs>
--- a/correctGCBias.xml Sat Nov 16 07:54:13 2013 -0500 +++ b/correctGCBias.xml Fri Nov 29 08:59:04 2013 -0500 @@ -16,6 +16,9 @@ correctGCBias + + @THREADS@ + --bamfile '$temp_bam_path' --GCbiasFrequenciesFile $GCbiasFrequenciesFile
--- a/deepTools_macros.xml Sat Nov 16 07:54:13 2013 -0500 +++ b/deepTools_macros.xml Fri Nov 29 08:59:04 2013 -0500 @@ -46,7 +46,7 @@ <requirement type="package" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a">deepTools</requirement> <requirement type="package" version="0.1">ucsc_tools</requirement> <requirement type="package" version="1.7.1">numpy</requirement> - <requirement type="package" version="0.7.6">pysam</requirement> + <requirement type="package" version="0.7.7">pysam</requirement> <requirement type="package" version="0.1.19">samtools</requirement> <yield /> </requirements>
--- a/readme.rst Sat Nov 16 07:54:13 2013 -0500 +++ b/readme.rst Fri Nov 29 08:59:04 2013 -0500 @@ -29,7 +29,7 @@ Citation ======== -deeptools are currently under review. In the meantime please refere to +deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools. ======= @@ -39,25 +39,23 @@ - v1.0: Initial public release -=============================== -Wrapper Licence (MIT/BSD style) -=============================== +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: -Permission to use, copy, modify, and distribute this software and its -documentation with or without modifications and for any purpose and -without fee is hereby granted, provided that any copyright notices -appear in all copies and that both those copyright notices and this -permission notice appear in supporting documentation, and that the -names of the contributors or copyright holders not be used in -advertising or publicity pertaining to distribution of the software -without specific prior permission. +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. -THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL -WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE -CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT -OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE -OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE -OR PERFORMANCE OF THIS SOFTWARE. - +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE.
--- a/tool_dependencies.xml Sat Nov 16 07:54:13 2013 -0500 +++ b/tool_dependencies.xml Fri Nov 29 08:59:04 2013 -0500 @@ -4,16 +4,16 @@ <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="numpy" version="1.7.1"> - <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="796c0081adad" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="matplotlib" version="1.2.1"> <repository changeset_revision="9d164359606b" name="package_matplotlib_1_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="scipy" version="0.12.0"> - <repository changeset_revision="303d29ec30e5" name="package_scipy_0_12" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d277bf006c3e" name="package_scipy_0_12" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> - <package name="pysam" version="0.7.6"> - <repository changeset_revision="9d817cc2c290" name="package_pysam_0_7_6" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="pysam" version="0.7.7"> + <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="ucsc_tools" version="0.1"> @@ -59,8 +59,8 @@ <actions> <!-- populate the environment variables from the dependend repos --> <action type="set_environment_for_install"> - <repository changeset_revision="f3f4b6121444" name="package_pysam_0_7_5" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> - <package name="pysam" version="0.7.5" /> + <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="pysam" version="0.7.7" /> </repository> </action> <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>