# HG changeset patch
# User rnateam
# Date 1399376965 14400
# Node ID 768a67f6ae18faf622ba0083bb9a5aac128e02c4
Uploaded
diff -r 000000000000 -r 768a67f6ae18 blockclust.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/blockclust.xml Tue May 06 07:49:25 2014 -0400
@@ -0,0 +1,186 @@
+
+ Non-coding RNA clustering from deep sequencing read profiles
+
+ blockclust
+ eden
+ R_3_0_1
+ samtools
+ mcl
+ blockclust_rlibs
+
+ echo '1.0'
+
+
+ #if str($tool_mode.operation) == "pre":
+ #set $outputdir = $tags_bed.extra_files_path
+ BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed
+ #elif str($tool_mode.operation) == "clust":
+ #set $outputdir = $clusters.extra_files_path
+ #set $accept_bed=list()
+ #set $reject_bed=list()
+ ## prepare annotations
+ #if str($tool_mode.reference) == "hg19":
+ $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed")
+ $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.reject.bed")
+ #elif str($tool_mode.reference) == "mm10":
+ $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed")
+ $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed")
+ #elif str($tool_mode.reference) == "dm3":
+ $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed")
+ $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed")
+ #elif str($tool_mode.reference) == "rheMac3":
+ $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.accept.bed")
+ $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/rheMac3/rheMac3.reject.bed")
+ #elif str($tool_mode.reference) == "panTro4":
+ $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.accept.bed")
+ $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/panTro3/panTro4.reject.bed")
+ #elif str($tool_mode.reference) == "xenTro3":
+ $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.accept.bed")
+ $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/xenTro3/xenTro3.reject.bed")
+ #elif str($tool_mode.reference) == "celWS235":
+ $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.accept.bed")
+ $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/celWS235/celWS235.reject.bed")
+ #elif str($tool_mode.reference) == "tair10":
+ $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.accept.bed")
+ $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/tair10/tair10.reject.bed")
+ #end if
+ BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config
+ -t $tool_mode.input_bbo
+ -a #echo ''.join( $accept_bed )
+ -r #echo ''.join( $reject_bed )
+ -o $outputdir
+ #if str($tool_mode.pred.enable_pred) == "yes":
+ -p
+ -pm $tool_mode.pred.pred_mode
+ -md \$BLOCKCLUST_DATA_PATH/models
+ -x 3;
+ #if str($tool_mode.pred.pred_mode) == "nearest_neighbour":
+ cp #echo os.path.join($outputdir,'nearest_neighbour_predictions.txt')# $nearest_neighbour_pred_bed;
+ #elif str($tool_mode.pred.pred_mode) == "model_based":
+ cp #echo os.path.join($outputdir,'model_based_predictions.txt')# $model_based_pred_bed;
+ #end if
+ #else:
+ ;
+ #end if
+
+ cp #echo os.path.join($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')# $sim_tab_out
+ #elif str($tool_mode.operation) == "post":
+ #set $outputdir = $clusters_bed.extra_files_path
+ BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o $outputdir;
+ cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist;
+ cp #echo os.path.join($outputdir, 'hclust_tree_clusters.pdf')# $cluster_hclust
+ #end if
+
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+ tool_mode["operation"]=="pre"
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+ tool_mode["operation"]=="clust"
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+ tool_mode["operation"]=="clust"
+
+
+
+ ((
+ tool_mode["operation"] == 'clust' and
+ tool_mode["pred"]["enable_pred"] == "yes" and
+ tool_mode["pred"]["pred_mode"] == "model_based"
+ ))
+
+
+
+
+ ((
+ tool_mode["operation"] == 'clust' and
+ tool_mode["pred"]["enable_pred"] == "yes" and
+ tool_mode["pred"]["pred_mode"] == "nearest_neighbour"
+ ))
+
+
+
+ tool_mode["operation"]=="clust"
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+ tool_mode["operation"]=="post"
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+ tool_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 768a67f6ae18 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue May 06 07:49:25 2014 -0400
@@ -0,0 +1,98 @@
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+ https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ape_3.0-11.tar.gz
+ https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/plyr_1.8.tar.gz
+ https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/digest_0.6.4.tar.gz
+ https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/gtable_0.1.2.tar.gz
+ https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/dichromat_2.0-0.tar.gz
+ https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/colorspace_1.2-4.tar.gz
+ https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/munsell_0.4.2.tar.gz
+ https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/labeling_0.2.tar.gz
+ https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/scales_0.2.3.tar.gz
+ https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/proto_0.3-10.tar.gz
+ https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/reshape2_1.2.2.tar.gz
+ https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ggplot2_0.9.3.1.tar.gz
+ https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/squash_1.0.1.tar.gz
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+ https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-1.0.tar.gz
+ make
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+ $INSTALL_DIR/bin
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+ $INSTALL_DIR/bin
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+ $INSTALL_DIR/bin
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+ $INSTALL_DIR/bin
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+ $INSTALL_DIR/data/
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+ $INSTALL_DIR/data/
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+ $INSTALL_DIR/data/annotations
+ https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz
+ tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/
+ https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/hg19.tar.gz
+ tar xfvz hg19.tar.gz -C $INSTALL_DIR/data/annotations/
+ https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/mm10.tar.gz
+ tar xfvz mm10.tar.gz -C $INSTALL_DIR/data/annotations/
+ https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/panTro4.tar.gz
+ tar xfvz panTro4.tar.gz -C $INSTALL_DIR/data/annotations/
+ https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz
+ tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/
+ https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/celWS235.tar.gz
+ tar xfvz celWS235.tar.gz -C $INSTALL_DIR/data/annotations/
+ https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/tair10.tar.gz
+ tar xfvz tair10.tar.gz -C $INSTALL_DIR/data/annotations/
+ https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/models.tar.gz
+ tar xfvz models.tar.gz -C $INSTALL_DIR/data/
+
+ $INSTALL_DIR/bin
+ $INSTALL_DIR/data
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