Mercurial > repos > bgruening > deeptools
changeset 15:351cd1f8791b draft
Uploaded
| author | bgruening |
|---|---|
| date | Thu, 28 Nov 2013 12:58:28 -0500 |
| parents | b0d64a9930d6 |
| children | d0667be9cb0c |
| files | bamCorrelate.xml bigwigCompare.xml computeGCBias.xml deepTools_macros.xml tool_dependencies.xml |
| diffstat | 5 files changed, 61 insertions(+), 66 deletions(-) [+] |
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--- a/bamCorrelate.xml Thu Nov 14 05:43:15 2013 -0500 +++ b/bamCorrelate.xml Thu Nov 28 12:58:28 2013 -0500 @@ -15,6 +15,15 @@ bamCorrelate + #if $mode.modeOpt == "bins": + bins + --binSize '$mode.binSize' + --numberOfSamples '$mode.numberOfSamples' + #else: + BED-file + --BED $mode.region_file + #end if + @THREADS@ --bamfiles #echo " ".join($files) @@ -31,13 +40,6 @@ --outFileCorMatrix '$outFileCorMatrix' #end if - #if $mode.modeOpt == "bins": - --binSize '$mode.binSize' - --numberOfSamples '$modenumberOfSamples' - #else: - --BED $mode.region_file - #end if - ## options available in both modes #if $mode.advancedOpt.showAdvancedOpt == "yes":
--- a/bigwigCompare.xml Thu Nov 14 05:43:15 2013 -0500 +++ b/bigwigCompare.xml Thu Nov 28 12:58:28 2013 -0500 @@ -29,6 +29,10 @@ #end if </command> + <stdio> + <regex match="Error:" /> + <regex match="EXception:" /> + </stdio> <inputs> <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" /> <param name="bigwigFile2" format="bigwig" type="data" label="Input bigwig file" />
--- a/computeGCBias.xml Thu Nov 14 05:43:15 2013 -0500 +++ b/computeGCBias.xml Thu Nov 28 12:58:28 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/deepTools_macros.xml Thu Nov 14 05:43:15 2013 -0500 +++ b/deepTools_macros.xml Thu Nov 28 12:58:28 2013 -0500 @@ -40,14 +40,14 @@ <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> <macro name="requirements"> <requirements> - <requirement type="package" version="1.5.1_91b873c095bb4ca44da99e57d8b49784508aa98b">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="0.1.19">samtools</requirement> <requirement type="package" >samtools</requirement> <requirement type="package" >deepTools</requirement> <requirement type="package" >ucsc_tools</requirement> + <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="0.7.7">pysam</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> <yield /> </requirements> </macro>
--- a/tool_dependencies.xml Thu Nov 14 05:43:15 2013 -0500 +++ b/tool_dependencies.xml Thu Nov 28 12:58:28 2013 -0500 @@ -12,8 +12,8 @@ <package name="scipy" version="0.12.0"> <repository changeset_revision="3c1bf479158c" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="pysam" version="0.7.6"> - <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <package name="pysam" version="0.7.7"> + <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="ucsc_tools" version="0.1"> @@ -54,17 +54,17 @@ <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme> </package> - <package name="deepTools" version="1.5.1_91b873c095bb4ca44da99e57d8b49784508aa98b"> + <package name="deepTools" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a"> <install version="1.0"> <actions> <!-- populate the environment variables from the dependend repos --> <action type="set_environment_for_install"> - <repository changeset_revision="a4e35f23093f" name="package_pysam_0_7_5" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="pysam" version="0.7.5" /> + <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.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> - <action type="shell_command">git reset --hard 91b873c095bb4ca44da99e57d8b49784508aa98b</action> + <action type="shell_command">git reset --hard 323fa6bf083c9d40e5092a6364a4ab8fee57507a</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command"> export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && @@ -73,7 +73,7 @@ <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> <!-- disable the config file of deepTools --> <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable> </action>