| Previous changeset 0:d957e25e18a3 (2013-11-14) Next changeset 2:b5da81864541 (2013-11-15) |
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modified:
bamCorrelate.xml bigwigCompare.xml deepTools_macros.xml tool_dependencies.xml |
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| diff -r d957e25e18a3 -r a22ccc261bb3 bamCorrelate.xml --- a/bamCorrelate.xml Thu Nov 14 16:39:18 2013 -0500 +++ b/bamCorrelate.xml Fri Nov 15 07:57:48 2013 -0500 |
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| @@ -33,7 +33,7 @@ #if $mode.modeOpt == "bins": --binSize '$mode.binSize' - --numberOfSamples '$modenumberOfSamples' + --numberOfSamples '$mode.numberOfSamples' #else: --BED $mode.region_file #end if |
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| diff -r d957e25e18a3 -r a22ccc261bb3 bigwigCompare.xml --- a/bigwigCompare.xml Thu Nov 14 16:39:18 2013 -0500 +++ b/bigwigCompare.xml Fri Nov 15 07:57:48 2013 -0500 |
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| @@ -29,6 +29,12 @@ #end if </command> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <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" /> |
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| diff -r d957e25e18a3 -r a22ccc261bb3 deepTools_macros.xml --- a/deepTools_macros.xml Thu Nov 14 16:39:18 2013 -0500 +++ b/deepTools_macros.xml Fri Nov 15 07:57:48 2013 -0500 |
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| @@ -40,7 +40,7 @@ <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="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> |
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| diff -r d957e25e18a3 -r a22ccc261bb3 tool_dependencies.xml --- a/tool_dependencies.xml Thu Nov 14 16:39:18 2013 -0500 +++ b/tool_dependencies.xml Fri Nov 15 07:57:48 2013 -0500 |
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| @@ -54,7 +54,7 @@ <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 --> @@ -64,7 +64,7 @@ </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 && |