| Previous changeset 10:9cc3a577f80d (2016-12-05) Next changeset 12:bda8b9986fae (2017-03-31) |
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Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca |
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modified:
bamCompare.xml deepTools_macros.xml repository_dependencies.xml tool_dependencies.xml |
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| diff -r 9cc3a577f80d -r 8f2a1286b61c bamCompare.xml --- a/bamCompare.xml Mon Dec 05 08:12:20 2016 -0500 +++ b/bamCompare.xml Tue Jan 24 04:59:05 2017 -0500 |
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| @@ -114,6 +114,7 @@ <option value="ratio">Compute the ratio of the number of reads</option> <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option> <option value="add">Compute the sum of number of reads</option> + <option value="mean">Compute the mean of the number of reads between the two files</option> <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option> <option value="first">Returns the scaled value of the first BAM file</option> <option value="second">Returns the scaled value of the second BAM file</option> @@ -125,6 +126,7 @@ <expand macro="pseudocount" /> </when> <when value="add" /> + <when value="mean" /> <when value="first" /> <when value="second" /> <when value="reciprocal_ratio"> |
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| diff -r 9cc3a577f80d -r 8f2a1286b61c deepTools_macros.xml --- a/deepTools_macros.xml Mon Dec 05 08:12:20 2016 -0500 +++ b/deepTools_macros.xml Tue Jan 24 04:59:05 2017 -0500 |
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| @@ -98,11 +98,11 @@ </xml> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.4.1</token> + <token name="@WRAPPER_VERSION@">2.4.2</token> <xml name="requirements"> <requirements> <requirement type="package" version="2.7.10">python</requirement> - <requirement type="package" version="2.4.1">deeptools</requirement> + <requirement type="package" version="2.4.2">deeptools</requirement> <yield /> </requirements> <expand macro="stdio" /> @@ -299,7 +299,7 @@ <param argument="--sortRegions" type="select" label="Sort regions" help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> <option value="no">no ordering</option> - <option value="descend">descending order</option> + <option value="descend" selected="true">descending order</option> <option value="ascend">ascending order</option> </param> </xml> @@ -450,10 +450,10 @@ #end for #else: #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): - ln -s "${f.bamfile}" "./${counter}.bam" && - ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" && + ln -s "${f.bamfiles}" "./${counter}.bam" && + ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" && #silent $files.append('%s.bam' % $counter) - #silent $labels.append("'%s'" % ($f.bamfile.display_name)) + #silent $labels.append("'%s'" % ($f.bamfiles.display_name)) #end for #end if ]]> @@ -471,9 +471,9 @@ #end for #else: #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): - ln -s "${f.bigwig}" "${counter}.bw" && + ln -s "${f.bigwigfiles}" "${counter}.bw" && #silent $files.append('%s.bw' % $counter) - #silent $labels.append("'%s'" % ($f.bigwig.display_name)) + #silent $labels.append("'%s'" % ($f.bigwigfiles.display_name)) #end for #end if ]]> |
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| diff -r 9cc3a577f80d -r 8f2a1286b61c repository_dependencies.xml --- a/repository_dependencies.xml Mon Dec 05 08:12:20 2016 -0500 +++ b/repository_dependencies.xml Tue Jan 24 04:59:05 2017 -0500 |
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| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories> - <repository changeset_revision="74b09c8e5f6e" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="df883cc67fbd" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |
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| diff -r 9cc3a577f80d -r 8f2a1286b61c tool_dependencies.xml --- a/tool_dependencies.xml Mon Dec 05 08:12:20 2016 -0500 +++ b/tool_dependencies.xml Tue Jan 24 04:59:05 2017 -0500 |
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| @@ -3,7 +3,7 @@ <package name="python" version="2.7.10"> <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="deeptools" version="2.4.1"> - <repository changeset_revision="e9855a43ac53" name="package_python_2_7_deeptools_2_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="deeptools" version="2.4.2"> + <repository changeset_revision="efc55c226f11" name="package_python_2_7_deeptools_2_4_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |