--- /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 @@
+<tool id="blockclust" name="BlockClust" version="1.0.0">
+    <description>Non-coding RNA clustering from deep sequencing read profiles</description>
+    <requirements>
+        <requirement type="package" version="1.0">blockclust</requirement>
+        <requirement type="package" version="1.1">eden</requirement>
+        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
+        <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="12.135">mcl</requirement>
+        <requirement type="package" version="1.0">blockclust_rlibs</requirement>
+    </requirements>
+    <version_command>echo '1.0'</version_command>
+    <command>
+
+        #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
+    </command>
+    <inputs>
+        <conditional name="tool_mode">
+            <param name="operation" type="select" label="Select mode of operation">
+                <option value="pre">Pre-processing </option>
+                <option value="clust">Clustering</option>
+                <option value="post">Post-processing</option>
+            </param>
+            <when value="pre">
+                <param name="reads_bam" type="data" format="bam" label="BAM file containing alignments" />
+            </when>
+            <when value="clust">
+                <param name="input_bbo" type="data" format="tabular" label="Input blockgroups file" />
+                <param name="reference" type="select" label="Select reference genome">
+                    <option value="hg19">Human (hg19)</option>
+                    <option value="mm10">Mouse (mm10)</option>
+                    <option value="dm3">Fly (dm3)</option>
+                    <option value="rheMac3">Monkey (rheMac3)</option>
+                    <option value="panTro4">Chimp (panTro4)</option>
+                    <option value="xenTro3">Frog (xenTro3)</option>
+                    <option value="celWS235">C. elegans (celWS235)</option>
+                    <option value="tair10">Arabidopsis thaliana (tair10)</option>
+                </param>
+                <conditional name="pred">
+                    <param name="enable_pred" type="select" label="Would you like to perform classification?">
+                        <option value="no">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="yes">
+                        <param name="pred_mode" type="select" label="Mode of classification">
+                            <option value="model_based">Model based</option>
+                            <option value="nearest_neighbour">Nearest neighbour</option>
+                        </param>
+                    </when>
+                </conditional>
+            </when>
+            <when value="post">
+                <param name="cmsearch_out" type="data" format="tabular" label="Output of cmsearch tool" />
+                <param name="clusters_bed" type="data" format="bed" label="BED file containing clusters (output of BlockClust)" />
+                <param name="sim_tab_in" type="data" format="tabular" label="Pairwise similarities file" />
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}">
+            <filter> tool_mode["operation"]=="pre"</filter>
+        </data>
+        <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" >
+            <filter> tool_mode["operation"]=="clust"</filter>
+        </data>
+        <data format="bed" name="clusters" label="BlockClust: Clustering BED on ${on_string}">
+            <filter> tool_mode["operation"]=="clust"</filter>
+        </data>
+        <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based prediction BED on ${on_string}">
+            <filter>
+            ((
+                tool_mode["operation"] == 'clust' and 
+                tool_mode["pred"]["enable_pred"] == "yes" and
+                tool_mode["pred"]["pred_mode"] == "model_based"
+             ))
+             </filter>
+        </data>
+        <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbour prediction BED on ${on_string}">
+            <filter>
+            ((
+                tool_mode["operation"] == 'clust' and 
+                tool_mode["pred"]["enable_pred"] == "yes" and
+                tool_mode["pred"]["pred_mode"] == "nearest_neighbour"
+             ))
+             </filter>
+        </data>
+        <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}">
+            <filter> tool_mode["operation"]=="clust"</filter>
+        </data>
+        <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" >
+            <filter> tool_mode["operation"]=="post"</filter>
+        </data>
+        <data format="pdf" name="cluster_hclust" label="BlockClust: Hierarchical clustering plot of cluster centroids on ${on_string}" >
+            <filter> tool_mode["operation"]=="post"</filter>
+        </data>
+    </outputs>
+    <help>
+
+.. 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] 
+
+
+    </help>
+</tool>