Mercurial > repos > bgruening > deeptools_compute_matrix
diff deepTools_macros.xml @ 1:275ed3e83de0 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
author | bgruening |
---|---|
date | Mon, 15 Feb 2016 10:34:00 -0500 |
parents | 14cb57237e46 |
children | a842285199d9 |
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--- a/deepTools_macros.xml Mon Jan 25 20:26:32 2016 -0500 +++ b/deepTools_macros.xml Mon Feb 15 10:34:00 2016 -0500 @@ -72,12 +72,12 @@ </xml> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.0.1</token> + <token name="@WRAPPER_VERSION@">2.1.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="2.7.10">python</requirement> <requirement type="binary">@BINARY@</requirement> - <requirement type="package" version="2.0.1">deepTools</requirement> + <requirement type="package" version="2.1.0">deepTools</requirement> <yield /> </requirements> <expand macro="stdio" /> @@ -104,6 +104,7 @@ <param name="clustering_options" type="select" label="Clustering algorithm"> <option value="none">No clustering</option> <option value="kmeans">Kmeans clustering</option> + <option value="hclust">Hierarchical clustering</option> </param> <when value="kmeans"> <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" @@ -112,6 +113,15 @@ If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software."/> </when> + <when value="hclust"> + <param name="n_hclust" type="integer" value="0" label="number of clusters to compute." + help="WARNING: This option causes the tool to run for a very long time! When this option is + set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage. + This only works for data that is not grouped, otherwise only the first group will be clustered. + Note that you must have used the '--missingDataAsZero' option within computeMatrix! + If more specific clustering methods are required it is advisable to save the underlying matrix and + run the clustering using other software."/> + </when> <when value="none" /> </conditional> </when> @@ -126,6 +136,11 @@ --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans #end if #end if + #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': + #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: + --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust + #end if + #end if #end if </token> @@ -293,6 +308,12 @@ </xml> <xml name="multiple_input_bams"> + <param argument="--bamfiles" type="data" format="bam" min="1" + label="Bam file" multiple="true" + help="The BAM file must be sorted."/> + </xml> + + <xml name="multiple_input_bams_min2"> <param argument="--bamfiles" type="data" format="bam" min="2" label="Bam file" multiple="true" help="The BAM file must be sorted."/> @@ -310,6 +331,7 @@ help="Title of the plot, to be printed on top of the generated image." /> </xml> + <token name="@multiple_input_bams@"> <![CDATA[ #set files=[]