fix #969 #970
fix #969 #970
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I think this error needs to be fixed on planemo. What do you think if we just merge it regardless? The issue is that the generated pc2 is different from the local one, but the local one is correct. At least I get the same value when i run it locally. I can also fix it if you can direct me to where I can find |
galaxy/wrapper/plotPCA.xml
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| <param name="outFileFormat" value="png" /> | |||
| <param name="outFileNameData" value="True" /> | |||
| <output name="outFileName" file="plotPCA_result2.png" ftype="png" compare="sim_size" delta="12000" /> | |||
| <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" /> | |||
| <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" compare="sim_size" delta="12000" /> | |||
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this is not good, why is the difference so high? The idea of such tests is that we spot errors because the output changes dramatically. If the output is actually intended to change than the file plotPCA_result2.tabular should be updated to reflect the new "truth".
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It is indeed high. plotPCA test in planemo generates 2.49319462166397e-32 for pc2 instead of 1.2325951644078315e-32 in plotPCA_result2.tabular . I should not change this though, since it is actually correct. This is actually what the cmd version of deeptools generates too. What is your suggestion?
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You can check the command that planemo creates. Planemo uses the same version as the CLI version, so either the arguments are different or something strange happens here.
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I would say the latter. Maybe some difference in the version of some package or so.
Though, let me check the planemo args one more time, in case I over looked something.
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@bgruening That test passed now even without alpha. This is how i meant by being passed time to time. |
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Wired, we also should move here to container based testing. Thanks @LeilyR! |
* Fixes for 3.4.2 * disable azure on OSX * Closes #945 * computeMatricOperation dataRange (#951) * Added dataRange to computeMatricOperation to return min,max,median and 10th and 90th percentile. * fixed pep8 * more pep8 fix * fixed test_sieve of azure tests * one more fix for test_sieve * imported pysam to test_readFiltering.py * updated hash values for test_sieve * fixed galaxy computeMatrixOperation.xml * More fixes for galaxy wrapper * fixed a little typo in bamCompare (#967) * save the output matrix of the plotheatmap in a format to be compatible with running plotheatmap on it again (#968) * Plot profile color map (#971) * Now colors can be set by user for any heatmap in plotProfile. A bug in tick index for plotting heatmap is also fixed. * added a small description * pep8 fix * added sortUsingSamples and clusterUsingSamples to the galaxy wrapper * [WIP] added auto to plotheatmap #908 (#982) * added auto to plotheatmap * fixed lint, added warning message, updated the help for zmin, zmax * galaxy test plotPCA * lower down the delat for potPCA galaxy test * fix #969 (#970) * fix #969 * PEP8 * updated changes.txt * fixed a little bug in parseCommon.py which caused flake8 failure. * [WIP] added auto to plotheatmap #908 (#982) * added auto to plotheatmap * fixed lint, added warning message, updated the help for zmin, zmax * galaxy test plotPCA * lower down the delat for potPCA galaxy test * updated version and changes * removed alpha from plotPCA test * removed compare="sim_size" * fixed plotHeatmap.xml by removing size from the the params and adding anitizer for the 2 new params. * upated change.txt * updated the doc html Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>
* Fixes for 3.4.2 * disable azure on OSX * Closes deeptools#945 * computeMatricOperation dataRange (deeptools#951) * Added dataRange to computeMatricOperation to return min,max,median and 10th and 90th percentile. * fixed pep8 * more pep8 fix * fixed test_sieve of azure tests * one more fix for test_sieve * imported pysam to test_readFiltering.py * updated hash values for test_sieve * fixed galaxy computeMatrixOperation.xml * More fixes for galaxy wrapper * fixed a little typo in bamCompare (deeptools#967) * save the output matrix of the plotheatmap in a format to be compatible with running plotheatmap on it again (deeptools#968) * Plot profile color map (deeptools#971) * Now colors can be set by user for any heatmap in plotProfile. A bug in tick index for plotting heatmap is also fixed. * added a small description * pep8 fix * added sortUsingSamples and clusterUsingSamples to the galaxy wrapper * [WIP] added auto to plotheatmap deeptools#908 (deeptools#982) * added auto to plotheatmap * fixed lint, added warning message, updated the help for zmin, zmax * galaxy test plotPCA * lower down the delat for potPCA galaxy test * fix deeptools#969 (deeptools#970) * fix deeptools#969 * PEP8 * updated changes.txt * fixed a little bug in parseCommon.py which caused flake8 failure. * [WIP] added auto to plotheatmap deeptools#908 (deeptools#982) * added auto to plotheatmap * fixed lint, added warning message, updated the help for zmin, zmax * galaxy test plotPCA * lower down the delat for potPCA galaxy test * updated version and changes * removed alpha from plotPCA test * removed compare="sim_size" * fixed plotHeatmap.xml by removing size from the the params and adding anitizer for the 2 new params. * upated change.txt * updated the doc html Co-authored-by: Devon Ryan <dpryan79@users.noreply.github.com>
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