# HG changeset patch
# User rnateam
# Date 1382368052 14400
# Node ID 91fb7edca34472ed2498b08e4d1ab1327950e600
Uploaded
diff -r 000000000000 -r 91fb7edca344 blockclust.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/blockclust.xml Mon Oct 21 11:07:32 2013 -0400
@@ -0,0 +1,121 @@
+
+ Non-coding RNA clustering from deep sequencing read profiles
+
+ blockclust
+
+
+
+ #set $blockclust_data_path = \$BLOCKCLUST_DATA_PATH
+ #if str($mode.operation) == "pre":
+ #set $outputdir = $tags_bed.extra_files_path
+ BlockClustPipeLine.pl -m PRE -bam $mode.reads_bam -tbed $tags_bed;
+ #end if
+
+ #if str($mode.operation) == "clust":
+ #set $outputdir = $clusters.extra_files_path
+ #set $accept_bed=list()
+ #set $reject_bed=list()
+ ## prepare annotations
+ #if str($mode.reference) == "hg19":
+ $accept_bed.append("$blockclust_data_path/annotations/hg19/hg19.accept.bed")
+ $reject_bed.append("$blockclust_data_path/annotations/hg19/hg19.reject.bed")
+ #elif str($mode.reference) == "mm10":
+ $accept_bed.append("$blockclust_data_path/annotations/mm10/mm10.accept.bed")
+ $reject_bed.append("$blockclust_data_path/annotations/mm10/mm10.reject.bed")
+ #elif str($mode.reference) == "dm3":
+ $accept_bed.append("$blockclust_data_path/annotations/dm3/dm3.accept.bed")
+ $reject_bed.append("$blockclust_data_path/annotations/dm3/dm3.reject.bed")
+ #end if
+ BlockClustPipeLine.pl -m TEST -f SEQUENCE -c $blockclust_script_path/blockclust.config
+ -t $mode.input_bbo
+ -a #echo ''.join( $accept_bed )
+ -r #echo ''.join( $reject_bed )
+ -o $outputdir;
+ cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters;
+ cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot;
+ cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out;
+ #end if
+
+ #if str($mode.operation) == "post":
+ #set $outputdir = $clusters_bed.extra_files_path
+ BlockClustPipeLine.pl -m POST -cbed $mode.clusters_bed -cm $mode.cmsearch_out -tab $mode.sim_tab_in -o $outputdir;
+ cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist;
+ #end if
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+ mode["operation"]=="pre"
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+ mode["operation"]=="clust"
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+ mode["operation"]=="clust"
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+ mode["operation"]=="clust"
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+ mode["operation"]=="post"
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+ mode["operation"]=="post"
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+
+
+.. class:: infomark
+
+**What it does**
+
+Clusters the read profiles (i.e., blockgroups) from the blockbuster tool.
+
+**Inputs**
+
+BlockClust needs output of tool blockbuster as input
+
+**Output**
+
+BlockClust produces a fasta file containing clusters.
+
+------
+
+**Licenses**
+
+If **BlockClust** is used to obtain results for scientific publications it
+should be cited as [1]_.
+
+**References**
+
+.. [1]
+
+------
+
+
+
diff -r 000000000000 -r 91fb7edca344 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Oct 21 11:07:32 2013 -0400
@@ -0,0 +1,28 @@
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+ https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-1.0.tar.gz
+ make
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+ BlockClust
+ $INSTALL_DIR/bin
+
+
+ BlockClustPipeLine.pl
+ $INSTALL_DIR/bin
+
+ https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0.tar.gz
+ tar xfvz blockclust-data-1.0.tar.gz -C $INSTALL_DIR/data/
+
+ $INSTALL_DIR/bin
+ $INSTALL_DIR/data
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