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comparison blockclust.xml @ 6:6721468f2f9f draft

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author rnateam
date Wed, 09 Jul 2014 13:01:56 -0400
parents 49e600128a73
children c1cc480c53da
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5:a50bd507edfe 6:6721468f2f9f
63 63
64 cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters; 64 cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters;
65 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot; 65 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot;
66 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out 66 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out
67 #elif str($tool_mode.operation) == "post": 67 #elif str($tool_mode.operation) == "post":
68 BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o ./; 68 BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -rfam \$BLOCKCLUST_DATA_PATH/rfam_map.txt -o ./;
69 #end if 69 #end if
70 </command> 70 </command>
71 <inputs> 71 <inputs>
72 <conditional name="tool_mode"> 72 <conditional name="tool_mode">
73 <param name="operation" type="select" label="Select mode of operation"> 73 <param name="operation" type="select" label="Select mode of operation">
165 165
166 1) Pre-processing - converts given mapped reads (BAM) into BED file of tags 166 1) Pre-processing - converts given mapped reads (BAM) into BED file of tags
167 167
168 2) Clustering and classification - of given input blockgroups (output of blockbuster tool) as explained in the original paper. 168 2) Clustering and classification - of given input blockgroups (output of blockbuster tool) as explained in the original paper.
169 169
170 3) Post-processing - extracts distribution of clusters searched against Rfam database and plots hierarchical clustering made out of centroids of each BlockClust predicted cluster. 170 3) Post-processing - plots for overview of predicted clusters.
171 171
172 For a thorough analysis of your data, we suggest you to use complete blockclust workflow, which contains all three modes of operation. 172 For a thorough analysis of your data, we suggest you to use complete blockclust workflow, which contains all three modes of operation.
173 173
174 **Inputs** 174 **Inputs**
175 175
197 * Pairwise similarities of all input blockgroups 197 * Pairwise similarities of all input blockgroups
198 * BED file containing predicted clusters 198 * BED file containing predicted clusters
199 * BED file containing prediction of blockgroups by pre-compiled SVM binary classification model. 199 * BED file containing prediction of blockgroups by pre-compiled SVM binary classification model.
200 200
201 3. Post-processing: 201 3. Post-processing:
202 * Distribution of clusters with annotations searched against Rfam database 202 * Plot of distribution of ncRNA families per predicted cluster (overview of cluster precissions). The annotation of ncRNA families are retrieved by searching cluster instances against Rfam database.
203 * Hierarchical clustering made out of centroids of each BlockClust predicted cluster 203 * Hierarchical clustering made out of centroids of each BlockClust predicted cluster
204 204
205 ------ 205 ------
206 206
207 **References** 207 **References**