Mercurial > repos > bgruening > deeptools_bam_compare
changeset 5:7aa5951c56b7 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 8b9cdb8dc4a8fedd2b2286e7afab6529e49a9d22-dirty
| author | bgruening |
|---|---|
| date | Tue, 22 Dec 2015 13:47:00 -0500 |
| parents | 0408832052db |
| children | 0da0ae5c854e |
| files | bamCompare.xml deepTools_macros.xml static/images/plotCorrelation_galaxy_bw_heatmap_output.png |
| diffstat | 3 files changed, 11 insertions(+), 16 deletions(-) [+] |
line wrap: on
line diff
--- a/bamCompare.xml Mon Dec 21 19:09:44 2015 -0500 +++ b/bamCompare.xml Tue Dec 22 13:47:00 2015 -0500 @@ -74,13 +74,13 @@ <param argument="--bamFile2" format="bam" type="data" label="Second BAM file (e.g. control sample)" help="The BAM file must be sorted."/> - <param argument="--binSize" type="integer" value="50" min="1" + <param argument="--binSize" type="integer" value="50" min="1" label="Bin size in bp" help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported."/> <conditional name="scaling"> - <param name="method" type="select" + <param name="method" type="select" label="Method to use for scaling the largest sample to the smallest"> <option value="readCount" selected="true">read count</option> <option value="SES">signal extraction scaling (SES), check the bamFingerprint plot before using it!</option> @@ -101,7 +101,7 @@ </conditional> <conditional name="comparison"> - <param name="type" type="select" + <param name="type" type="select" label="How to compare the two files" 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 @@ -218,7 +218,7 @@ .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png -You can find more details on the bamCompare wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare +You can find more details on the bamCompare doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/bamCompare.html **Output files**:
--- a/deepTools_macros.xml Mon Dec 21 19:09:44 2015 -0500 +++ b/deepTools_macros.xml Tue Dec 22 13:47:00 2015 -0500 @@ -40,10 +40,10 @@ </xml> <token name="@HEATMAP_OPTIONS@"> - #if $plotting_type.zMin: + #if str($plotting_type.zMin) != "": --zMin $plotting_type.zMin #end if - #if $plotting_type.zMax: + #if str($plotting_type.zMax) != "": --zMax $plotting_type.zMax #end if --colorMap '$plotting_type.colorMap' @@ -107,7 +107,11 @@ </param> <when value="kmeans"> <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" - help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/> + help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. + Only works for data that is not grouped, otherwise only the first group will be clustered. + If more specific clustering methods are required it is advisable to save the underlying matrix and + run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) + if a cluster has very few members compared to the total number or regions. (default: 0 [do not cluster])."/> </when> <when value="none" /> </conditional> @@ -408,7 +412,6 @@ <when value="no" /> <when value="yes"> <yield /> - <param name="saveData" type="boolean" label="Save the data underlying the average profile"/> <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> </when> </conditional> @@ -456,14 +459,6 @@ </xml> <xml name="output_graphic_outputs"> - <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> - <filter> - (( - output['showOutputSettings'] == 'yes' and - output['saveData'] is True - )) - </filter> - </data> <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> <filter> ((