Mercurial > repos > bgruening > deeptools_bigwig_compare
changeset 11:f90c8a697ee9 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca
| author | bgruening |
|---|---|
| date | Tue, 24 Jan 2017 04:51:01 -0500 |
| parents | 163f2951146c |
| children | efc677b291c5 |
| files | bigwigCompare.xml deepTools_macros.xml repository_dependencies.xml tool_dependencies.xml |
| diffstat | 4 files changed, 20 insertions(+), 18 deletions(-) [+] |
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--- a/bigwigCompare.xml Mon Dec 05 08:06:20 2016 -0500 +++ b/bigwigCompare.xml Tue Jan 24 04:51:01 2017 -0500 @@ -49,15 +49,16 @@ help="The default is to output the log2ratio between the two samples. The reciprocal ratio returns the negative of the inverse of the ratio if the ratio is less than 0. The resulting values are interpreted as negative - fold changes. To output the scaled values from the first or second BAM file, + fold changes. To output the scaled values from the first or second bigWig file, select 'first' or 'second'."> - <option value="log2" selected="true">Compute log2 of the number of reads ratio</option> - <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="log2" selected="true">Compute log2 of the signal ratio</option> + <option value="ratio">Compute the ratio signals</option> + <option value="subtract">Compute difference (subtract input from treatment) of the signal</option> + <option value="add">Compute the sum of the signals</option> + <option value="mean">Compute the mean of the signal in 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> + <option value="first">Returns the scaled value of the first bigWig file</option> + <option value="second">Returns the scaled value of the second bigWig file</option> </param> <when value="log2"> <expand macro="pseudocount" /> @@ -67,6 +68,7 @@ </when> <when value="subtract" /> <when value="add" /> + <when value="mean" /> <when value="first" /> <when value="second" /> <when value="reciprocal_ratio">
--- a/deepTools_macros.xml Mon Dec 05 08:06:20 2016 -0500 +++ b/deepTools_macros.xml Tue Jan 24 04:51:01 2017 -0500 @@ -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 ]]>
--- a/repository_dependencies.xml Mon Dec 05 08:06:20 2016 -0500 +++ b/repository_dependencies.xml Tue Jan 24 04:51:01 2017 -0500 @@ -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>
--- a/tool_dependencies.xml Mon Dec 05 08:06:20 2016 -0500 +++ b/tool_dependencies.xml Tue Jan 24 04:51:01 2017 -0500 @@ -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>